Global food security could be imperilled by the combined pressures from the effects of continuall... more Global food security could be imperilled by the combined pressures from the effects of continually evolving climatic conditions, demographics and other socio-economic factors, the demands of the livestock, bioenergy and fibre industries for food-based substrates, the static or decreasing availability of natural resources for agriculture and the impracticality of increased use of economically and environmentally costly agricultural inputs. The optimal harnessing of plant genetic resources for food and agriculture (PGRFA) in manners that translate their repertoire of hidden potentials into significantly enhanced crop productivities has been severally identified as crucial to achieving the required considerably significant increases in food production. The scope of the problems and the plausible means for addressing them compel the devising of novel and more efficient ways for deploying PGRFA in need-based crop improvement programmes. We posit a continuum approach to the management of ...
Single Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers were used ... more Single Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers were used to survey gamma ray induced genetic variation in a set of 13 originally produced structural barley (H. vulgare L.) mutants from cv. Freya; including 8 single translocation lines, 3 double translocation lines and 2 multiple reconstructed karyotypes. Both marker systems contributed to the evaluation of the radiation induced DNA alterations and revealed in general 0.49% polymorphisms in the studied genotypes. AFLPs were observed with 3 out of 10 PstI/MseI primer combinations. Transmissible microsatellite instability at loci with perfect (AT)n repeats located in the introns of the rubisco activase and waxy was documented in three mutant lines. The results emphasize that in addition to point mutations, small indels (2bp) form the major group of the gamma induced DNA alterations.
The industrial starch market is undergoing major expansion, but certain specific industrial uses ... more The industrial starch market is undergoing major expansion, but certain specific industrial uses cannot be satisfied by native starches and, therefore, chemical or physical modification is necessary. Mutations in the cassava starch biosynthesis pathways were discovered at CIAT (Cali, Colombia) few years ago. A starch mutation induced by gamma rays radiation resulted in a deeply modified branching pattern of amylopectin as well as other starch characteristics and properties. These modifications include changes in starch granule ultrastructure (e.g. decreased starch crystallinity), a weak organized structure, and increased susceptibility to mild acid and enzymatic raw starch hydrolysis (fastest and most efficient hydrolysis of all studied native starches). This mutation could offer interesting advantages for the production of bioethanol. Surprisingly this mutation also results in increased proportion of amylopectin. Hydrolysis was more dependent on granule morphology than on starch ch...
A decade ago CIAT began the search of what it called "High-Value Cassava". What was the... more A decade ago CIAT began the search of what it called "High-Value Cassava". What was then only a promise has gradually became a reality. In the area of starch quality traits an amylosefree (waxy) mutation was identified and has now been successfully introgressed to be released as commercial varieties. Part of this work is financially supported by the private starch sector. A small-granule mutation was also identified and found to be particularly suitable for processes requiring starch hydrolysis (e.g. sweeteners and ethanol). Moreover, CIAT has also identified a high-amylose genotype with as much as 42% amylose (whereas cassava starch typically has around 20%). Breeding methodologies to exploit these traits have been developed and tested. On the nutritional side, during the past decade, the increases in carotenoids content in the roots have been remarkable, and there seems to be no plateau in the progress made. Protocols for efficient selection in carotenoids have also been...
Despite the economic importance of cassava, studies of diversity, population structure, and domes... more Despite the economic importance of cassava, studies of diversity, population structure, and domestication have been limited, and have not been performed at whole genome level. In this study, we addressed these issues using RAD-seq to discover more than 500.000 genome-wide SNP genetic markers for over 450 cassava accessions from the International Center for Tropical Agriculture (CIAT) germplasm collection, and a wide representation of wild relative species of the genus Manihot. Preliminary results from cassava accessions using 11,480 newly discovered SNPs revealed a complex pattern of population structure and clustered into five main subpopulations, without correlation to their geographical distribution. Differentiation between subpopulations was low to moderate, suggesting recent divergence and possible genetic flow between subpopulations. In addition, using 5,137 SNPs we could find a strong differentiation between cassava and wild relative species. Based on genetic differences, we ...
International Journal of Food Science & Technology, 2021
Summary“Consumers have their say: assessing preferred quality traits of roots, tubers and cooking... more Summary“Consumers have their say: assessing preferred quality traits of roots, tubers and cooking bananas, and implications for breeding” special issue, brings together new knowledge about quality traits required for roots, tubers and bananas (RTB) varieties to successfully meet diverse user preferences and expectations, along the variety development and RTB value chains (production, processing, marketing, food preparation, consumption). Key RTB crops in sub‐Saharan Africa are cassava, yams, sweetpotatoes, potatoes and bananas/plantains. They are mainly consumed directly as boiled pieces or pounded in the form of smooth, not sticky, and stretchable dough. They are also stewed, steamed or fried. Cassava, the most widely grown RTB, is generally boiled, stewed or steamed in Eastern and Southern Africa, and in West and Central Africa is usually processed directly into derivative products, e.g. whole root fermentation through retting or heap fermentation; fermentation/dewatering of the m...
Journal of the Swedish Seed Association publishes, in Swedish or English, articles, notes, commen... more Journal of the Swedish Seed Association publishes, in Swedish or English, articles, notes, commentaries, reviews as well as proceedings of meetings and seminars. All scientific original papers are subject to a referee procedure. The submission of original articles in the field of plant breeding and related areas is encouraged.
This chapter reviews the ways cassava yields can be improved sustainably to keep pace with a risi... more This chapter reviews the ways cassava yields can be improved sustainably to keep pace with a rising population. It also looks more broadly at improving the role cassava can play in improving farmers’ and consumers’ lives – through income generation, improved food security, better nutrition, and a healthier environment
Microspore embryogenesis is the developmental plasticity of juvenile male gametophytes to switch ... more Microspore embryogenesis is the developmental plasticity of juvenile male gametophytes to switch from pollen to embryo development upon exposure to in vitro stress. It is a common method for obtaining haploid and doubled haploid plants in breeding programs for development of superior varieties via haploid-diploidization which allows fast development of homozygous lines from heterozygous parents. In cassava, obtaining haploidization through traditional methods of successive selfing is difficult because of cassava’s long reproductive cycle, high heterozygosity, and inbreeding depression. As a first step towards microspore embryogenesis, callus induction following heat treatment has not been investigated in cassava. We used two elite Ugandan cassava varieties, hereafter called “genotypes”, NASE3 and NASE14, for the study of callus induction. Heat stress of 40°C for 0, 6, 12, 18 and 24hrs and Murashige and Skoog medium supplemented with 2-9% sucrose, and 2,4-dichlorophenoxy acetic acid ...
Breeding cassava relies on a phenotypic recurrent selection that takes advantage of the vegetativ... more Breeding cassava relies on a phenotypic recurrent selection that takes advantage of the vegetative propagation of this crop. Successive stages of selection (single row trial-SRT; preliminary yield trial-PYT; advanced yield trial-AYT; and uniform yield trials UYT), gradually reduce the number of genotypes as the plot size, number of replications and locations increase. An important feature of this scheme is that, because of the clonal, reproduction of cassava, the same identical genotypes are evaluated throughout these four successive stages of selection. For this study data, from 14 years (more than 30,000 data points) of evaluation in a sub-humid tropical environment was consolidated for a meta-analysis. Correlation coefficients for fresh root yield (FRY), dry matter content (DMC), harvest index (HIN), and plant type score (PTS) along the different stages of selection were estimated. DMC and PTS measured in different trials showed the highest correlation coefficients, indicating a relatively good repeatability. HIN had an intermediate repeatability, whereas FRY had the lowest value. The association between HIN and FRY was lower than expected, suggesting that HIN in early stages was not reliable as indirect selection for FRY in later stages. There was a consistent decrease in the average performance of clones grown in PYTs compared with the earlier evaluation of the same genotypes at SRTs. A feasible explanation for this trend is the impact of the environment on the physiological and nutritional status of the planting material and/or epigenetic effects. The usefulness of HIN is questioned. Measuring this variable takes considerable efforts at harvest time. DMC and FRY showed a weak positive association in SRT (r = 0.21) but a clearly negative one at UYT (r = −0.42). The change in the relationship between these variables is the result of selection. In later stages of selection, the plant is forced to maximize productivity on a dry weight basis either by maximizing FRY or DMC, but not both. Alternatively, the plant may achieve high dry root yield by simultaneously attaining "acceptable" (but not maximum) levels of FRY and DMC.
Genetic distance and specific combining ability in cassava The International Center for Tropical ... more Genetic distance and specific combining ability in cassava The International Center for Tropical Agriculture (CIAT) believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture. CIAT is committed to creating and sharing knowledge and information openly and globally. We do this through collaborative research as well as through the open sharing of our data, tools, and publications.
Cassava is a highly heterozygous species; hence, current methods used in classical cassava breedi... more Cassava is a highly heterozygous species; hence, current methods used in classical cassava breeding cannot match the urgent need to high yielding varieties. Recently, progress was made through androgenesis and gynogenesis as pathways for raising doubled cassava haploid lines to overcome problems associated with cassava's inherent reproductive biology, but these efforts were limited (no candidate cassava plantlets were regenerated). For the first time, this study shows that pollen irradiation coupled with self-pollination and embryo rescue regenerated 62 candidate cassava plantlets. Plants of an elite cassava variety, Nase14, served as a mother plant and as the pollen donor for the irradiation. Irradiation dosages of 50 to 250 Gray studied across five pollination events and 300 or 500 Gray in one pollination event caused a reduction in pollen germination up to 67.0%. By 15 days after pollination (DAP) with irradiated pollen, up to 89.7% of the pollinated flowers had aborted. By embryo rescue time (42 DAP), significant differences were observed in number of fruits, seeds and embryos generated, with the non-irradiated pollen treatments having significantly higher numbers. Sixteen (16) heterozygous SSR markers in the parent and ploidy analysis showed that none of the regenerated plants was haploid or homozygous. However, the plantlets resulting from pollination with non-irradiated pollen had 56.2% homozygous loci, while progeny derived from irradiated treatments had frequencies of homozygous loci between 28.1 and 55.0%. This is the first time to use irradiated pollen in cassava as a pathway to generate candidate plantlets as an initial step in double haploid production.
Because of its long growing season and sensitivity to low temperatures, cassava (Manihot esculent... more Because of its long growing season and sensitivity to low temperatures, cassava (Manihot esculenta Crantz) is exclusively a crop of the tropics and subtropics. This effective exclusion from production in most of the developed world has had a strong and largely negative influence on the research investment in the crop. In spite of being one of the world's major calorie producers for human sustenance (second most important source of calo ries in sub-Saharan Africa after maize), cassava is little known in the developed world. Research investment into the crop was sparse until two centers of the CGIAR Consortium – the International Center for Tropical Agriculture (CIAT) and the International Institute of Tropical Agriculture (IITA) – began research on the crop in the mid-1970s. Cassava produces better than many crops on acid and low-fertility soils, and under periodic or even extended droughts. Because it has no specific maturity period, there is no period of growth during which it ...
starch content in the roots, and low for defensive traits (pest and disease resistance) and plant... more starch content in the roots, and low for defensive traits (pest and disease resistance) and plant architecture. The present article considers the potential impact of different technologies for maximizing gains for key traits in cassava, and highlights the advantages of integrating them. Exploiting heterosis would be optimized through the implementation of reciprocal recurrent selection. The advantages of using inbred progenitors would allow shifting the current cassava phenotypic recurrent selection method into line improvement, which in turn would allow designing outstanding hybrids rather than finding them by trial and error.
Global food security could be imperilled by the combined pressures from the effects of continuall... more Global food security could be imperilled by the combined pressures from the effects of continually evolving climatic conditions, demographics and other socio-economic factors, the demands of the livestock, bioenergy and fibre industries for food-based substrates, the static or decreasing availability of natural resources for agriculture and the impracticality of increased use of economically and environmentally costly agricultural inputs. The optimal harnessing of plant genetic resources for food and agriculture (PGRFA) in manners that translate their repertoire of hidden potentials into significantly enhanced crop productivities has been severally identified as crucial to achieving the required considerably significant increases in food production. The scope of the problems and the plausible means for addressing them compel the devising of novel and more efficient ways for deploying PGRFA in need-based crop improvement programmes. We posit a continuum approach to the management of ...
Single Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers were used ... more Single Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers were used to survey gamma ray induced genetic variation in a set of 13 originally produced structural barley (H. vulgare L.) mutants from cv. Freya; including 8 single translocation lines, 3 double translocation lines and 2 multiple reconstructed karyotypes. Both marker systems contributed to the evaluation of the radiation induced DNA alterations and revealed in general 0.49% polymorphisms in the studied genotypes. AFLPs were observed with 3 out of 10 PstI/MseI primer combinations. Transmissible microsatellite instability at loci with perfect (AT)n repeats located in the introns of the rubisco activase and waxy was documented in three mutant lines. The results emphasize that in addition to point mutations, small indels (2bp) form the major group of the gamma induced DNA alterations.
The industrial starch market is undergoing major expansion, but certain specific industrial uses ... more The industrial starch market is undergoing major expansion, but certain specific industrial uses cannot be satisfied by native starches and, therefore, chemical or physical modification is necessary. Mutations in the cassava starch biosynthesis pathways were discovered at CIAT (Cali, Colombia) few years ago. A starch mutation induced by gamma rays radiation resulted in a deeply modified branching pattern of amylopectin as well as other starch characteristics and properties. These modifications include changes in starch granule ultrastructure (e.g. decreased starch crystallinity), a weak organized structure, and increased susceptibility to mild acid and enzymatic raw starch hydrolysis (fastest and most efficient hydrolysis of all studied native starches). This mutation could offer interesting advantages for the production of bioethanol. Surprisingly this mutation also results in increased proportion of amylopectin. Hydrolysis was more dependent on granule morphology than on starch ch...
A decade ago CIAT began the search of what it called "High-Value Cassava". What was the... more A decade ago CIAT began the search of what it called "High-Value Cassava". What was then only a promise has gradually became a reality. In the area of starch quality traits an amylosefree (waxy) mutation was identified and has now been successfully introgressed to be released as commercial varieties. Part of this work is financially supported by the private starch sector. A small-granule mutation was also identified and found to be particularly suitable for processes requiring starch hydrolysis (e.g. sweeteners and ethanol). Moreover, CIAT has also identified a high-amylose genotype with as much as 42% amylose (whereas cassava starch typically has around 20%). Breeding methodologies to exploit these traits have been developed and tested. On the nutritional side, during the past decade, the increases in carotenoids content in the roots have been remarkable, and there seems to be no plateau in the progress made. Protocols for efficient selection in carotenoids have also been...
Despite the economic importance of cassava, studies of diversity, population structure, and domes... more Despite the economic importance of cassava, studies of diversity, population structure, and domestication have been limited, and have not been performed at whole genome level. In this study, we addressed these issues using RAD-seq to discover more than 500.000 genome-wide SNP genetic markers for over 450 cassava accessions from the International Center for Tropical Agriculture (CIAT) germplasm collection, and a wide representation of wild relative species of the genus Manihot. Preliminary results from cassava accessions using 11,480 newly discovered SNPs revealed a complex pattern of population structure and clustered into five main subpopulations, without correlation to their geographical distribution. Differentiation between subpopulations was low to moderate, suggesting recent divergence and possible genetic flow between subpopulations. In addition, using 5,137 SNPs we could find a strong differentiation between cassava and wild relative species. Based on genetic differences, we ...
International Journal of Food Science & Technology, 2021
Summary“Consumers have their say: assessing preferred quality traits of roots, tubers and cooking... more Summary“Consumers have their say: assessing preferred quality traits of roots, tubers and cooking bananas, and implications for breeding” special issue, brings together new knowledge about quality traits required for roots, tubers and bananas (RTB) varieties to successfully meet diverse user preferences and expectations, along the variety development and RTB value chains (production, processing, marketing, food preparation, consumption). Key RTB crops in sub‐Saharan Africa are cassava, yams, sweetpotatoes, potatoes and bananas/plantains. They are mainly consumed directly as boiled pieces or pounded in the form of smooth, not sticky, and stretchable dough. They are also stewed, steamed or fried. Cassava, the most widely grown RTB, is generally boiled, stewed or steamed in Eastern and Southern Africa, and in West and Central Africa is usually processed directly into derivative products, e.g. whole root fermentation through retting or heap fermentation; fermentation/dewatering of the m...
Journal of the Swedish Seed Association publishes, in Swedish or English, articles, notes, commen... more Journal of the Swedish Seed Association publishes, in Swedish or English, articles, notes, commentaries, reviews as well as proceedings of meetings and seminars. All scientific original papers are subject to a referee procedure. The submission of original articles in the field of plant breeding and related areas is encouraged.
This chapter reviews the ways cassava yields can be improved sustainably to keep pace with a risi... more This chapter reviews the ways cassava yields can be improved sustainably to keep pace with a rising population. It also looks more broadly at improving the role cassava can play in improving farmers’ and consumers’ lives – through income generation, improved food security, better nutrition, and a healthier environment
Microspore embryogenesis is the developmental plasticity of juvenile male gametophytes to switch ... more Microspore embryogenesis is the developmental plasticity of juvenile male gametophytes to switch from pollen to embryo development upon exposure to in vitro stress. It is a common method for obtaining haploid and doubled haploid plants in breeding programs for development of superior varieties via haploid-diploidization which allows fast development of homozygous lines from heterozygous parents. In cassava, obtaining haploidization through traditional methods of successive selfing is difficult because of cassava’s long reproductive cycle, high heterozygosity, and inbreeding depression. As a first step towards microspore embryogenesis, callus induction following heat treatment has not been investigated in cassava. We used two elite Ugandan cassava varieties, hereafter called “genotypes”, NASE3 and NASE14, for the study of callus induction. Heat stress of 40°C for 0, 6, 12, 18 and 24hrs and Murashige and Skoog medium supplemented with 2-9% sucrose, and 2,4-dichlorophenoxy acetic acid ...
Breeding cassava relies on a phenotypic recurrent selection that takes advantage of the vegetativ... more Breeding cassava relies on a phenotypic recurrent selection that takes advantage of the vegetative propagation of this crop. Successive stages of selection (single row trial-SRT; preliminary yield trial-PYT; advanced yield trial-AYT; and uniform yield trials UYT), gradually reduce the number of genotypes as the plot size, number of replications and locations increase. An important feature of this scheme is that, because of the clonal, reproduction of cassava, the same identical genotypes are evaluated throughout these four successive stages of selection. For this study data, from 14 years (more than 30,000 data points) of evaluation in a sub-humid tropical environment was consolidated for a meta-analysis. Correlation coefficients for fresh root yield (FRY), dry matter content (DMC), harvest index (HIN), and plant type score (PTS) along the different stages of selection were estimated. DMC and PTS measured in different trials showed the highest correlation coefficients, indicating a relatively good repeatability. HIN had an intermediate repeatability, whereas FRY had the lowest value. The association between HIN and FRY was lower than expected, suggesting that HIN in early stages was not reliable as indirect selection for FRY in later stages. There was a consistent decrease in the average performance of clones grown in PYTs compared with the earlier evaluation of the same genotypes at SRTs. A feasible explanation for this trend is the impact of the environment on the physiological and nutritional status of the planting material and/or epigenetic effects. The usefulness of HIN is questioned. Measuring this variable takes considerable efforts at harvest time. DMC and FRY showed a weak positive association in SRT (r = 0.21) but a clearly negative one at UYT (r = −0.42). The change in the relationship between these variables is the result of selection. In later stages of selection, the plant is forced to maximize productivity on a dry weight basis either by maximizing FRY or DMC, but not both. Alternatively, the plant may achieve high dry root yield by simultaneously attaining "acceptable" (but not maximum) levels of FRY and DMC.
Genetic distance and specific combining ability in cassava The International Center for Tropical ... more Genetic distance and specific combining ability in cassava The International Center for Tropical Agriculture (CIAT) believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture. CIAT is committed to creating and sharing knowledge and information openly and globally. We do this through collaborative research as well as through the open sharing of our data, tools, and publications.
Cassava is a highly heterozygous species; hence, current methods used in classical cassava breedi... more Cassava is a highly heterozygous species; hence, current methods used in classical cassava breeding cannot match the urgent need to high yielding varieties. Recently, progress was made through androgenesis and gynogenesis as pathways for raising doubled cassava haploid lines to overcome problems associated with cassava's inherent reproductive biology, but these efforts were limited (no candidate cassava plantlets were regenerated). For the first time, this study shows that pollen irradiation coupled with self-pollination and embryo rescue regenerated 62 candidate cassava plantlets. Plants of an elite cassava variety, Nase14, served as a mother plant and as the pollen donor for the irradiation. Irradiation dosages of 50 to 250 Gray studied across five pollination events and 300 or 500 Gray in one pollination event caused a reduction in pollen germination up to 67.0%. By 15 days after pollination (DAP) with irradiated pollen, up to 89.7% of the pollinated flowers had aborted. By embryo rescue time (42 DAP), significant differences were observed in number of fruits, seeds and embryos generated, with the non-irradiated pollen treatments having significantly higher numbers. Sixteen (16) heterozygous SSR markers in the parent and ploidy analysis showed that none of the regenerated plants was haploid or homozygous. However, the plantlets resulting from pollination with non-irradiated pollen had 56.2% homozygous loci, while progeny derived from irradiated treatments had frequencies of homozygous loci between 28.1 and 55.0%. This is the first time to use irradiated pollen in cassava as a pathway to generate candidate plantlets as an initial step in double haploid production.
Because of its long growing season and sensitivity to low temperatures, cassava (Manihot esculent... more Because of its long growing season and sensitivity to low temperatures, cassava (Manihot esculenta Crantz) is exclusively a crop of the tropics and subtropics. This effective exclusion from production in most of the developed world has had a strong and largely negative influence on the research investment in the crop. In spite of being one of the world's major calorie producers for human sustenance (second most important source of calo ries in sub-Saharan Africa after maize), cassava is little known in the developed world. Research investment into the crop was sparse until two centers of the CGIAR Consortium – the International Center for Tropical Agriculture (CIAT) and the International Institute of Tropical Agriculture (IITA) – began research on the crop in the mid-1970s. Cassava produces better than many crops on acid and low-fertility soils, and under periodic or even extended droughts. Because it has no specific maturity period, there is no period of growth during which it ...
starch content in the roots, and low for defensive traits (pest and disease resistance) and plant... more starch content in the roots, and low for defensive traits (pest and disease resistance) and plant architecture. The present article considers the potential impact of different technologies for maximizing gains for key traits in cassava, and highlights the advantages of integrating them. Exploiting heterosis would be optimized through the implementation of reciprocal recurrent selection. The advantages of using inbred progenitors would allow shifting the current cassava phenotypic recurrent selection method into line improvement, which in turn would allow designing outstanding hybrids rather than finding them by trial and error.
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Papers by CLAIR HERSHEY