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Population Structure Analysis and Selection of Core Set among Common Bean Genotypes from Jammu and Kashmir, India

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Abstract

Understanding the genetic diversity of a crop is useful for its effective utilization in breeding programmes. For better understanding of the genetic variability in common bean, the first and foremost step is to study its genetic diversity. In the present investigation, 138 genotypes of common bean collected from various regions of Jammu and Kashmir, India, representing major common bean growing areas of this region, were evaluated using 23 SSRs. These SSRs were found highly polymorphic and possess high values for various parameters indicating their high discriminatory power. The average PIC value observed was 0.692, with 0.730 as average gene diversity value, and 0.267 as heterozygosity. Twenty-three SSRs produced a total of 251 alleles. The dendrogram generated with un-weighted neighbour joining cluster analysis grouped genotypes into three main clusters with various degrees of sub-clustering within the clusters. The model-based STRUCTURE analysis using 23 SSR markers identified a population with 3 sub-populations which corresponds to distance-based groupings with average F ST value and expected heterozygosity of 0.1497 and 0.6696, respectively, within the sub-population, as such high level of genetic diversity was observed within the population. Further, Core Hunter II was used to identify a core set of 96 diverse genotypes. This core set of diverse 96 genotypes is a potential resource for association mapping studies and can be used by breeders as a material to make desirable genetic crosses to generate elite varieties for the fulfilling global market needs. These findings have further implications in common bean breeding as well as conservation programs.

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Acknowledgements

SMZ is grateful to SERB, DST, New Delhi for financial support of this work (Project sanction order No. SR/FT/LS-27/ 2011).

Contribution of Authors

RM was involved in laboratory experiments and was also involved in data analysis. SMZ has designed experiment and has guided molecular experiments, analysis and manuscript preparation. RS has helped in data analysis and manuscript correction. SF and HS helped in data analysis. RKS helped in manuscript preparation.

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Authors and Affiliations

  1. School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu and Kashmir, 180009, India

    Reetika Mahajan, Ravinder Singh, Romesh Kumar Salgotra & Sufia Farhat

  2. Division of Biotechnology, S K University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India

    Sajad Majeed Zargar

  3. Départment de phytologie-FSAA, Université Laval, Québec, QC, G1V 0A6, Canada

    Humaira Sonah

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  1. Reetika Mahajan
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Supplementary Figure1

Jammu and Kashmir Map. Red triangle indicates the region of common bean collection. (PPTX 155 kb)

Supplementary Figure 2

NJ tree dendrogram. Red colour indicates population I, green colour indicates population II and Blue colour indicates population III and grey colour admixture. (PPTX 84 kb)

Supplementary Figure 3

Graphical representation of the optimal number of groups in STRUCTURE inferred using the criterion of Evanno et al. (2005). The analysis was based on data obtained using 23 microsatellite markers. (PPTX 122 kb)

Supplementary Figure 4

Core Set of 96 diverse common bean genotypes. (PPTX 114 kb)

Supplementary Table 1

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Mahajan, R., Zargar, S.M., Singh, R. et al. Population Structure Analysis and Selection of Core Set among Common Bean Genotypes from Jammu and Kashmir, India. Appl Biochem Biotechnol 182, 16–28 (2017). https://doi.org/10.1007/s12010-016-2307-1

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