Biotechnology

The r p l locus of maize controls race-specific resistance to the common rust fungus Puccinia sorghi. Four mutant or recombinant bpl alleles (rpl-NC3, Rpl-D27, Rpl-MDl9, and Rpl-KrlN) were identified. They condition necrotic phenotypes in the absence of the rust pathogen. These Rpl lesion mimics fall into three different phenotypic classes: (1) The rpl-NC3 and Rpl-D27 alleles require rust infection or other biotic stimulus to initiate necrotic lesions. These alleles react strongly to all maire rust biotypes tested and also to nonhost rusts. (2) The Rpl-MDl9 allele, which has a similar phenotype, also requires a biotic stimulus to initiate lesions. However, Rpl-MDl9 shows the race specificity of the Rpl-D gene.

The microsatellite or simple sequence repeat (SSR) marker is the most preferred marker because of its many desirable properties. It is important to increase the genic and genomic resources particularly in legumes because the SSR markers currently available in chickpea, pigeonpea, horsegram, blackgram, and cowpea are very limited. In the present study, 201 pairs of SSR markers comprising of 172 genic and 29 genomic SSRs were screened against 11 chickpea genotypes, among which 153 produced monomorphic and 48 produced polymorphic bands. The polymorphic information content ranged from 0.152 to 0.373 for both genic and genomic SSRs. Among the polymorphic markers, two-three alleles were detected for genic and two-four alleles for genomic SSRs. A unique banding pattern could be found for all the genotypes within 48 polymorphic SSR markers and cultivar specific markers could be identified for seed purity test. We have also studied the ability of chickpea genic and genomic SSRs to amplify distantly related but important legumes viz., horsegram, blackgram, cowpea, pigeonpea, and soybean. Out of 201 chickpea SSR primer pairs, 66.7% in blackgram, 62.2% in horsegram, 61.7% in redgram, 54.7% in cowpea, and 62.7% in soybean produced amplification. The transferability of about 60.0% of the chickpea SSRs to distantly related legumes could be considered successful. In the present study, 134, 133, 126, 124, and 110 new SSR primers for blackgram, horsegram, soybean, redgram, and cowpea pulse crops, respectively, were identified. It is an important addition to the already available genomic resources in these crops. In addition, among genic primer pairs, 12 in horsegram, three in soybean, 13 in redgram, and eight in cowpea, and among genomic primer pairs, two in horsegram and four in redgram were polymorphic even in the two-three genotypes tested indicating their potentially for application in genetic studies and mapping.

Peanut production, quality and trade is predominantly affected by aflatoxin contamination especially
under rainfed conditions making produce unfit for human and animal consumption because of its
carcinogenic effect. Hence, finding the resistance source is the need of the hour for aflatoxin
resistance breeding. Attempts are therefore being made to use different genomic approaches to tackle
this challenge. In the first approach, RNAsequencing
of resistant (J 11, ICGV 91278) and susceptible
(JL 24) genotypes has been carried out to study the resistance to invitro
and preharvest
colonization
of seeds by Aspergillus flavus (strain AF114).
The preliminary results in the invitro
seed colonization
showed several differentially expressed genes in control and infected samples of resistant and
susceptible genotypes, which provide the insights of the probable resistance mechanisms. In the
second approach, peanut ‘reference set’ was screened for aflatoxin contamination across four
environments at Niger and the analysis is underway to identify markertrait
associations for aflatoxin
contamination. As there are no biparental
populations reported for aflatoxin resistance in peanut,
multiparent
advanced generation intercross (MAGIC) populations are being developed for aflatoxin
resistance along with other important agronomic traits as the third approach. In summary, combined
approaches will provide entities responsible for aflatoxin contamination and their use in aflatoxinfree
peanut improvement.

Contamination of crops with aflatoxin is a serious global threat to food safety. Aflatoxin production by Aspergillus flavus is exacerbated by drought stress in the field and by oxidative stress in vitro. We examined transcriptomes of three toxigenic and three atoxigenic isolates of A. flavus in aflatoxin conducive and non-conducive media with varying levels of H2O2 to investigate the relationship of secondary metabolite production, carbon source, and oxidative stress. We found that toxigenic and atoxigenic isolates employ distinct mechanisms to remediate oxidative damage, and that carbon source affected the isolates' expression profiles. Iron metabolism, monooxygenases, and secondary metabolism appeared to participate in isolate oxidative responses. The results suggest that aflatoxin and aflatrem biosynthesis may remediate oxidative stress by consuming excess oxygen and that kojic acid production may limit iron-mediated, non-enzymatic generation of reactive oxygen species. Toget...

Aflatoxin contamination, caused by fungal pathogen Aspergillus flavus, is a major quality and health problem delimiting the trade and consumption of groundnut (Arachis hypogaea L.) worldwide. RNAseq approach was deployed to understand the host-pathogen interaction by identifying differentially expressed genes (DEGs) for resistance to in-vitro seed colonization (IVSC) at four critical stages after inoculation in J 11 (resistant) and JL 24 (susceptible) genotypes of groundnut. About 1,344.04 million sequencing reads have been generated from sixteen libraries representing four stages in control and infected conditions. About 64% and 67% of quality filtered reads (1,148.09 million) were mapped onto A (A. duranensis) and B (A. ipaёnsis) subgenomes of groundnut respectively. About 101 million unaligned reads each from J 11 and JL 24 were used to map onto A. flavus genome. As a result, 4,445 DEGs including defense-related genes like senescence-associated proteins, resveratrol synthase, 9s-lipoxygenase, pathogenesis-related proteins were identified. In A. flavus, about 578 DEGs coding for growth and development of fungus, aflatoxin biosynthesis, binding, transport, and signaling were identified in compatible interaction. Besides identifying candidate genes for IVSC resistance in groundnut, the study identified the genes involved in host-pathogen cross-talks and markers that can be used in breeding resistant varieties. Aflatoxins are a group of carcinogenic mycotoxins produced mainly by Aspergillus flavus and A. parasiticus. They are considered to be a threat to human health, global food safety, and security 1, 2. Maize (Zea mays L.) and groundnut (Arachis hypogaea L.) are the most susceptible crops to aflatoxin contamination and serve as the main source of aflatoxin exposure for humans. The aflatoxins were reported as growth retardants in children 3 and immune-suppressors leading to AIDS 4, 5. Aflatoxin B1 produced by A. flavus and A. parasiticus in groundnut is considered to be the major cause of liver cancer along with the chronic infection with hepatitis B and C viruses and acute aflatoxicosis 6. Groundnuts tend to be colonized and contaminated by Aspergillus spp. at pre-harvest, during harvest, post-harvest drying, in storage and also during transport covering the whole value chain 7, 8. Use of cultivars resistant to seed invasion by Aspergillus spp. is one of the possible means of reducing aflatoxin contamination during groundnut storage with no extra input cost for the farmers. Development of aflatoxin resistant groundnut varieties has been a challenging task for breeders due to lack of availability of reliable resistance sources, poor understanding of plant-fungus interactions and large environmental influence. Three types of resistance mechanisms namely in-vitro seed colonization resistance (IVSC), resistance to pre-harvest aflatoxin contamination

The infection of maize and peanut with Aspergillus flavus and subsequent contamination with aflatoxin pose a threat to global food safety and human health, and is exacerbated by drought stress. Drought stress-responding compounds such as reactive oxygen species (ROS) are associated with fungal stress responsive signaling and secondary metabolite production, and can stimulate the production of aflatoxin by A. flavus in vitro. These secondary metabolites have been shown to possess diverse functions in soil-borne fungi including antibiosis, competitive inhibition of other microbes, and abiotic stress alleviation. Previously, we observed that isolates of A. flavus showed differences in oxidative stress tolerance which correlated with their aflatoxin production capabilities. In order to better understand these isolate-specific oxidative stress responses, we examined the transcriptional responses of field isolates of A. flavus with varying levels of aflatoxin production (NRRL3357, AF13, a...

Aflatoxin contamination, caused by fungal pathogen Aspergillus flavus, is the major quality and health problem delimiting the trade and consumption of groundnut (Arachis hypogaea L.) worldwide. Three types of aflatoxin resistance mechanisms namely, resistance to in-vitro seed colonization (IVSC), pre-harvest aflatoxin contamination (PAC) and aflatoxin production (AP) have been reported in groundnut. Transcriptome sequencing approach was used to study the differentially expressed genes that differ in-vitro seed colonization (IVSC) in resistant (J 11) and susceptible (JL 24) genotypes. A total of 1,344 million raw reads with an average of 84 million reads per sample were generated from 16 libraries from four different stages of fungal infection. A total of 737.75 and 770.83 million reads were mapped on the progenitor genomes- A subgenome (A. duranensis) and B subgenome (A. ipaensis) of cultivated groundnut (A. hypogaea), respectively. In groundnut, defense related genes like senescenc...

Rice root growth encompasses a remarkable genetic diversity in terms of growth patterns, architecture, and environmental adaptations. In order to harness this valuable diversity for improving rice response to drought, an understanding of key root traits and effective drought response mechanisms is necessary. A trait-based approach with precise understanding of the target environment, including temporal and spatial heterogeneity, is a possible path toward the use of roots and dehydration avoidance traits for improved drought resistance in rice. The ability to grow deep roots is currently the most accepted target trait for improving drought resistance, but genetic variation has been reported for a number of traits that may affect drought response. Here, we review variation in rice root response to drought from a physiological perspective in terms of morphology and function with respect to the different growth environments (upland and lowland) commonly used by farmers. Recent advances in linking physiology and breeding are also presented.

Molecular markers are becoming essential components in breeding programs involving gene pyramiding. Using marker-assisted selection in a backcross-breeding program, four bacterial blight resistant genes namely Xa4, xa5, xa13 and Xa21 have been introgressed into the hybrid rice parental lines KMR3, PRR78, IR58025B, Pusa 6B and the popular cv. Mahsuri. Only foreground selection was done using markers. Conventional breeding strategy was adopted for background selection. The pyramids showed very high level of disease resistance to 10 highly virulent isolates of Xanthomonas oryzae pv. oryzae. Grain quality parameters of the pyramids were on par with that of the original genotype. This work reports the successful application of marker-assisted breeding for pyramiding simultaneously four bacterial blight resistant genes into multiple backgrounds. These lines can be used directly or can be used as donors of bacterial blight (BB) resistance breeding.

Rice root growth encompasses a remarkable genetic diversity in terms of growth patterns, architecture, and environmental adaptations. In order to harness this valuable diversity for improving rice response to drought, an understanding of key root traits and effective drought response mechanisms is necessary. A trait-based approach with precise understanding of the target environment, including temporal and spatial heterogeneity, is a possible path toward the use of roots and dehydration avoidance traits for improved drought resistance in rice. The ability to grow deep roots is currently the most accepted target trait for improving drought resistance, but genetic variation has been reported for a number of traits that may affect drought response. Here, we review variation in rice root response to drought from a physiological perspective in terms of morphology and function with respect to the different growth environments (upland and lowland) commonly used by farmers. Recent advances in linking physiology and breeding are also presented.

The aim of this work was to improve early season drought tolerance in the upland rice variety Kalinga III, a variety that was not used for mapping drought-related traits. It was used as a recurrent parent in backcrossing with marker-assisted selection (MAS) with the Philippines variety Azucena as the donor parent of five carrier chromosomes for introgression. Four target segments carried a QTL for root traits and the fifth carried a recessive gene for aroma. We summarise the marker-assisted selection in three backcross (BC) generations and further pyramid crosses to stack multiple target segments from Azucena. We combined MAS with client-oriented breeding in bulk populations selected for QTLs from the BC2 generation. Phenotypic evaluation of the resultant bulks and near-isogenic lines was carried out. Screens for root traits were conducted in soil-filled pipes under field conditions in Bangalore, India. Over three years, six bulks and four advanced BC3 lines (known as PY lines) were evaluated by farmers in their own fields in eastern India. In addition replicated drought trials were carried out under upland conditions in three locations (two in eastern India and one in western India). The results demonstrate the complexities of selecting for root traits with low heritability and the effect of the evaluation environment. None-the-less, some of the products of this programme were shown to outperform Kalinga III and were acceptable to upland farmers in eastern India.

tomary statistical analyses are found to be inadequate in discerning the effects of different yield components Improvement of grain yield in the rainfed lowland rice (Oryza on yield (Zobel et al., 1989). Hence, studying grain yield sativa L.) ecosystem is important because that ecosystem covers a under varying moisture conditions and employing more considerable area. The objectives of this study were first to find relationship(s) among grain yield and its components, second to assess reliable statistical analyses may lead to better underthe influence of root morphological characters on grain yield, and standing of the influence of various traits on grain yield. finally to find the relationship of molecular marker heterozygosity Ample genetic variability for root morphological with heterosis-performance of yield related characters in rainfed lowtraits and other components (primary traits) of drought land rice. Nine backcrosses involving transgressants for maximum resistance has been documented over the past few deroot length in rice from a doubled haploid mapping population of cades. These studies have been conducted on specific IR64/Azucena along with parents were evaluated simultaneously for primary trait(s) of interest and its (their) contribution grain yield and related characters as well as root traits under conto drought resistance (Ludlow and Muchow, 1990; trasting moisture regimes. Grain yield showed maximum reduction Acevedo and Fereres, 1993; Sadiq et al., 1994; Hemaunder severe moisture stress conditions. Significant negative correlamalini et al., 2000). Even after several well designed tion between drought tolerance index and grain yield was observed in the well-watered conditions only. Multiple linear regression analysis experiments across crops, consensus on selecting for revealed total dry weight (root ϩ shoot dry weight) as the most either grain yield (potential or actual) and/or drought significant variable under well-watered conditions because it could resistance traits eludes plant breeders. This could be explain as much as 30% of variability in grain yield, followed by root because of the differences in intensity of drought (timing number. Under severe stress conditions, root dry weight explained and severity), differences in the intrinsic potential of 20% of variability in grain yield. The relationships between yield the crop to tolerate stress [like sorghum, Sorghum biand root related characters were determined. General heterozygosity, color (L.) Moench, and rice), and the constraints of based on molecular marker data, was found to be correlated with the study itself as standardized protocols for assessing hybrid performance and heterosis of yield related characters. Among drought resistance are conspicuously absent (Blum, the nine backcrosses, P331 ϫ IR64 and P124 ϫ IR64 were selected 1999). to map quantitative trait loci for root morphological characters and grain yield.