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New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]

Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pi...

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Autores principales: Bohra, Abhishek, Jha, Rintu, Pandey, Gaurav, Patil, Prakash G., Saxena, Rachit K., Singh, Indra P., Singh, D., Mishra, R. K., Mishra, Ankita, Singh, F., Varshney, Rajeev K., Singh, N. P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374739/
https://www.ncbi.nlm.nih.gov/pubmed/28408910
http://dx.doi.org/10.3389/fpls.2017.00377
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author Bohra, Abhishek
Jha, Rintu
Pandey, Gaurav
Patil, Prakash G.
Saxena, Rachit K.
Singh, Indra P.
Singh, D.
Mishra, R. K.
Mishra, Ankita
Singh, F.
Varshney, Rajeev K.
Singh, N. P.
author_facet Bohra, Abhishek
Jha, Rintu
Pandey, Gaurav
Patil, Prakash G.
Saxena, Rachit K.
Singh, Indra P.
Singh, D.
Mishra, R. K.
Mishra, Ankita
Singh, F.
Varshney, Rajeev K.
Singh, N. P.
author_sort Bohra, Abhishek
collection PubMed
description Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R(2) = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable genomic resource for pigeonpea research community, particularly in South Asia and East Africa where pigeonpea is primarily grown.
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spelling pubmed-53747392017-04-13 New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh] Bohra, Abhishek Jha, Rintu Pandey, Gaurav Patil, Prakash G. Saxena, Rachit K. Singh, Indra P. Singh, D. Mishra, R. K. Mishra, Ankita Singh, F. Varshney, Rajeev K. Singh, N. P. Front Plant Sci Plant Science Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R(2) = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable genomic resource for pigeonpea research community, particularly in South Asia and East Africa where pigeonpea is primarily grown. Frontiers Media S.A. 2017-03-31 /pmc/articles/PMC5374739/ /pubmed/28408910 http://dx.doi.org/10.3389/fpls.2017.00377 Text en Copyright © 2017 Bohra, Jha, Pandey, Patil, Saxena, Singh, Singh, Mishra, Mishra, Singh, Varshney and Singh. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Bohra, Abhishek
Jha, Rintu
Pandey, Gaurav
Patil, Prakash G.
Saxena, Rachit K.
Singh, Indra P.
Singh, D.
Mishra, R. K.
Mishra, Ankita
Singh, F.
Varshney, Rajeev K.
Singh, N. P.
New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
title New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
title_full New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
title_fullStr New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
title_full_unstemmed New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
title_short New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
title_sort new hypervariable ssr markers for diversity analysis, hybrid purity testing and trait mapping in pigeonpea [cajanus cajan (l.) millspaugh]
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374739/
https://www.ncbi.nlm.nih.gov/pubmed/28408910
http://dx.doi.org/10.3389/fpls.2017.00377
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