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Maize Breeding
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Maize Breeding
4
Firoz Hossain, Vignesh Muthusamy, Jayant S. Bhat,
Rajkumar U. Zunjare, Santosh Kumar, Nitish R. Prakash,
and Brijesh K. Mehta
Abstract
Maize has emerged as an important crop for food, feed and various applications.
Utilization of hybrid technology has resulted in a quantum jump in grain produc-
tion worldwide. However, ever-increasing population pressure coupled with
climate change warrant many fold increase in productivity in a shorter time
frame. Emergence of newer diseases and insect-pests further pose a great chal-
lenge to even sustain the production. Malnutrition has become a major health
issue, thereby causing severe socio-economic losses. However, discovery of new
genes and quantitative trait loci (QTLs) for higher grain yield, plant architecture,
resistance/tolerance to various biotic and abiotic stresses, nutritional quality and
specialty traits, and also availability of suitable donors provide great opportunity
to breed improved hybrids with higher productivity, better resilience to biotic and
abiotic stresses, and higher nutritional quality. Genomics-assisted breeding, dou-
bled haploid and gene editing technology provide great impetus to further
accelerate the breeding cycle. Here, we discussed the present status, opportunities
and challenges in maize breeding.
F. Hossain (*) · V. Muthusamy · J. S. Bhat · R. U. Zunjare

ICAR-Indian Agricultural Research Institute, New Delhi, India
S. Kumar
ICAR-Indian Agricultural Research Institute, Gauria Karma, Jharkhand, India
N. R. Prakash
ICAR-Central Soil Salinity Research Institute, Regional Research Station, Canning, India
B. K. Mehta
ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
# The Author(s), under exclusive licence to Springer Nature Singapore Pte 221
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_4
222 F. Hossain et al.
Keywords
Zea mays · Corn · Genomics · Markers · Gene · QTL · Specialty traits
4.1 Introduction
Maize assumes great significance as food, feed and raw material for diverse indus-
trial applications, thereby serving as a source of livelihood to millions of people
worldwide (Prasanna et al. 2020a; Hossain et al. 2021). Globally, maize is produced
to a volume of 1148 million metric tons with cultivation of 197 million hectares area
(FAOSTAT 2019). Maize is an important cereal crop in as many as 169 countries
across North America, South America, Africa, Asia and Europe. Maize grains are
consumed in various forms such as flat bread, porridge, boiled and roasted grains/
cobs (Hossain et al. 2019a). Besides, maize possesses diverse usage as food in the
form of sweet corn, baby corn, popcorn, waxy corn, high amylose maize and high oil
maize (Hossain et al. 2019b; Pal et al. 2020; Chhabra et al. 2021). Maize, together
with rice and wheat, provides at least 30% of the food calories to more than 4.5
billion people in 94 developing countries (Shiferaw et al. 2011). Considering the
share of calories among all-staple crops, maize contributes 61% in Mesoamerica,
45% in Eastern and Southern Africa, 29% in the Andean region, 21% in West and
Central Africa and 4% in South Asia (Shiferaw et al. 2011). The contribution to
protein by maize is also in the similar tune (Mesoamerica: 62%, Eastern and
Southern Africa: 43%, Andean region: 28%, West and Central Africa: 22% and
South Asia: 4%). Maize grains are the principal component of animal feed, espe-
cially in the poultry and piggery industry (Gao 2002; Panda et al. 2013; Rajasekhar
et al. 2020). Besides, it serves as a source of raw material to corn syrup, emulsifier,
textile, paper and adhesive industries (Bao et al. 2012; Devi et al. 2017). To meet the
requirement of ever-increasing population and growing animal feed industry, the
demand for maize will be doubled by 2050 in the developing world (Rosengrant
et al. 2009).
Gradual progression from open pollinated (OP) varieties to single cross hybrid
technology helped to realize the highest potential for grain heterosis (Andorf et al.
2019). Furthermore, modification in plant architectural traits from wide leaf angle to
shorter leaf angle enabled the maize hybrids to grow under high density, thereby
further enhancing the grain yield. Maize production is increased by two-fold during
the past 40 years due to enhanced grain yield resulting from improved crop cultivars
coupled with the better responsiveness to fertilizer, water and pesticides (Evenson
and Gollin 2003). However, climate change quite often increases frequent crop
failures and decreases grain production. Lack of well-distributed rainfall pattern
would further lead to water scarcity and eventually occurrence of drought stress
which may lead to complete failure of the crop (Brown and Funk 2008; Funk and
Brown 2009). Increase in heat has become a major issue to healthy crop production
as each degree day spent above 30 C reduces the final yield by 1% under optimal
rain-fed conditions and by 1.7% under drought conditions (Lobell et al. 2011).
4 Maize Breeding 223
Incidence of biotic stress has also become a major limiting factor to maize
production.
Of various biotic stresses, fall army worm (FAW) has recently caused havoc
throughout the world, causing as much as complete loss of crop (Israni et al. 2020).
Considerable loss has also been attributed to diseases like grey leaf spot (GLS) and
maize lethal necrosis (MLN). Post-harvest loss up to 80% has been reported in the
tropics due to infestation by grain weevils and grain borers (Hossain et al. 2007;
Zunjare et al. 2014, 2015a, b, c, 2016). Malnutrition caused due to consumption of
unbalanced diet has emerged as one of the major health concerns particularly in the
developing and under-developed world (Bouis et al. 2019; Virk et al. 2021).
Globally, around two billion people suffer from malnutrition (Global Nutrition
Report 2020). Nearly 45% of deaths among children under age 5 are linked to
malnutrition (Global Nutrition Report 2018). Globally, 149.2 million (22.0%) chil-
dren (<5 years) are stunted, while 45.4 million (6.7%) children (below 5 years)
possess child wasting (UNICEF-WHO-WB 2021). Malnutrition contributes to loss
in 11% gross domestic product (GDP) in Asia and Africa, while malnutrition in all
its forms could cost society up to US$3.5 trillion per year (Global Nutrition Report
2016, 2018). Among various avenues, breeding for improved maize hybrid would
remain as the most sustainable and cost-effective avenues to combat the combined
challenges of increasing demand, frequent occurrence of biotic and abiotic stresses
and nutritional disorders.
4.2 Origin of Maize
Maize, as a crop is documented to be grown for 10,000 years (Schnable et al. 2009).
Adult plant morphology of maize is very unique among all cereals, having single
culm, separate male and female inflorescence and human-dependent seed dispersal,
which are thought to have been evolved through few major mutations (Doebley
1992). Morphological resemblances and cytological studies have confirmed its close
relatedness to teosinte (Doebley and Stec 1991). Role of humans in developing and
establishing maize as a crop species has also been documented because of presence
of great variability in maize and continuous selection by ancient people (Yu and
Buckler 2006). Establishing the scientific theory of origin and domestication of
maize was a daunting task because of absence of very close and morphologically
similar plant species (Wang et al. 2017a). Several theories regarding origin of maize
have been proposed and described below.
4.2.1 Tripartite Hypothesis (Mangelsdorf and Reeves 1938)
This hypothesis states that maize originated from an unknown plant which was
having similar ear morphology. Such unknown plant is now extinct. Accordingly,
teosinte is the offspring of maize and Tripsacum.
4.2.2 Catastrophic Sexual Transmutation Hypothesis (Iltis 1983)
According to this hypothesis, sudden sexual transmutation in teosinte was responsi-

ble for development of maize plant. The ear of maize is result of morphological
change in central spike of teosinte resulting from a phenomenon called “genetic
assimilation”.
4.2.3 Tripsacum–Zea Diploperennis Hypothesis (Eubanks 1995)
It is the modified version of tripartite hypothesis. According to this hypothesis,

maize plant evolved from the cross between Zea diploperennis and Tripsacum
dactyloides.
4.2.4 Teosinte Hypothesis (Beadle 1939)
According to this hypothesis, ancient people cultivated teosinte and selected the
morphologically useful plant forms. Maize plants arose due to major mutations in
few loci of teosinte.
Of these, teosinte hypothesis is the most accepted and validated, using modern
genomics associated studies (Doebley 1990; Doebley and Stec 1991; Dorweiler et al.
1993; Matsuoka et al. 2002; Wang et al. 2005; Dong et al. 2019). Beadle (1939) had
predicted teosinte as a sole progenitor of maize and carried out a planned experiment
using a very large recombinant population (F2) derived from crossing teosinte with a
primitive maize landrace. He reported that at least five major mutations were
responsible for converting teosinte into maize. Later on, during the 1990s, a research
group led by Prof. J.F. Doebley at University of Wisconsin, Madison, United States,
had redeveloped and studied the recombinant mapping population using the same
parent as done by Prof. Beadle in the 1930s. They also confirmed the role of at least
five major mutations in developing maize from teosinte in a series of selection events
practiced by ancient cultivators. Several studies have now been carried out to
understand the molecular basis of domestication of maize (Dong et al. 2019).
The mutation present in teosinte glume architecture1 (tga1) gene found in
chromosome 4S was responsible for development of naked kernels (Dorweiler
et al. 1993). This gene encodes a SBP (SQUAMOSA promoter binding protein-
like) family transcription factor. A single nucleotide polymorphism (SNP) at posi-
tion 18 of the ORF in this protein caused a gain-of-function mutation acting as
transcriptional repressor responsible for naked kernel in maize (Wang et al. 2015).
Similarly, single culm developed in maize with respect to tillering habits in teosinte
was found to be governed by teosinte branched1 (tb1) gene (Doebley et al. 1997).
The gene tb1 is a TCP-domain containing transcription factor whose higher expres-
sion in maize reduces the branching and tillering habits. The higher expression is due
to the presence of “Hopscotch” and “Tourist” transposon at ~58–69 kb upstream of
coding region (Studer et al. 2011). Similarly, other genes such as grassy tiller1 (gt1),
enhancer of tb1.2 (etb1.2), barren stalk1 (ba1), barren stalk2 (ba2) have been found
to be associated with branching habits in teosinte and maize intercross populations
(Prakash et al. 2020).
4.3 Species Distribution
Genus Zea consist of five species, that is, Zea diploperennis (diploperennial teosinte,
native of Western Mexico), Zea luxurians (Florida teosinte or Guatemalan teosinte,
native of Mexico, Guatemala and Honduras), Zea mays (Southern Mexico, include
cultivated maize, grown across the world), Zea nicaraguensis (Nicaraguan teosinte),
and Zea perennis (perennial teosinte, native of western Mexico). Among these, Zea
mays include four sub-species Zea mays ssp. mays (cultivated corn), Zea mays ssp.
parviglumis (Balsas teosinte), Zea mays ssp. mexicana (Mexican teosinte), Zea mays
ssp. huehuetenangensis (found on western highlands of Guatemala) (Hossain et al.
2016; Prakash et al. 2020). Among all the species documented under the genus Zea,
maize (Zea mays ssp. mays) is the only one which is being cultivated. The other
sub-species under Zea mays along with other species under Zea is collectively
considered as ‘teosinte’. It is now well established that maize is originated from
Zea mays ssp. parviglumis (also known as balsas teosinte). All the teosinte species
are commonly found in Mexico and northern part of South America.
However, maize has lost many variations present in these teosintes and acquired
new variations arising out of mutations. Doebley (1990) has estimated 25% loss of
gene diversity in maize from balsas teosinte. Later on, through various mutation and
selection by indigenous people, several plant forms of maize were developed, such
as waxy corn, popcorn, sweetcorn, pod corn (Smykal et al. 2018). Cultivated maize
has spread to North America, Europe, Asia, Australia and Africa by European
travelers of the colonial era. After introduction of maize into a different continent,
the variations present in them had led to adaptation to local conditions, and temper-
ate and tropical varieties began to evolve (Prasanna et al. 2010).
4.4 Types of Grains
Maize is of the most produced grain crops on this planet, and this has only been
possible due to the presence of enormous diversity and mutant forms, making it
suitable to be cultivated across environments and ecological conditions (Prasanna
et al. 2012). The various maize forms used in cultivation are given below.
4.4.1 Flint Corn (Zea mays ssp. mays var. indurata)
Complete kernel including outer portion is made up of hard starch.

4.4.2 Dent Corn (Zea mays ssp. mays var. indentata)
Only kernel is made up of hard starch. It has dent-like structure on top of the grain.
4.4.3 Sweet Corn (Zea mays ssp. mays var. saccharata)
Sugar content is high at milking stage (up to 20% as compared to other maize types).
4.4.4 Flour Corn (Zea mays ssp. mays var. amylacea)
Kernel is made up of soft starch, and it is easy to grind and used in making chappatis.
4.4.5 Popcorn (Zea mays ssp. mays var. everta)
Small size kernel which burst and turn inside out after heating. The bursting during
heating is because of formation of steam in the grain.
4.4.6 Waxy Corn (Zea mays ssp. mays var. ceratina)
These are waxy grains which are sticky after cooking. The waxiness of kernel is due
to the presence of low amylose and high amylopectin content (almost 100%).
4.4.7 Pod Corn (Zea mays ssp. mays var. tunicata)
These are podded grains covered inside glumes.

The various forms of maize with specialized usage are a type of mutations
selection occurring in the natural population. Most commonly used corn is of flint
type. Sweet corn has evolved through mutation in genes regulating sugar metabo-
lism, such as sugary1 (su1) and shrunken2 (sh2). Waxy corn is developed by
mutation at waxy1 (wx1) locus in maize. Similarly, pod corn is having mutation at
tunicate locus (Yadav et al. 2015).
4.5 Floral Biology
Maize is a monoecious type of plant with separate female and male flowers borne on
single plant. The main shoot of plant terminates into male inflorescence referred to as
‘tassel’, while the female inflorescence is called ‘silk’ that develop into the ‘ear’. The
modified leaf sheaths of several layers that surrounds around ear are known as
‘husks’. Being protandrous in nature, male flowers mature before female flowers
with a gap of 2–3 days. The genetic mechanisms of monoecism and protandry are the
key factors for anemophily (pollination due to wind) in maize (Kumar et al. 2011;
Tripathi et al. 2011). There are two functional florets in each of the male flower
spikelet, and each floret is composed of pair of thin layers (lemma and palea), three
anthers, one rudimentary pistil and two lodicules. Kiesselbach (1949) has reported
about 2000 to 7500 pollen grains per anther per floret.
Nearly 14 106 pollen grains can be produced by each plant tassel considering
mean of 7000 anthers/tassel and 2000 pollen grains/anther (Kiesselbach 1949).
The pollen grains are very small, lighter in weight and easily carried away by
wind. The female flower formed in the row with development progresses toward
the tip of the ear. The elongated style into thread-like structure known as ‘silks’
covered with numerous small hairs on which pollen grains fall leading to the base of
the silk where fertilization occurs. The pollen grains germinate and enter the embryo
sac within 12–28 h. Self- and cross-pollination are two important practices in maize
breeding. In the breeding nursery, hand pollination is usually followed for
accomplishing self- and cross-pollination, thus it is a labour and cost-intensive
process for maize breeders. Self-pollination is required for development and main-
tenance of inbreds varieties, while cross-pollination is essential to generate
variability and hybrid seed production.
To accomplish self-pollination, ear of plant is covered with ‘silk bag’ before the
silk emerges out. The fresh pollen grains (yellowish in colour) from tassel of same
plant are collected in the morning through bagging tassel with a ‘tassel bag’ wrapped
the previous day evening. The collected fresh pollen grains are placed on silk hairs of
the same plant with no outside exposure to ensure proper self-pollination. For cross-
pollination, pollen grains collected from desired male parent is transferred to well-
covered silk of desired female parent. The proper record of parents involved in
crossing, date of crossing, and breeding scheme is to be clearly written with water-
proof pencil on the tag fixed on the female parent. The plant-to-plant crossing is
generally carried out for generation of genetic variability and introgression of genes.
However, the large-scale hybrid seed production, fixed ratio of female rows to male
rows sown in the field. Tassel of female plant is removed before initiation of pollen
shedding, so that the pollen of male parent is used in the seed production plot.
Removal of tassel as soon as it emerges out of flag leaf is called ‘detasseling’ and is
necessary to avoid selfing in female rows.
4.6 Varietal Development
Most of the U.S. maize production traces to the U.S. Corn Belt dent corn, which was
the product of hybridization between two corn races, Northern flints and Southern
dents (Anderson and Brown 1952). Decades before the Mendel’s laws of inheri-
tance, farmer-breeders in the United States cherished the benefits of out-crossing,
and by 1813, new cultivars were being developed through controlled pollinations.
Lorain (1814) was the first to describe the effect of crossing dent and flint corns, and
also elaborated the potential of crossed seeds for farmers. Later, corn producers and
breeders crossed the Northern flints corn and Southern dents corn to combine the
favourable traits of both, and several new varieties of corn were developed for a quite
long time. The new varieties were somewhat high yielding, early in flowering, more
tolerant to drought and were more adapted to local environments (Anderson and
Brown 1952). Sturtevant (1899) documented the popular use of 323 OP varieties of
dent corn and 69 varieties of flint corn. Robert Reid crossed ‘Gordon Hopkins’, a
semi-gourd dent corn and ‘Little Yellow’, a native Indian flint corn, and developed a
new cultivar known as Reid’s Yellow Dent (Troyer 1999). The OP varieties devel-
oped by farmers and corn breeders dominated the corn production in the U.S. Corn
Belt for over 50 years. The OP varieties were the source material for the develop-
ment of inbreds initially by successive generations of self-pollination/inbreeding.
4.7 Hybrid Development
In the early twentieth century, farmer breeders, U.S. public sector breeders and
private seed producers bred OP varieties but with little gain in maize yield (Hallauer
2008). W.J. Beal was the first to use detasseling in crossing plots to make hybrids in
1881 (Beal 1881). Shull (1908) proposed that the maize yield can be increased by
selfing of parental lines over several cycles to develop inbreds, and then crossing
between inbreds to generate hybrids, the phenomenon termed as ‘hybrid vigour’, or
heterosis (Crabb 1947). At the same time (1909–1912), Edward M. East also
discovered the hybrid vigour at Harvard University’s Bussey Institution in associa-
tion with Connecticut Agricultural Experiment Station. The discovery of hybrid
vigour proved to be a turning point for U.S. maize production and economy (Crabb
1947). Though the potential of hybrid breeding was known since eighteenth century,
no commercial hybrid was developed until 1921. The reasons behind non-popularity
of single cross hybrids were the parental inbreds with poor vigour, very low yield,
low weed competitive ability and susceptibility to corn pests (Hallauer 2008).
Furthermore, low yield of parental inbreds increased the cost of hybrid seed
production.
The major breakthrough came in hybrid maize breeding when Donald F. Jones
created double-cross hybrid ‘Burr-Leaming’ in 1918, which was first produced
commercially in 1921 (Jones 1927). The use of double-cross hybrids greatly reduced
the cost of hybrid seed production, making the hybrid technology feasible for
farmers. A double cross hybrid is essentially the progeny of two single cross hybrids.
The first-generation hybrids overcame the weaknesses of inbreds as they gave
significantly higher seed yield with fewer diseases, insect-pest infestation and
weed issues. At the same time that double cross hybrids were produced and
commercialized, a number of technological advances were adopted in corn produc-
tion viz., (1) use of chemical fertilizers such as inorganic nitrogen fertilizer since
1945 (Gardner 2009), (2) mechanization which facilitated uniform harvesting and
other cultivation practices, thus saved time and labour inputs, and (3) improved
agronomic practices which significantly improved maize productivity in the United
States (Crow 1998; Troyer 2003).
Adoption of these technologies resulted in rapid shift of farmers toward double

cross hybrids. In 1940, about 50% area of maize production in the United States was
under double-cross hybrids, which reached to about 90% by 1950 (Griliches 1957).
During the double-cross hybrid era, the U.S. national average production increased
by ~1 bu./acre every year (Crow 1998). There were other contributing reasons, such
as uniformity in flowering and plant stature, that were aesthetically pleasing and
suitable for machine harvesting, and their better adaptation to different habitats
(Crow 1998) and tolerance to drought than open pollinated varieties (Crabb 1947).
Eventually, breeders could generate inbred varieties with higher productivity and
adaptability which was enough to use them as seed producers to achieve commercial
viability, and single cross hybrids (based on two parental lines) become popular and
grown widely throughout the world (Crow 1998).
With the availability of more vigorous and high yielding inbred lines along with
technological advances in maize production, the production of single hybrids
became more feasible. This again shifted the trend from double cross hybrids to
single cross hybrids in the United States. In the 1950s, many small- and medium-
sized private seed companies were established, but initially dependent on the public
sector hybrids to build their business (Fitzgerald 1990). The adoption of single cross
hybrids resulted in significant increase in U.S. national annual yield by an average of
1.71 bu./acre (Crow 1998). It has now been established that the hybrids developed
from genetically diverse parents are more often highly heterotic than generated from
similar inbreds (Hallauer and Miranda 1988). Following this observation, geneti-
cally similar maize lines were grouped together to generate distinct diverse groups
called ‘heterotic groups’. A heterotic group denotes a group of related or unrelated
genotypes from the same or different populations, which display similar combining
ability and heterotic response when crossed with genotypes from other genetically
distinct germplasm groups (Melchinger and Gumber 1998; Ricci et al. 2007). The
inter-group hybrids typically display more heterosis than intra-heterotic group
hybrids. Several heterotic groups have been described in the United States, viz.,
Reid Yellow Dent, Lancaster Sure Crop, European flints and Minnesota 13 (Dubreuil
and Charcosset 1999; Troyer 2006).
4.8 Genetic Resources
Maize is bestowed with enormous genetic diversity, and several landraces are
reported across the globe that offer opportunity for genetic enhancement to meet
the growing challenges. Wide variation for yield, stress tolerance and nutritional
quality are present in a diverse array of landraces or populations worldwide.
Landraces are heterogeneous in nature and are selectively grown by farmers for
specific characteristics like adaptation, yield, use in a specific diet form, nutritive
value and stress tolerance (Louette and Smale 2000). Some of the notable global land
races of maize that have been used in maize improvement programmes include
Tuxpeno, Bolita, Jala, Chalqueno, Nal-Tel, Palomero, Suwan-1, La Posta Sequia,
Conica, Conica Nortena, Bolita, Oloton, etc., (Louette et al. 1997; Prasanna 2012).
Wide variation for landraces in maize has also been reported in India, particularly in
Sikkim and northeastern Region of the country (Prasanna 2010). Some notable
examples are Murli makai, Kaali makai, Rathi makai, Paheli makai, Seti makai,
Putali makai, Chaptey makai, Gadbade makai, Bancharey makai, Kukharey makai,
Kuchungdari, Kuchungtakmar, etc. (Prasanna and Sharma 2005). These landraces
from India have been well-characterised both at phenotypic and molecular level for
its effective use in the breeding programme (Sharma et al. 2010). One of the most
promising landraces that has been well characterised is Murli makai (Sikkim Primi-
tive) that possess prolificacy (more ears per plant) and stay green in character
(Dhawan 1964; Prasanna 2012; Prakash et al. 2019; Prakash et al. 2021).
The most important consideration is use of these unique land races in the breeding
programme for development of inbreds with specific target traits (Prakash et al.
2019). Broadening of germplasm offers novel trait combinations to the breeders, and
it must be a continuous process. One such example is GEM’ (Germplasm Enhance-
ment of Maize) project, a cooperative effort of United States Department of Agricul-
ture (USDA) with many institutions and industries that aim to utilise diverse maize
genetic resources from around the world to widen the germplasm base of the
commercial hybrid corn in the United States. Such efforts are required globally in
the breeding programmes across the continents for germplasm enhancement and
utilisation in maize.
Different methods have been used to improve germplasm and develop potential
lines. The most important procedure for maize breeding is the recurrent selection
scheme; wherein cyclical improvement of the lines can be achieved. Among recur-
rent selection schemes, the reciprocal recurrent selection (RRS) is the most useful in
inter population improvement. The RRS applied may be half-sib RRS (HS-RRS;
Comstock et al. 1949) or full-sib RRS (FS-RRS; Hallauer and Eberhart 1970) for
developing lines with high general combining ability (GCA) and specific combining
ability (SCA) and to develop heterotic pools. The homozygous lines developed by
this are crossed to opposite heterotic pools, and highly heterotic hybrids can be
commercialized. This traditional recurrent selection schemes are upgraded by
marker technologies and using genomic selection (RRGS) which have shown lot
of promise.
Once the improved lines are available, these lines can be utilized to produce an
array of maize varieties and hybrids that include composites, synthetics, conven-
tional hybrids (single cross, double cross, three-way cross, modified single and three
way cross, and multiple cross) and non-conventional hybrids (inter-varietal hybrids,
inter-family hybrids, top cross, double top cross, and poly cross). The procedure of
development of composites and synthetics are similar, but they differ in the compo-
nent lines used. Composites are the OP populations developed by inter-mating of
outstanding lines (germplasm inbreds, OPVs, hybrids, advance generation lines) and
subsequently maintained by mass selection from isolated plantings, while synthetic
varieties are OP populations derived from the inter-crossing of selfed plants (homo-
zygous lines) or lines and subsequently maintained by routine mass selection
procedures from isolated plantings (Lonnquist 1961) and are proposed by Hayes
and Garber (1919).
4.9 Key Loci for Economically Important Traits
4.9.1 Grain Yield and Component Traits
The ear and kernel related traits are the important contributing traits for maize yield.
Two major quantitative trait loci (QTLs) for kernel row number (KRN4 and KRN1)
(Chuck et al. 2014; Wang et al. 2019) and one major quantitative trait locus (QTL)
for kernel size and weight (qHKW1) (Raihan et al. 2016) have been cloned using
map-based approaches. The ear and kernel-related genomic regions have undergone
selection during maize domestication and improvement (Liu et al. 2015a; Wang
et al. 2019). In addition, many secondary traits like nutrient uptake, photosynthesis,
translocation, sink size, transpiration and respiration also influence the yield levels in
maize. Grain yield is also affected by maturity duration, standability, and resistance
to biotic and abiotic stresses (Gong et al. 2015). Besides, well-developed root
system, strong stem, short plant height, low ear placement, ability to stay green at
maturity, etc., contribute to good standability, which in turn contributes enormously
toward higher yield.
High density planting is a practical approach to increase maize productivity per
unit area. It is predicted that a gain of 20% in maize productivity is possible if
planting density is increased by 15,000 plants/ha. Hence, breeding varieties suitable
to high density planting by targeting leaf architectural traits is an important task.
Among the multiple leaf traits important for high density planting, leaf angle is an
important target trait (Li et al. 2015). Breeding for narrow leaf angle leads to more
upright leaves, which helps in increasing the leaf area index and improve photosyn-
thetic efficiency by reducing shade syndrome (Sakamoto et al. 2006). During the last
century, maize breeders placed higher emphasis on shoot phenotypes (York et al.
2015). The recent understanding on root architecture makes it possible to modify
root traits to make maize more water- and nutrition-efficient, and also suitable for
high density planting.
The narrower xylem vessel reduces the root hydraulic conductance, and thereby
saves soil moisture for later use (Meister et al. 2014). By controlling the expression
of root-water channel-related genes, such as aquaporin, the water channels in the
roots can be modulated (Hachez et al. 2012). Besides, QTL mapping has identified
the maize genomic regions that govern root architecture in water uptake (Zurek et al.
2015). In dry and nitrogen- (N) deficient soils, a deeper root, reduced maize lateral
root branching, a smaller number of crown roots would optimize N and water use
(Lynch 2013; Zhan and Lynch 2015; Saengwilai et al. 2014). The shallow axial root
growth angles many shorter laterals, and long root hairs will enhance phosphorus
(P) utilization by maize (Lynch 2013).
4.9.2 Plant Architecture
The genetic variation for morphological traits is of great importance for plant
breeders. The majority of the genes responsible for differences in morphology and
growth rate between maize and teosinte are either transcription factors or molecules
regulating transcription factors (Yang and Xu 2013). Several candidate genes with
regulatory function have been identified. The liguleless1 (lg1) and liguleless2 (lg2)
genes are associated with leaf ligule and auricle development in maize (Tian et al.
2011). ZmCLA4 is the functional gene for leaf angle QTL qLA4–1 in maize (Zhang
et al. 2014). qLA4–1 is the major QTL that negatively controls the leaf angle by ~15
with semi-dominant effect. Two QTLs, Upright Plant Architecture1 (UPA1) and
Upright Plant Architecture1 (UPA2), control the upright plant architecture in maize
(Tian et al. 2019). The brd1 (brassino steroid C-6 oxidase1) and ZmRAVL1 are the
underlying genes for these two QTLs.
The UPA2 functions by altering the protein binding affinity of another leaf angle
gene, drooping leaf1 (Strable et al. 2017). ZmGA3ox2 is the functional gene for plant
height QTLs, qPH3.1 and dwarf1 in maize (Teng et al. 2013). qPH3.1 is the major
QTL for plant height with a 10.0 cm additive effect and 3.7 cm dominant effect.
qPH1 is another major QTL for plant height explaining 17.7 cm additive and 7.8 cm
dominant effects (Xing et al. 2015). The presence of transposable element (TE) in
tb1 enhances its expression in maize which represses the axillary growth and leads to
formation of female inflorescence, besides promoting apical dominance (Doebley
et al. 2006). Another most important gene in maize domestication is tga1, which
codes for a SBP transcription factor, and is responsible for naked grain phenotype in
maize instead of kernels encased in a hardened fruitcase in teosinte (Wang et al.
2005). A single amino acid substitution (lysine to asparagine) at sixth amino acid of
tga1 changes its specificity to target site in maize leading to naked grain phenotype.
4.9.3 Flowering Time
Flowering time is a complex trait associated with adaptation of maize in different

climatic regions. A large number of QTLs for flowering time in maize has been
identified, of them three QTLs, vegetative to generative transition 1 (Vgt1),
ZmCCT10 (CCT transcription factor) and ZmCCT9, were mapped and cloned
(Salvi et al. 2007; Hung et al. 2012; Yang et al. 2013; Huang et al. 2018). Associa-
tion analysis identified significant association of three polymorphisms (G/A/
indel324, Mite and ATindel434) in Vgt1 with flowering time in maize (Salvi et al.
2007). The insertion of TE upstream of ZmCCT10 changes the promotor methyla-
tion levels that would alter the expression pattern of ZmCCT10 (Yang et al. 2013).
ZmCCT9 is the functional gene for days to anthesis QTL, qDTA9 which was
confirmed by knocking out of ZmCCT9 function resulted in earlier flowering
under long day conditions (Huang et al. 2018).
4.9.4 Nutritional Quality
Maize is an important source of carbohydrate, protein, lipids, minerals and certain

vitamins (Prasanna et al. 2001). Several genes involved in starch biosynthesis in
maize endosperm have been mapped and cloned using well-known starch mutants
(James et al. 2003). Among them, su1 and sh2 has been widely used in sweet corn
breeding (Lertrat and Pulam 2007). The sh2 gene encodes large subunit of
ADP-glucose pyrophosphorylase and accumulates six times more sugars compared
to ordinary maize (Bhave et al. 1990; Mehta et al. 2017). The su1 gene codes for
isoamylose-type starch debranching enzyme (DBE) and retains two to three times
higher sugar and ten times higher water-soluble phytoglycogens than ordinary maize
(James et al. 1995). Several maize mutants with reduced zeins and enhanced
non-zeins have been well-characterized (Gupta et al. 2015).
The mutant opaque2 (o2) located on chromosome-7 encodes less active leucine
zipper transcriptional factor leading to enhanced lysine and tryptophan in maize
endosperm (Schmidt et al. 1992). opaque16 (o16), another recessive mutant of
Robertson’s Mutator (Mu) stock, located on chromosome-8 was found to be
associated with enhanced lysine and tryptophan in maize endosperm (Yang et al.
2005; Hossain et al. 2008a, b, 2017; Sarika et al. 2017). These two genes have been
shown to enhance lysine and tryptophan content in the introgressed versions of high
yielding maize hybrids adapted to different climatic conditions (Sarika et al.
2018a, b; Prasanna et al. 2020a). Among the genes governing carotenoids biosyn-
thesis, the favourable alleles of lcyE (lycopene epsilon cyclase) and crtRB1 (-
β-carotene hydroxylase) have been found to be responsible for enhancement of
provitamin-A (proA) carotenoids in maize kernels (Harjes et al. 2008; Yan et al.
2010).
The favourable allele of lcyE reduces lycopene flux by 30% in α-branch, and
thereby diverts lycopene flux toward β-branch of the carotenoids biosynthesis
pathway, resulting in three-fold enhancements in proA (Vignesh et al. 2013; Zunjare
et al. 2017, 2018a, b). The favourable allele of crtRB1 enhances proA concentration
in maize kernels by limiting the enzymatic activity involved in β-carotene conver-
sion in β-branch (Muthusamy et al. 2016; Zunjare et al. 2018c). The ZmVTE4 and
ZmPORB2 encoding γ-tocopherol methyltransferase and protochlorophyllide oxido-
reductase, respectively, enhance kernel provitamin-E (proE) content in maize
(Li et al. 2012; Zhan et al. 2019). The favourable allele of diglyceride acyltransferase
(DGAT1–2) which encodes type I acyl-coenzyme A: diacylglycerol acyltransferase
leads to higher oil content in maize endosperm and embryo (Zheng et al. 2008). The
insertion of an extra amino acid (phenylalanine) at position 469 of DGAT1–2 causes
enhancement of its enzymatic activity and results in increased oil and oleic acid.
Zmfatb gene which codes for acyl-ACP thioesterase enhances palmitic acid content
in maize (Li et al. 2011). An 11 bp InDel in the last exon of Zmfatb affects the
enzyme activity by introducing a premature stop codon.
4.10 Specialty Traits
4.10.1 Sweet Corn
Two genes affecting the starch metabolism, viz., su1 (chromosome 4) and sh2
(chromosome 3), have been extensively used for development of sweet corn
cultivars, where the sh2 is located upstream of the pathway, while enzyme coded
by su1 affects step downstream of the pathway (Hossain et al. 2015; Chhabra et al.
2019a, b, 2020, 2021). Sugary varieties (su1su1) at the milky ripening stage contain
nearly three times more reducing sugar and sucrose, ten times more water-soluble
phytoglycan (WSP) and one-third of starch content of normal maize (Fisher and
Boyer 1983; James et al. 1995; Feng et al. 2008). Besides, sugary kernels have
creamy texture with good flavour and appear wrinkled and glossy upon maturity
(Creech 1965). However, the sugar level after the harvest declines much faster in the
su1 types (Garwood et al. 1976). On the other hand, the sh2-based sweet corn types
popularly called ‘super sweet’ or ‘extra sweet corn’ accumulate sugar in place of
starch.
At milky ripening stage, the content of reducing sugars and sucrose in the kernel
is about six-fold higher than the ordinary maize (Feng et al. 2008; Khanduri et al.
2011; Solomon et al. 2012). However, the content of WSP is similar to normal
maize, and starch content is about one-third of the ordinary maize. By virtue of
higher amount of sugars in sh2sh2 mutant, kernels contain decreased amount of total
carbohydrates at the mature seed stage, and the kernels get collapsed and look
shrunken with degree of opaqueness (Creech 1965). The depletion of sugar level
is much slower in sh2 type even without refrigeration; thus, varieties have extended
shelf life and are better suited for prolonged storage. Sweet corn cultivars with
combination of su1 and sh2 have often been used in commercial sweet corn
development (Lertrat and Pulam 2007). Furthermore, sugary enhancer1 (se1) (chro-
mosome 2), a modifier of su1, has been used in combination with su1 in sweet corn
development. Now, brittle2 (bt2) (chromosome 4) based sweet corn cultivars have
also been developed and commercialized worldwide. Furthermore, sweet corn has
now been biofortified with high lysine, tryptophan, proA and proE (Feng et al. 2015;
Mehta et al. 2020a, b, 2021; Baveja et al. 2021).
4.10.2 Popcorn
Popping percentage and popping volume are two most important characters for
popcorn (Pal et al. 2020). Several mapping studies have reported many major
genomic regions for popping traits with >10% phenotypic variance (Lu et al.
2003; Babu et al. 2006; Li et al. 2007a, b; Liu et al. 2007a; Yongbin et al. 2012).
Recently, Meta-QTL analyses revealed three QTLs located on chromosome
1 (metaQTL1_1, metaQTL1_5 and metaQTL1_7) and one QTL on chromosome
6 (metaQTL6_2) as significant QTL responsible for popping traits (Kaur et al. 2021).
4.10.3 Baby Corn
Among various genes, teosinte branched1 (tb1) has been identified as the key gene
(on chromosome 1) determining prolificacy (Doebley et al. 1995, 1997; Doebley
2004). Wills et al. (2013) identified a ‘prol1.1’ major QTL located on chromosome
1 for prolificacy. Prakash et al. (2021) identified a novel QTL ‘qProl-SP-8.05’ from
‘Sikkim Primitive’ on chromosome 8. It is a prolific maize landrace with five to nine
ears per plant. QTL mapping identified a major QTL (bin: 8.05) explaining 31.7%
and 29.2% of phenotypic variance in two mapping populations.
4.10.4 Waxy Corn
Waxy maize is originated from the cultivated flint maize through mutation in Wx1
locus (Fan et al. 2008; Zheng et al. 2013). Wx1 is mapped on the short arm of
chromosome 9 (Klosgen et al. 1986; Mason-Gamer et al. 1998). Wx1 codes granule-
bound starch synthase (GBSS-I) gene which catalyses amylose synthesis from ADP
glucose in amyloplasts of maize endosperm. Different types of mutation, such as
insertion of transposon, retroposon and fragments of few nucleotides and deletion of
nucleotides, result in mutant allele (wx1) (Devi et al. 2017; Hossain et al. 2019b).
These mutations create the synthesis of altered transcript with premature stop codon
or change in amino acids in key domain or splicing or translational errors that in turn
stops the activity of wild-type Wx1 allele or inhibits the activity of GBSS-I, which
results in lower amylose and higher amylopectin in grain (Bao et al. 2012; Zhang
et al. 2013). Generally, GBSS-I is highly active in non-waxy maize and its product
(amylose) cannot be fully changed into amylopectin by starch branching enzyme.
GBSS-I coded by recessive gene wx1 possesses reduced activity (Liu et al. 2007b).
Most of the amylose synthesized by low activity of GBSS-I are transformed into
amylopectin by starch branching enzyme. Amylopectin is only accumulated in
endosperm, and the phenotype appears as waxy (Wessler et al. 1986).
4.10.5 High Amylose Maize
The recessive amylose extender1 (ae1) mutation (present on chromosome 5) that

codes for starch branching enzyme (sbe2b) enhances amylose to a level of 50–60%
from 25 to 30% found in traditional maize (Li et al. 2008). The ae1.1 is a null allele,
also called ae1-ref, which does not produce a SBE2b protein product (Vineyard and
Bear 1952). A second variant ae1.2, known as ae1-Elmore, produces a catalytically
inactive and truncated protein (Liu et al. 2012). Increase in amylose content by ae1
was only 50%. Maize starch with amylose content of >60% is the result of high
amylose modifier genes in the maize ae1 background. A major modifier gene of ae1
has been reported to be SbeIa, which can increase amylose up to 70–80% in the
presence of ae1 (Garwood et al. 1976; Hedman and Boyer 1982). Second modifier
called modifier of amylose extender1 (mae1) has also been reported (Krzywdzinski
2016).
4.11 Biotic Stress Tolerance
Diseases are the most important factors for yield loss in maize. Many QTLs for
disease resistance in maize has been identified; however, only few genes have been
validated (Yang et al. 2017; Liu et al. 2020a). The maize Hm1 gene governing
resistance against maize leaf blight was the first gene to be cloned and elucidated at
molecular level in plants (Johal and Briggs 1992). It is a dominant gene which is
located on chromosome 1 and codes for NADPH-dependent HC-toxin reductase
which inactivates HC toxin. The Rp1-D is another resistance gene conferring
resistance toward common rust in maize (Collins et al. 1999). Six resistance genes,
viz., ZmWAK, ZmHtn1, ZmTrx, Rcg1, ZmCCT10 and ZmAuxRp1, with relatively
large effects have also been cloned in maize (Zuo et al. 2015; Hurni et al. 2015;
Wang et al. 2017b; Ye et al. 2019). The ZmWAK gene codes for a wall-associated
kinase-specific 730 residue receptor-like protein which represses the fungal growth
(Sporisorium reilianum) in above ground tissues (Zuo et al. 2015). The ZmHtn1
gene mapped on chromosome 8 also encodes wall-associated receptor-like kinases
to confer resistance toward northern leaf blight (Hurni et al. 2015).
The ZmTrxh mapped on chromosome 6 lacks two canonical cysteines in its
thioredoxin active-site motif required to reduce disulfide bridges and provide resis-
tance to sugarcane mosaic virus (Liu et al. 2017a). Rcg1 is a major QTL located on
chromosome 4 which encodes a NB-LRR domain and provides resistance to
anthracnose stalk rot (Frey et al. 2011). ZmCCT10, a gene that controls the flowering
time in maize is also associated with resistance to Gibberella stalk rot (Yang et al.
2013). The CACTA-like transposable element in ZmCCT10 is the causal variant,
which alters its DNA methylation and histone modification, and results in greater
disease resistance (Wang et al. 2017b). ZmAuxRP1 encodes DUF966 protein and
also confers resistance to Gibberella stalk rot by affecting the biosynthesis of both
IAA and benzoxazinoids (Ye et al. 2019). Among insect-pest, FAW severely limits
maize production by causing severe damage to the growing young leaves. Womack
et al. (2020) identified two major QTLs (bin: 4.06 and 9.03) that explained 35.7% of
the phenotypic variance over all environments.
Resistance sources to foliar diseases of maize including maydis leaf blight (MLB,
southern corn leaf blight, or SCLB) (Bhat et al. 2012), turcicum leaf blight (TLB,)
northern corn leaf blight, or NCLB) (Ayiga-Aluba et al. 2015; Bhat et al. 2017;
Kurosawa et al. 2017), gray leaf spot (GLS) (Dhami et al. 2015), polysora and
common rust, downy mildew (DM), some viral diseases, Aspergillus contamination
(Hooda et al. 2012; Badu-Apraku and Fakorede 2017) have been identified and are
incorporated successfully through conventional breeding. In addition, multiple dis-
ease resistance (MDR) in maize has been reported (Martins et al. 2019). International
Maize and Wheat Improvement Center (CIMMYT) has developed a multiple borer
resistance (MBR) source population utilizing diverse germplasm obtained from
different organizations.
MBR population was developed by adopting recombination and recurrent selec-
tion under artificial insect epidemics against Southwestern corn borer (SWCB),
sugarcane borer (SCB), European corn borer (ECB) and fall armyworm (FAW)
Table 4.1 Secondary and tertiary gene pool resources of maize for biotic stress tolerance
S. No. Biotic stress Germplasm Reference (s)
Secondary gene pool
1. Maize chlorotic dwarf virus Z. diploperennis Findley et al.
(1982)
2. H. turcicum, H. maydis Z. diploperennis Wei et al.
(2003)
3. Corn smut disease downy mildew Z. mays spp. mexicana Mammadov
et al. (2018)
4. H. turcicum, H. maydis Z. diploperennis Mammadov
et al. (2018)
5. Fusarium spp. Z. spp. mexicana Pasztor and
Borsos (1990)
6. Striga-parasitic weed Z. diploperennis Yallou et al.
(2009)
7. Northern leaf blight Teosinte Ott (2008)
8. Ustilago maydis Teosinte Chavan and
Smith (2014)
9. Corn borer Z. mays spp. mexicana Pasztor and
Borsos (1990)
10. Asiatic corn borer Z. mexicana, Ramirez
Z. diploperennis. Z. perennis (1997)
11. Corn rootworm T. dactyloides Prischmann
et al. (2009)
12. S. frugiferda Z. diploperennis Farias-Rivera
et al. (2003)
Tertiary gene pool
13. C. graminicola, H. turcicum, T. dactyloides Bergquist
H. maydis, E stewartii, P. sorghi (1979)
14. Rust disesase T. dactyloides Mammadov
et al. (2018)
15. H. turcicum (Ht gene) T. floridanum Hooker and
Perkins (1980)
16. P. sorghi (RpTd gene) T. dactyloides Bergquist
(1981)
(Mihm 1985). As teosintes are more resistant to insects and pathogen than the
improved maize cultivars, understanding the underlying defence mechanisms of
teosintes would present novel strategies to breed for biotic stress resistance in
modern maize. Exploring the genetic variation for resistance and other agronomic
traits among wild and landrace of maize has long been advocated (Flint-Garcia
2013). Over the years, many research efforts have been directed towards the
identification/development of resistant sources against various biotic stresses.
Besides primary gene pool, resistant sources from secondary and tertiary gene
pools have also been identified (Table 4.1).
4.12 Abiotic Stress Tolerance
Initial attempt of QTL mapping for drought tolerance in maize was executed using
Polj17 (drought-resistant) and F-2 (drought-sensitive) to generate F2 population
(Lebreton et al. 1995). In this study, QTLs for abscisic acid (ABA) content and
stomata conductance were mapped. Since then, numbers of studies have been
recorded on QTL mapping in maize for important morpho-physiological traits
drought stress condition. In different studies of QTL mapping, many QTLs were
identified for morphological traits like male flowering, female flowering, anthesis
and silking interval (ASI), yield and cob number (Ribaut et al. 1996; Ribaut et al.
1997; Agrama and Moussa 1996; Sari-Gorla et al. 1999). Later, considering the
importance of root and its related traits imparting the tolerance to drought, different
QTLs for root architecture and root-associated traits along with yield traits have been
identified, viz., one QTL for root trait (Landi et al. 2010), 22 QTLs for root-
associated traits, such as root density, root dry weight, sugar concentration and
leaf ABA content through composite interval mapping in F2:3 population (Rahman
et al. 2011). Similarly, Trachsel et al. (2016) identified a total of 17 QTLs for
stomatal conductance, leaf water content, ASI, and grain yield.
Besides, association mapping is another important approach for better resolution
of QTLs as it utilizes the historical recombination events in natural populations
known as association panel. Setter et al. (2011) conducted association mapping to
identify single nucleotide polymorphisms (SNPs) related to genes involved in
carbohydrate and ABA metabolite accumulation during drought stress. Aldehyde
oxidase gene is found to regulate silk ABA concentration under drought stress.
Later, SNP-based genome-wide association mapping was conducted using 5000
inbred lines as association panel (Li et al. 2016). The study revealed significant
association of SNPs with drought tolerance associated candidate genes. However,
most of the identified QTLs identified till date are of minor effect except few major
QTLs. The mQTL study conducted using three populations and several
environments revealed seven genomic regions for grain yield and one genomic
region for ASI. Among these, six mQTL on grain yield mapped on chromosomes
1, 4, 5 and 10 under moisture stress and optimal environments and hence classify as
stable QTLs.
Though hundreds of QTLs for drought tolerance have been mapped, only few of
them have been cloned (Liu and Qin 2021). Two large effects on genes SDG140 and
Hp322 were identified for drought tolerance in maize (Lu et al. 2010). SDG140 gene
which encodes a SET-domain protein is the underlying gene for HP71 haplotype of
drought tolerance. Hp322 includes two closely linked SNPs from a gene encoding
aldo-keto reductase and provides enhanced drought tolerance. Four genes,
ZmNAC111 ZmVPP1, ZmTIP1 and Zmabh2, have been identified to be responsible
for seedling drought tolerance in maize (Mao et al. 2015; Wang et al. 2016; Zhang
et al. 2019; Liu et al. 2020b). Two genes, ZmPYL8 and ZmPYL12, which encodes the
abscisic acid receptors, facilitate drought tolerance in maize (He et al. 2018). Maize
ABP2 (ABRE binding protein 2) gene codes for bZIP transcription factor which
enhances the expression of stress-responsive, and carbon metabolism-related genes

result in enhanced tolerance to both drought and salt (Na et al. 2018).
Several QTLs for heat stress tolerance in maize has been mapped using biparental
and genome-wide association mapping approaches, and few candidate genes have
also been identified (Frey et al. 2016; Gao et al. 2019; Inghelandt et al. 2019;
Longmei et al. 2021). Frey et al. (2016) identified two QTL hotspots separately on
chromosome 2 and 3 for heat tolerance with respect to grain yield, which explained
7–13% of the variance. The low variance of these QTLs explained the multigenic
inheritance of tolerance to heat in maize. Frey et al. (2016) also identified three heat
tolerance genes (GRMZM2G115658; GRMZM2G537291 on chromosome 2; and
GRMZM2G324886 on chromosome 3) in the above identified QTL hotspot regions.
The gene GRMZM2G324886 codes for calcicylin binding protein involved in
calcium signalling in response to stress condition. QTL for heat susceptibility
index (leaf scorching trait) has been found on chromosome 9 and QTL for heat
susceptibility index (grain yield) were reported on chromosome 2 and 3, which
suggested the involvement of different genomic regions in regulation of genetic
mechanisms for leaf scorching and grain yield (Frey et al. 2016).
Inghelandt et al. (2019) identified six QTLs for heat susceptibility index of the
five traits at the seedling stage which exhibited 7–9% of the phenotypic variance.
Eleven QTLs have been mapped for pollen germination and pollen tube (Frova and
Sari-Gorla 1994). The pollen germination ability is correlated with the cellular
membrane stability since QTLs for both the traits map to common region on the
short arm of chromosome 8 (Ottaviano et al. 1991). Qin et al. (2007) reported that
higher expression of ZmDREB2A gene in maize may induce heat responsive genes
which may further provide adaptability under high temperature stress. QTLs
controlling leaf temperature, ASI and grain yield have been mapped in maize on
chromosome 7 (Sanguineti et al. 1999).
Transcriptome study in maize in response to heat stress identified 1029
upregulated and 828 downregulated DEGs, and the analysis indicated the central
role of protein processing in endoplasmic reticulum in response to heat stress (Qian
et al. 2019). They also identified 167 putative transcription factors associated with
heat stress response of maize belonging to the TF family of MYB, AP2-EREBP,
b-ZIP, bHLH, NAC and WRKY. Heat stress triggers the endoplasmic reticulum
stress which causes heat-induced upregulation of ZmbZIP60, and study by Li et al.
(2018) concluded that upstream region of ZmbZIP60 is vital in its upregulation under
heat stress.
Waterlogging tolerance in maize is governed by complex genetic mechanism
with involvement of multiple genomic regions (Mano and Omori 2007). Mano et al.
(2005) reported two QTLs on chromosomes 4 and 8 governing adventitious root
formation under waterlogging condition. Mano et al. (2009) also identified three
QTLs for adventitious root formation under waterlogging condition on
chromosomes 3, 7 and 8 from the backcross population derived from the cross
Mi29 teosinte (Z. nicaraguensis). Composite interval mapping of F2 population of
cross between F1649 and H84 reported that a single QTL of chromosome 1 is
responsible for the severity of leaf injury due to waterlogging (Mano et al. 2015).
Qiu et al. (2007) reported chromosomes 4 and 9 as the hot spots for several QTLs
governing root dry weight, shoot dry weight, total dry weight and plant height. Zaidi
et al. (2015) identified 22 candidate genes from several identified QTLs located on
chromosome1, 3, 4, 5, 7, 8 and 10 for grain yield and other secondary traits
associated with waterlogging tolerance.
A total of 7 out of 55 uniformly distributed QTLs among all the 10 chromosomes
were identified as the candidate genes for waterlogging tolerance. These candidate
genes were lying on the previously identified QTLs located on chromosomes 1, 4,
6, 7 and 9 (Osman et al. 2013). Transcriptome analysis has identified the rapid
induction in TFs families bZIP, AP2/ERF, bHLH, NAC and MYB under
waterlogging condition (Yu et al. 2020). A genome-wide analysis in the inbred
line HZ32 revealed 38 out of 184 AP2/ERF genes identified in maize which
responds to waterlogging stress (Du et al. 2014). In addition to all these genes and
transcription factors, non-coding RNAs also play key role in making adaptive
changes in morphology and metabolism of plants in response to waterlogging stress
(Yu et al. 2020). The gene ZmEREB180 of the ERF-VII family in maize have been
found to play key role in regulating the adventitious root growth, and overexpression
of ZmEREB180 also enhances the tolerance level against waterlogging stress
(Yu et al. 2019).
4.13 Genomics-Assisted Breeding
Conventional breeding achieved success in developing maize varieties with

enhanced yield, quality and stress tolerance through crossing and selection over
years (Liu and Qin 2021). However, this is tedious, time-consuming and inefficient
for complex traits. Genomics-assisted breeding approaches, such as marker-assisted
backcross breeding (MABB), forward breeding (FB) and genomic selection (GS),
are considered to be efficient tools for accelerating genetic gain by increasing
selection intensity and reducing selection cycles by two to three years (Gilliham
et al. 2017; Prasanna et al. 2021). Bouchez et al. (2002) introgressed favourable
alleles of three QTLs for earliness and grain yield through three cycles of marker-
assisted backcrossing. Marker-assisted introgression of o2, crtRB1 and vte4 has been
used to improve protein quality (Gupta et al. 2013; Hossain et al. 2018, 2019a, c;
Sarika et al. 2018a; Jompuk et al. 2020), proA content (Muthusamy et al. 2014; Liu
et al. 2015b; Zunjare et al. 2018a) and proE content (Feng et al. 2015; Das et al.
2021), respectively, in maize. In recent years, multi-nutrient-rich inbred lines and
hybrids, especially combinations of quality protein maize (QPM), proA, proE and
low phytate, have been developed through MABB (Bhatt et al. 2018; Goswami et al.
2019; Mehta et al. 2020b; Baveja et al. 2021; Das et al. 2021; Singh et al. 2021).
Several proA-rich and three QPM + proA-rich hybrids developed by MABB have
been released for commercial cultivation worldwide (Prasanna et al. 2020a). MABB
have also been used for improving disease resistance and abiotic stress tolerance in
maize. Zhao et al. (2012) introgressed qHSR1 QTL into 10 inbred lines of maize
which resulted in significant improvement for head smut resistance. Marker-assisted
backcrossing of H5 haplotype of ZmCCT showed to enhance resistance to stalk rot in

maize inbreds and hybrids (Li et al. 2017). The marker-assisted pyramiding of
sugarcane mosaic virus (Scmv1) and Scmv2 QTLs into F7 maize line resulted in
complete resistance to sugarcane mosaic virus (Xing et al. 2006).
Yang et al. (2017) developed near isogenic lines with qMdr9.02 locus containing
multiple disease resistance genes via maker-assisted selection, which possessed
resistance to southern corn leaf blight and GLS. Using MABB, resistance to maize
lethal necrosis (MLN) has been introgressed into over 30 elite drought-tolerant
maize lines (Prasanna et al. 2020b). Similarly, Awata et al. (2021) introgressed
QTL for resistance to MLN into nine elite but MLN susceptible lines. Ribaut and
Ragot (2007) showed drought tolerance in MABB-derived test cross maize hybrids
over control hybrids. Wang et al. (2016) intogressed ZmVPP1 QTL into drought
susceptible inbred, Shen5003 through four cycles of marker-assisted backcrossing.
The improved progenies with homozygous ZmVPP1 showed enhanced drought
tolerance than Shen5003.
FB is a simple form of population improvement using molecular markers tightly
linked to genomic regions of high importance. FB is being used for improvement of
maize populations with favourable alleles of large effect genes/QTLs for disease
resistance, such as maize streak virus and MLN, and nutritional quality traits, such as
proA (Prasanna et al. 2020c). Duo et al. (2021) applied marker-assisted pedigree
selection (MAPS) for improvement of proA in sub-tropically adapted maize inbreds.
The resultant inbreds and hybrids showed significantly higher proA than traditional
hybrids indicating the feasibility of MAPS for improving nutritional traits. Marker-
assisted recurrent selection (MARS) is useful to accumulate favourable alleles from
several genomic regions within a single population. Abdulmalik et al. (2017) applied
MARS in a bi-parental population to increase the frequency of favourable alleles for
drought tolerance.
GS is a powerful tool to take account of all the major or minor QTLs spread
throughout the genome and is especially useful for complex traits (Santantonio et al.
2020). GS is conducted in a training population by combining genotypic and
phenotypic data to estimate the marker effects (breeding values) of the individuals
that have been genotyped but not phenotyped in a population to be tested
(Meuwissen et al. 2001). GS helps in population improvement by rapid cycling
and higher genetic gain per cycle through the use of markers. GS has been applied in
maize for improvement of grain yield (Beyene et al. 2015; Zhang et al. 2017),
drought and water logging tolerance (Vivek et al. 2017; Das et al. 2020), disease
resistance (Technow et al. 2013; Sitonik et al. 2019; Nyaga et al. 2019; Liu et al.
2020c; Kuki et al. 2020; Holland et al. 2020), and kernel oil (Hao et al. 2019) and
zinc content (Guo et al. 2020; Mageto et al. 2020).
4.14 Doubled Haploid Technology
Maize breeding exploiting the doubled haploid (DH) technology based on in vivo
haploid induction has gained wide significance and become an invaluable tool due to
the fastest and most efficient route to produce completely homozygous lines for
maize breeding programmes (Ren et al. 2017). DH lines in maize is produced in four
steps, viz., haploid induction using the haploid inducer line, identification of
haploids, chromosome doubling and selfing of the doubled haploid maintain DH
line (Chaikam et al. 2019). The natural occurrence of haploid maize plants (~0.1%)
laid the base for in vivo DH production (Chase 1969). Haploid inducers may be the
paternal (used as female parent and haploid produced retain genome from the male
parent) or maternal inducers (used as male parent and retain genome from the female
parent). Paternal haploid induction has been reported through mutation in the ig1
gene (indeterminate gametophyte1) (Kermicle 1969; Evans 2007). However, it is not
being commonly used due to low haploid induction rate (HIR) of 1–2%, as well as
presence of anomaly in the cytoplasmic constitution of the resulting haploid
(Kermicle 1973, 1994).
Maternal haploid induction is quite successful and is being frequently used in
maize DH production due to high HIR of around 8–10%, and the haploid produced
retain the cytoplasmic and nuclear genome of the female parent without any
differences. At present, all the haploid inducers being used have been deduced
from the ancestral haploid inducer line Stock6 (HIR of ~3% of maternal haploids).
The currently available haploid inducers have the HIR of around 10%. In maize, two
major quantitative trait loci, qhir1 in bin 1.04 and qhir8 in bin 9.01, govern
significant haploid induction (Prigge et al. 2012). Dong et al. (2013) identified a
243 kb region with significant effect on haploid induction by fine-mapping a
3.57 Mb region between markers umc1917 and bnlg1811, targeting the QTL
qhir1. Kelliher et al. (2017), Liu et al. (2017b) and Gilles et al. (2017) reported
mtl/pla1/nld is the gene underlying the qhir1. 4 bp insertion near the terminal end of
the mtl gene causes the haploid induction. Zhong et al. (2019) cloned the gene
underlying qhir8 and found a non-Stock6-originating gene, dmp. They exhibited that
SNP substitution in dmp from thymine (T) to cytosine (C), at 131 bp from the
initiation codon ATG leads to amino acid substitution from methionine to threonine.
Enhanced ability of HIR by five to six times of dmp was observed in the presence
of mtl/pla1/nld. The first identified inducer ‘Stock 6’ had HIR of 1–3%. Efforts have
been made to enhance the HIR and several inducers like PHI (Rotarenco et al. 2010),
RWS (Rober et al. 2005), UH400 (Prigge et al. 2011) and MHI (Chalyk 1999) were
developed with HIR of ~6–15%, but all of them were adapted to temperate environ-
ment. Later on, tropically adapted inducer lines with HIR of around 6–14% were
also developed with the efforts of CIMMYT and the University of Hohenheim
(Prigge et al. 2012; Prasanna et al. 2012; Chaikam et al. 2016; Chaikam et al.
2018). DH technology is now the order of choice to all the maize breeders as lengthy
6–7 generation of inbreeding is bypassed, and completely homozygous plants are
achieved in two to three seasons.
4.15 Gene Editing Technology
Mutagenesis through physical and chemical agents and through Targeting Induced
Local Lesions in Genomes (TILLING) has been used to create variability (Slade
et al. 2005). Site-directed mutagenesis systems are now available for targeted
genome editing. Present-day genome editing tools such as zinc finger nucleases
(ZFNs), transcription activator like effector nucleases (TALENs) and clustered
regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated (Cas)
systems (Georges and Ray 2017). ZFN technology has been used to reduce phytate
content in maize seeds by targeting one of the inositol phosphate kinase (IPK)
homologues (Shukla et al. 2009). TALENs approach has been used to generate
heritable changes in maize gl2 locus (Char et al. 2015). In maize, various traits such
as grain composition, male sterility, lignin biosynthesis, herbicide tolerance, second-
ary metabolism and drought tolerance have been modified through CRISPR tech-
nology (Chilcoat et al. 2017).
The first use of CRISPR technology was reported for the maize IPK gene (Liang
et al. 2014). In addition, Shi et al. (2017) used the native maize GOS2 promoter to
both replace and supplement the native ARGOS8 promoter to achieve altered
expression of ARGOS8 and yield gains under drought high yield levels under
well-watered conditions. CIMMYT has started the MLN gene editing project
which uses CRISPR/Cas9 with the goal of deployment of resistant cultivars by
2025. Besides, transgene-free semi-dwarf maize plants were generated using
CRISPR-Cas9 technology by editing GA20ox3 gene (GA biosynthetic gene). Qi
et al. (2020) edited waxy locus in genetic background of ZC01 genotypes using
in vivo CRISPR/Cas9 tool and successfully obtained progenies rich in kernel
amylopectin. Recently, Liu et al. (2021) obtained genetic gain in multiple maize
grain-yield-related traits by engineering quantitative variation for yield-related traits.
This was done by engineering weak promoter alleles of CLE genes (a family of
genes that act as a brake to stop stem cell growth) and a null allele of a newly
identified partially redundant compensating CLE gene, using CRISPR-Cas9 genome
editing. Very recently, a new genome editing technology that does not require
double-stranded break in the DNA has been developed and is termed as prime
editing. This can achieve different types of editing such as any transition and
transversion mutations, as well as small indels. As this technology has wide flexibil-
ity to obtain different types of edits in the genome, it holds a great promise for
developing superior maize varieties with high yield, resistance to various abiotic and
biotic stresses, and quality of plant products (Marzec et al. 2020).
4.16 Future Thrust
Significant progress in understanding the genetics and efforts toward adopting newer
breeding methodologies and effective integration of omics tools have led to a
substantial genetic improvement of maize both in terms of productivity and total
production. Continued yield enhancement in maize with newer varieties year-after-
year has led to an imperative growth in area under cultivation of the maize crop. The
primary challenge in the future is going to be further enhancement of yield with
increased adaptation to the newer challenges. Despite the persistent yield growth,
breeding for stress tolerance particularly biotic stress is continuing to be an area that
need immediate attention. Although efforts have been made to understand the
genetics and to identify the gene(s)/loci governing disease resistance, their actual
use in breeding for resistant cultivars is still to reach its full potential.
With the changing climatic conditions and evolution of new races of pathogen,
breeding for resistance to disease of greater concern in the region is highly important.
In the most recent times, outbreak and rapid spread of FAW have created havoc in
maize cultivation as delay in control measures has led to a greater reduction in yield
and sometimes complete failure of the crop. This has also necessitated excessive use
of chemicals which has increased cost of production besides posing serious environ-
mental pollution. Besides, tolerance to abiotic stresses, particularly drought, heat and
water logging are very important as maize crop is sensitive to both moisture stress
and excessive moisture. Thus, widening of germplasm for multiple stress resistance/
tolerance and their use in crop improvement programme to breed high yielding
maize hybrids coupled with stress tolerance is very important.
Recently, considerable success has been achieved in development of high yield-
ing hybrids with enhanced nutritional quality (with one or more grain quality traits).
This offers hope for simultaneous improvement of multiple traits, and these
germplasms also need to be improved for stress tolerance for its wider adaptation
and adoption. Weeds continue to remain as one of the major yield-reducing factors in
maize production. Development of herbicide-tolerant maize genotypes will greatly
facilitate use of herbicides for weed management anytime during the crop growth.
This requires large-scale screening of available germplasm for herbicide tolerance or
use of mutation as a tool to create variation for such economically important traits.
Until recent times, breeders have been largely practising inbreeding for development
of more and more inbreds from the source population. By the virtue of process and
associated genetic effects, complete homozygosity could never be achieved in the
inbreds. Use of DH technology in the maize-breeding programmes needs to be
strengthened for rapid development of completely homozygous productive inbreds.
This will help in greatly reducing the time taken for inbred development besides
maximum realisation of heterosis. With the availability of gene-editing technology,
accelerated development of genotypes with target traits is very much possible, and
this will greatly facilitate in plant breeding. Furthermore, ‘speed breeding’ needs to
be explored in maize to accelerate the breeding cycle and development of hybrids in
a much shorter time frame.
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Chapter · May 2022

Firoz Hossain Vignesh Muthusamy

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Jayant Bhat Rajkumar U. Zunjare

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F. Hossain (*) · V. Muthusamy · J. S. Bhat · R. U. Zunjare

Zea mays · Corn · Genomics · Markers · Gene · QTL · Specialty traits

4.2 Origin of Maize

4.2.1 Tripartite Hypothesis (Mangelsdorf and Reeves 1938)

4.2.2 Catastrophic Sexual Transmutation Hypothesis (Iltis 1983)

According to this hypothesis, sudden sexual transmutation in teosinte was responsi-

4.2.3 Tripsacum–Zea Diploperennis Hypothesis (Eubanks 1995)

It is the modiﬁed version of tripartite hypothesis. According to this hypothesis,

4.2.4 Teosinte Hypothesis (Beadle 1939)

4.3 Species Distribution

4.4 Types of Grains

4.4.1 Flint Corn (Zea mays ssp. mays var. indurata)

Complete kernel including outer portion is made up of hard starch.

4.4.2 Dent Corn (Zea mays ssp. mays var. indentata)

4.4.3 Sweet Corn (Zea mays ssp. mays var. saccharata)

4.4.4 Flour Corn (Zea mays ssp. mays var. amylacea)

4.4.5 Popcorn (Zea mays ssp. mays var. everta)

4.4.6 Waxy Corn (Zea mays ssp. mays var. ceratina)

4.4.7 Pod Corn (Zea mays ssp. mays var. tunicata)

These are podded grains covered inside glumes.

4.5 Floral Biology

4.6 Varietal Development

4.7 Hybrid Development

Adoption of these technologies resulted in rapid shift of farmers toward double

4.8 Genetic Resources

4.9 Key Loci for Economically Important Traits

4.9.1 Grain Yield and Component Traits

4.9.2 Plant Architecture

4.9.3 Flowering Time

Flowering time is a complex trait associated with adaptation of maize in different

4.9.4 Nutritional Quality

Maize is an important source of carbohydrate, protein, lipids, minerals and certain

4.10 Specialty Traits

4.10.1 Sweet Corn

4.10.3 Baby Corn

4.10.4 Waxy Corn

4.10.5 High Amylose Maize

The recessive amylose extender1 (ae1) mutation (present on chromosome 5) that

4.11 Biotic Stress Tolerance

4.12 Abiotic Stress Tolerance

enhances the expression of stress-responsive, and carbon metabolism-related genes

4.13 Genomics-Assisted Breeding

Conventional breeding achieved success in developing maize varieties with

backcrossing of H5 haplotype of ZmCCT showed to enhance resistance to stalk rot in

4.14 Doubled Haploid Technology

4.15 Gene Editing Technology

4.16 Future Thrust

Chaikam V, Nair SK, Martinez L et al (2018) Marker-assisted breeding of improved maternal

Li Q, Yang X, Xu S et al (2012) Genome-wide association studies identiﬁed three independent

Prasanna BM, Palacios-Rojas N, Hossain F et al (2020a) Molecular breeding for nutritionally

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