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Arnau Gemma - One of the best experts on this subject based on the ideXlab platform.
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Genetic control of flowering in greater yam (Dioscorea alata L.)
'Springer Science and Business Media LLC', 2021Co-Authors: Cormier Fabien, Maledon Erick, Mournet Pierre, Vignes Hélène, Arnau Gemma, Cornet Denis, Martin Guillaume, Lachman Laurie, Faure Y., Chaïr HânaAbstract:Background: Greater yam (Dioscorea alata L.) is a major tropical and subtropical staple crop cultivated for its starchy tubers. Breeding of this dioecious species is hampered by its erratic flowering, yet little is currently known on the genetic determinism of its sexual reproduction. Result: Here we used a genome-wide association approach and identified a major genetic barrier to reproduction in yam on chromosome 1, as represented by two candidate genes. A deleterious effect on male fitness could be hypothesized considering the involvement of these two genes in male reproduction and the low frequency of this non-flowering dominant allele within the male genepool. We also extended the hypothesis of a XX/XY sex-determination system located on chromosome 6 in D. alata to encompass most of the species diversity. Moreover, a kompetitive allele-specific PCR (KASPar) marker was designed and validated that enables accurate cultivar sex estimation. The reconstruction of chromosome 6 associated with the detection of highly putative structural variations confirmed the possible involvement of a major part of the chromosome. Conclusion: The findings of this study, combined with proper estimation of accession ploidy levels to avoid endosperm incompatibility issues, could facilitate the design of future promising parental combinations in D. alata breeding programs. Moreover, the discovery of this genetic barrier to reproduction opens new avenues for gaining insight into yam reproductive biology and diversification
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Genetic control of flowering in greater yam (Dioscorea alata L.)
'Springer Science and Business Media LLC', 2021Co-Authors: Cormier Fabien, Maledon Erick, Mournet Pierre, Vignes Hélène, Arnau Gemma, Cornet Denis, Martin Guillaume, Lachman Laurie, Faure Yoana, Chaïr HânaAbstract:International audienceBackground Greater yam ( Dioscorea alata L.) is a major tropical and subtropical staple crop cultivated for its starchy tubers. Breeding of this dioecious species is hampered by its erratic flowering, yet little is currently known on the genetic determinism of its sexual reproduction. Result Here we used a genome-wide association approach and identified a major genetic barrier to reproduction in yam on chromosome 1, as represented by two candidate genes. A deleterious effect on male fitness could be hypothesized considering the involvement of these two genes in male reproduction and the low frequency of this non-flowering dominant allele within the male genepool. We also extended the hypothesis of a XX/XY sex-determination system located on chromosome 6 in D. alata to encompass most of the species diversity. Moreover, a kompetitive allele-specific PCR (KASPar) marker was designed and validated that enables accurate cultivar sex estimation. The reconstruction of chromosome 6 associated with the detection of highly putative structural variations confirmed the possible involvement of a major part of the chromosome. Conclusion The findings of this study, combined with proper estimation of accession ploidy levels to avoid endosperm incompatibility issues, could facilitate the design of future promising parental combinations in D. alata breeding programs. Moreover, the discovery of this genetic barrier to reproduction opens new avenues for gaining insight into yam reproductive biology and diversification
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A reference high-density genetic map of greater yam (Dioscorea alata L.)
'Springer Science and Business Media LLC', 2019Co-Authors: Cormier Fabien, Lawac Floriane, Maledon Erick, Gravillon Marie-claire, Nudol Elie, Mournet Pierre, Vignes Hélène, Chaïr Hâna, Arnau GemmaAbstract:Greater yam (Dioscorea alata L.) is a major staple food in tropical and subtropical areas. This study aimed to produce the first reference genetic map of this dioecious species using genotyping-by-sequencing. In this high-density map combining information of two F1 outcrossed populations, 20 linkage groups were resolved as expected and 1579 polymorphic markers were ordered. The consensus map length was 2613.5 cM with an average SNP interval of 1.68 cM. An XX/XY sex determination system was identified on LG6 via the study of sex ratio, homology of parental linkage groups and the identification of a major QTL for sex determination. Homology with the sequenced D. rotundata is described, and the median physical distance between SNPs was estimated at 139.1 kb. The effects of segregation distortion and the presence of heteromorphic sex chromosomes are discussed. This D. alata linkage map associated with the available genomic resources will facilitate quantitative trait mapping, marker-assisted selection and evolutionary studies in the important yet scarcely studied yam species
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A reference high-density genetic map of greater yam (Dioscorea alata L.)
'Springer Science and Business Media LLC', 2019Co-Authors: Cormier Fabien, Lawac Floriane, Maledon Erick, Gravillon Marie-claire, Nudol Elie, Mournet Pierre, Vignes Hélène, Chair Nana, Arnau GemmaAbstract:International audienceKey message This study generated the first high-density genetic map for D. alata based on genotyping-by-sequencing and provides new insight on sex determination in yam. Abstract Greater yam (Dioscorea alata L.) is a major staple food in tropical and subtropical areas. This study aimed to produce the first reference genetic map of this dioecious species using genotyping-by-sequencing. In this high-density map combining information of two F1 outcrossed populations, 20 linkage groups were resolved as expected and 1579 polymorphic markers were ordered. The consensus map length was 2613.5 cM with an average SNP interval of 1.68 cM. An XX/XY sex determination system was identified on LG6 via the study of sex ratio, homology of parental linkage groups and the identification of a major QTL for sex determination. Homology with the sequenced D. rotundata is described, and the median physical distance between SNPs was estimated at 139.1 kb. The effects of segregation distortion and the presence of heteromorphic sex chromosomes are discussed. This D. alata linkage map associated with the available genomic resources will facilitate quantitative trait mapping, marker-assisted selection and evolutionary studies in the important yet scarcely studied yam species
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Production of hybrid seeds by intraspecific crossing in yam Dioscorea alata L
'International Journal of Science and Research', 2019Co-Authors: Ehounou, Adou Emmanuel, Maledon Erick, Arnau Gemma, Kouakou A.m., N'zi J.c., Dibi K.b.e., Bakayoko Y., Essis B.s., N'zue Boni, Asfaw AsratAbstract:Manual crosses were carried out over two successive years on Dioscorea alata for the production of hybrid seeds between five females and seven males' parents with contrasting characteristics. A total of 22951 flowers were manually pollinated in both years (14145 in 2016 and 8806 in 2017) in 33 parental combinations. The ploidy levels of the parents were determined by flow cytometry. The crossed parents were all diploids except the female OA49 which was triploid. In both years the fruiting and seed rates were comparable (25.06% and 22.82%; 30.05% and 30.18%). A significant variation in fruiting rates was observed between the different parental combinations. Analysis of variance have shown that there is both a male effect on the fruit setting. The lowest rates were observed in combinations involving male clones 23 and Ma01 (2.04% and 2.77%) and the highest rates involved males TDa00/00128 and TDa00/00095 (48.25% and 33.91%). The triploid female OA49 is sterile. Females TDa01/00003, TDa01/00018, TDa99/00240 and TDa01/00295 gave comparable fruiting rates which are respectively (37.87%, 29.38%, 24.70% and 20.92%). For seeds production, there is no male and female effect. The fruiting rate according to the time slot depends on each male variety involved. For some males, the fruiting rate is influenced by the time slot of pollination while for others, there is no time slot effect on the fruiting rate
Cormier Fabien - One of the best experts on this subject based on the ideXlab platform.
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Genetic control of flowering in greater yam (Dioscorea alata L.)
'Springer Science and Business Media LLC', 2021Co-Authors: Cormier Fabien, Maledon Erick, Mournet Pierre, Vignes Hélène, Arnau Gemma, Cornet Denis, Martin Guillaume, Lachman Laurie, Faure Y., Chaïr HânaAbstract:Background: Greater yam (Dioscorea alata L.) is a major tropical and subtropical staple crop cultivated for its starchy tubers. Breeding of this dioecious species is hampered by its erratic flowering, yet little is currently known on the genetic determinism of its sexual reproduction. Result: Here we used a genome-wide association approach and identified a major genetic barrier to reproduction in yam on chromosome 1, as represented by two candidate genes. A deleterious effect on male fitness could be hypothesized considering the involvement of these two genes in male reproduction and the low frequency of this non-flowering dominant allele within the male genepool. We also extended the hypothesis of a XX/XY sex-determination system located on chromosome 6 in D. alata to encompass most of the species diversity. Moreover, a kompetitive allele-specific PCR (KASPar) marker was designed and validated that enables accurate cultivar sex estimation. The reconstruction of chromosome 6 associated with the detection of highly putative structural variations confirmed the possible involvement of a major part of the chromosome. Conclusion: The findings of this study, combined with proper estimation of accession ploidy levels to avoid endosperm incompatibility issues, could facilitate the design of future promising parental combinations in D. alata breeding programs. Moreover, the discovery of this genetic barrier to reproduction opens new avenues for gaining insight into yam reproductive biology and diversification
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Genetic control of flowering in greater yam (Dioscorea alata L.)
'Springer Science and Business Media LLC', 2021Co-Authors: Cormier Fabien, Maledon Erick, Mournet Pierre, Vignes Hélène, Arnau Gemma, Cornet Denis, Martin Guillaume, Lachman Laurie, Faure Yoana, Chaïr HânaAbstract:International audienceBackground Greater yam ( Dioscorea alata L.) is a major tropical and subtropical staple crop cultivated for its starchy tubers. Breeding of this dioecious species is hampered by its erratic flowering, yet little is currently known on the genetic determinism of its sexual reproduction. Result Here we used a genome-wide association approach and identified a major genetic barrier to reproduction in yam on chromosome 1, as represented by two candidate genes. A deleterious effect on male fitness could be hypothesized considering the involvement of these two genes in male reproduction and the low frequency of this non-flowering dominant allele within the male genepool. We also extended the hypothesis of a XX/XY sex-determination system located on chromosome 6 in D. alata to encompass most of the species diversity. Moreover, a kompetitive allele-specific PCR (KASPar) marker was designed and validated that enables accurate cultivar sex estimation. The reconstruction of chromosome 6 associated with the detection of highly putative structural variations confirmed the possible involvement of a major part of the chromosome. Conclusion The findings of this study, combined with proper estimation of accession ploidy levels to avoid endosperm incompatibility issues, could facilitate the design of future promising parental combinations in D. alata breeding programs. Moreover, the discovery of this genetic barrier to reproduction opens new avenues for gaining insight into yam reproductive biology and diversification
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Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)
'Oxford University Press (OUP)', 2020Co-Authors: Sharif, Bilal Muhammad, Cormier Fabien, Mournet Pierre, Kaoh Juliane, Burgarella Concetta, Causse Sandrine, Van, Kien Nguyen, Rajaonah, Mamy Tiana, Lakshan, Senanayake Ravinda, Waki JeffreyAbstract:International audienceBackground and Aims Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample.Methods We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach.Key Results Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool. which was later introduced to the Caribbean region.Conclusions Our results arc congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding. and this is likely to threaten future adaptation
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Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata L.)
'Oxford University Press (OUP)', 2020Co-Authors: Sharif, Bilal Muhammad, Cormier Fabien, Mournet Pierre, Kaoh Juliane, Burgarella Concetta, Causse Sandrine, Rajaonah, Mamy Tiana, Lakshan, Senanayake Ravinda, Nguyen Van Kien, Waki JeffreyAbstract:Background and Aims: Inferring the diffusion history of many human-dispersed species is still not straightforward due to unsolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers is still unsolved. Here, we address yam demographic and dispersal history using a worldwide sample. Methods: We characterized genome-wide patterns of genetic variation by genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using alleles frequency distribution and identity by descent approaches. Then, we addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. Key Results: Diploid genotypes were more frequent than triploids and tetraploids in all the continents. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. Triploids and tetraploids genetic make-up suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced in the Caribbean region. Conclusions: Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidisation. Both processes reduced the extent of diversity available for breeding, which most likely threaten future adaptation
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A reference high-density genetic map of greater yam (Dioscorea alata L.)
'Springer Science and Business Media LLC', 2019Co-Authors: Cormier Fabien, Lawac Floriane, Maledon Erick, Gravillon Marie-claire, Nudol Elie, Mournet Pierre, Vignes Hélène, Chaïr Hâna, Arnau GemmaAbstract:Greater yam (Dioscorea alata L.) is a major staple food in tropical and subtropical areas. This study aimed to produce the first reference genetic map of this dioecious species using genotyping-by-sequencing. In this high-density map combining information of two F1 outcrossed populations, 20 linkage groups were resolved as expected and 1579 polymorphic markers were ordered. The consensus map length was 2613.5 cM with an average SNP interval of 1.68 cM. An XX/XY sex determination system was identified on LG6 via the study of sex ratio, homology of parental linkage groups and the identification of a major QTL for sex determination. Homology with the sequenced D. rotundata is described, and the median physical distance between SNPs was estimated at 139.1 kb. The effects of segregation distortion and the presence of heteromorphic sex chromosomes are discussed. This D. alata linkage map associated with the available genomic resources will facilitate quantitative trait mapping, marker-assisted selection and evolutionary studies in the important yet scarcely studied yam species
Asiedu Robert - One of the best experts on this subject based on the ideXlab platform.
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A genetic linkage map of water yam (Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance
'Springer Science and Business Media LLC', 2019Co-Authors: Mignouna H.d., Asiedu Robert, Abang, Mathew M., Mank R.a., Ellis T.h.n., Bosch N.v.d., Peleman J.Abstract:A genetic linkage map of the tetraploid water yam (Dioscorea alata L.) genome was constructed based on 469 co-dominantly scored amplified fragment length polymorphism (AFLP) markers segregating in an intraspecific F1 cross. The F1 was obtained by crossing two improved breeding lines, TDa 95/00328 as female parent and TDa 87/01091 as male parent. Since the mapping population was an F1 cross between presumed heterozygous parents, marker segregation data from both parents were initially split into maternal and paternal data sets, and separate genetic linkage maps were constructed. Later, data analysis showed that this was not necessary and thus the combined markers from both parents were used to construct a genetic linkage map. The 469 markers were mapped on 20 linkage groups with a total map length of 1,233 cM and a mean marker spacing of 2.62 cM. The markers segregated like a diploid cross-pollinator population suggesting that the water yam genome is allo-tetraploid (2n = 4x = 40). QTL mapping revealed one AFLP marker E-14/M52-307 located on linkage group 2 that was associated with anthracnose resistance, explaining 10% of the total phenotypic variance. This map covers 65% of the yam genome and is the first linkage map reported for D. alata. The map provides a tool for further genetic analysis of traits of agronomic importance and for using marker-assisted selection in D. alata breeding programmes. QTL mapping opens new avenues for accumulating anthracnose resistance genes in preferred D. alata cultivars
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Identification and potential application of RAPD markers for anthracnose resistance in water yam (Dioscorea alata)
2019Co-Authors: Mignouna H.d., Abang, Mathew M., Onasanya A., Agindotan A., Asiedu RobertAbstract:Anthracnose, caused by Colletotrichum gloeosporioides, is the most severe foliar disease of water yam (Dioscorea alata) worldwide. The tetraploid breeding line, TDa 95/00328, is a source of dominant genetic resistance to the moderately virulent fast growing salmon (FGS) strain of C. gloeosporioides.Bulked segregant analysis was used to search for random amplified polymorphic DNA (RAPD) markers linked to anthracnose resistance in F1 progeny derived from a cross between TDa 95/00328 and the susceptible male parent, TDa 95-310. Two hundred and eighty decamer primers were screened using bulks obtained from pooled DNA of individuals comprising each extreme of the disease phenotype distribution. A single locus that contributes to anthracnose resistance in TDa 95/00328 was identified and tentatively named Dcg-1. We found two RAPD markers closely linked in coupling phase with Dcg-1, named OPI71700 and OPE6950, both of which were mapped on the same linkage group. OPI71700 appeared tightly linked to the Dcg-1 locus; it was present in all the 58 resistant F1 individuals and absent in all but one of the 13 susceptible genotypes (genetic distance of 2.3 cM). OPE6950 was present in 56 of the 58 resistant progeny and only one susceptible F1 plant showed this marker (6.8 cM). Bot
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Genotype x environment interaction in water yam (Dioscorea alata) yield trials in five yamgrowing sites in Nigeria
2018Co-Authors: Egesi, Chiedozie N., Ogunyemi S., Asiedu RobertAbstract:A randomised complete block experiment was conducted in the 1998 and 1999 cropping seasons in five major yam growing areas in the yam belt of Nigeria to evaluate the performance and yield stability of six genotypes of water yarn (Dioscorea alata L). Location, genotype and their interaction effects, significantly (P
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AFLP marker diversity in water yam (Dioscorea alata L.)
'CABI Publishing', 2018Co-Authors: Egesi, Chiedozie N., Ogunyemi S., Asiedu Robert, Ude G., Egunjobi J.k.Abstract:Amplified fragment length polymorphism (AFLP) markers were employed to assess intraspecific variability in water yam (Dioscorea alata L.). Fifty-three accessions of diverse geographic origins in West and Central Africa (Benin, Côte d'Ivoire, Ghana, Nigeria and Chad) and Puerto Rico were analysed using three AFLP primer combinations. Of the 342 amplification products generated, a mean of 53.4% were polymorphic. Genetic similarity coefficients ranged from 0.29 to 0.95. The accessions could be clustered into three major genetic groups with one outlier. Each group was a mixture of accessions of different geographical origin indicating that geography has not played a major role in the differentiation of the species. A few accessions clustered very tightly suggesting that there may be duplicate accessions in the collection. The wide genetic variation observed constitutes a good basis for genetic improvement of yam
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Reaction of Dioscorea alata (water yam) to anthracnose disease in Nigeria
2018Co-Authors: Aduramigba-modupe A.o., Asiedu Robert, Odebode A.c.Abstract:Anthracnose disease, caused by the pathogen Collectotrichum gloeosporioides Penz., is a serious challenge to the cultivation of Dioscorea alata, a major source of food and income for millions of farm households in the tropics. Five breeder’s lines and eighteen landraces of D. alata from IITA’s germplasm collection were screened in the field in three agroecological zones (southern guinea savanna, derived savannah and the humid forest) of Nigeria for two years. The objective was to study their reactions to anthracnose disease and investigate the influences of environment (E) and genotype x environment (G x E) interactions on these using the Additive Main Effects and Multiplicative Interaction (AMMI) model. Environments (E), obtained as location x year combination, genotypes (G) and G x E interactions were highly significant (P
Ranjana Bhattacharjee - One of the best experts on this subject based on the ideXlab platform.
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An EST-SSR based genetic linkage map and identification of QTLs for anthracnose disease resistance in water yam (Dioscorea alata L.)
2018Co-Authors: Ranjana Bhattacharjee, Christopher A Saski, Brian E Scheffler, Christian O. Nwadili, Agre Paterne, Joao Augusto, Antonio Lopez-montes, Joseph T. Onyeka, Lava P. Kumar, Ranajit BandyopadhyayAbstract:Water yam (Dioscorea alata L.) is one of the most important food yams with wide geographical distribution in the tropics. One of the major constraints to water yam production is anthracnose disease caused by a fungus, Colletotrichum gloeosporioides (Penz.). There are no economically feasible solutions as chemical sprays or cultural practices, such as crop rotation are seldom convenient for smallholder farmers for sustainable control of the disease. Breeding for development of durable genetic resistant varieties is known to offer lasting solution to control endemic disease threats to crop production. However, breeding for resistance to anthracnose has been slow considering the biological constraints related to the heterozygous and vegetative propagation of the crop. The development of saturated linkage maps with high marker density, such as SSRs, followed by identification of QTLs can accelerate the speed and precision of resistance breeding in water yam. In a previous study, a total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from two D. alata genotypes. A set of 380 EST-SSRs were validated as polymorphic when tested on two diverse parents targeted for anthracnose disease and were used to generate a saturated linkage map. Majority of the SSRs (60.2%) showed Mendelian segregation pattern and had no effect on the construction of linkage map. All 380 EST-SSRs were mapped into 20 linkage groups, and covered a total length of 3229.5 cM. Majority of the markers were mapped on linkage group 1 (LG 1) comprising of 97 EST-SSRs. This is the first genetic linkage map of water yam constructed using EST-SSRs. QTL localization was based on phenotypic data collected over a 3-year period of inoculating the mapping population with the most virulent strain of C. gloeosporioides from West Africa. Based on threshold LOD scores, one QTL was consistently observed on LG 14 in all the three years and average score data. This QTL was found at position interval of 71.1–84.8 cM explaining 68.5% of the total phenotypic variation in the average score data. The high marker density allowed identification of QTLs and association for anthracnose disease, which could be validated in other mapping populations and used in marker-assisted breeding in D. alata improvement programmes.
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genomic resources for water yam Dioscorea alata l analyses of est sequences de novo sequencing and gbs libraries
PLOS ONE, 2015Co-Authors: Christopher A Saski, Ranjana Bhattacharjee, Brian E Scheffler, Robert AsieduAbstract:The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp.) is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST)-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS) profiles on two yam (Dioscorea alata L.) genotypes (TDa 95/00328 and TDa 95-310) was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using different approaches in generating genomic resources provides a non-biased glimpse into the publicly available EST-sequences, yam genome, and GBS profiles with affirmation that the genomic complexity can be methodically unraveled and constitute a critical foundation for future studies in linkage mapping, germplasm analysis, and predictive breeding.
Christopher A Saski - One of the best experts on this subject based on the ideXlab platform.
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An EST-SSR based genetic linkage map and identification of QTLs for anthracnose disease resistance in water yam (Dioscorea alata L.)
2018Co-Authors: Ranjana Bhattacharjee, Christopher A Saski, Brian E Scheffler, Christian O. Nwadili, Agre Paterne, Joao Augusto, Antonio Lopez-montes, Joseph T. Onyeka, Lava P. Kumar, Ranajit BandyopadhyayAbstract:Water yam (Dioscorea alata L.) is one of the most important food yams with wide geographical distribution in the tropics. One of the major constraints to water yam production is anthracnose disease caused by a fungus, Colletotrichum gloeosporioides (Penz.). There are no economically feasible solutions as chemical sprays or cultural practices, such as crop rotation are seldom convenient for smallholder farmers for sustainable control of the disease. Breeding for development of durable genetic resistant varieties is known to offer lasting solution to control endemic disease threats to crop production. However, breeding for resistance to anthracnose has been slow considering the biological constraints related to the heterozygous and vegetative propagation of the crop. The development of saturated linkage maps with high marker density, such as SSRs, followed by identification of QTLs can accelerate the speed and precision of resistance breeding in water yam. In a previous study, a total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from two D. alata genotypes. A set of 380 EST-SSRs were validated as polymorphic when tested on two diverse parents targeted for anthracnose disease and were used to generate a saturated linkage map. Majority of the SSRs (60.2%) showed Mendelian segregation pattern and had no effect on the construction of linkage map. All 380 EST-SSRs were mapped into 20 linkage groups, and covered a total length of 3229.5 cM. Majority of the markers were mapped on linkage group 1 (LG 1) comprising of 97 EST-SSRs. This is the first genetic linkage map of water yam constructed using EST-SSRs. QTL localization was based on phenotypic data collected over a 3-year period of inoculating the mapping population with the most virulent strain of C. gloeosporioides from West Africa. Based on threshold LOD scores, one QTL was consistently observed on LG 14 in all the three years and average score data. This QTL was found at position interval of 71.1–84.8 cM explaining 68.5% of the total phenotypic variation in the average score data. The high marker density allowed identification of QTLs and association for anthracnose disease, which could be validated in other mapping populations and used in marker-assisted breeding in D. alata improvement programmes.
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genomic resources for water yam Dioscorea alata l analyses of est sequences de novo sequencing and gbs libraries
PLOS ONE, 2015Co-Authors: Christopher A Saski, Ranjana Bhattacharjee, Brian E Scheffler, Robert AsieduAbstract:The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp.) is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST)-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS) profiles on two yam (Dioscorea alata L.) genotypes (TDa 95/00328 and TDa 95-310) was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using different approaches in generating genomic resources provides a non-biased glimpse into the publicly available EST-sequences, yam genome, and GBS profiles with affirmation that the genomic complexity can be methodically unraveled and constitute a critical foundation for future studies in linkage mapping, germplasm analysis, and predictive breeding.