Development of genome-wide SSR markers in horsegram and their use for genetic diversity and cross-transferability analysis

Horsegram [ Macrotyloma uniflorum (Lam.) Verdc.] commonly known as kulthi or Madras gram is an important drought tolerant legume crop used as food and fodder in India and across the globe. Horsegram is tolerant to many biotic and abiotic stresses and considered a potential future food legume. Despit...

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Bibliographic Details
Published in:Molecular breeding 2017-08, Vol.37 (8), p.1-10, Article 103
Main Authors: Kaldate, Rahul, Rana, Maneet, Sharma, Vikas, Hirakawa, Hideki, Kumar, Rahul, Singh, Gagandeep, Chahota, Rakesh Kumar, Isobe, Sachiko N., Sharma, Tilak Raj
Format: Article
Language:English
Subjects:
Bayesian analysis
Biodiversity
Biomedical and Life Sciences
Biotechnology
Breeding
Crops
Drought
Drought resistance
Fodder
Food
Gene loci
Gene mapping
Gene sequencing
Genetic analysis
Genetic diversity
Genetic improvement
Genetic structure
Genetic variance
Genomes
Genomics
Germplasm
Heterozygosity
Legumes
Life Sciences
Macrotyloma uniflorum
Mapping
Markers
Molecular biology
Next-generation sequencing
Nucleotide sequence
Plant biology
Plant breeding
Plant Genetics and Genomics
Plant Pathology
Plant Physiology
Plant Sciences
Polymorphism
Population genetics
Principal components analysis
Species diversity
Structural analysis
Variance
Variance analysis
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Summary:Horsegram [ Macrotyloma uniflorum (Lam.) Verdc.] commonly known as kulthi or Madras gram is an important drought tolerant legume crop used as food and fodder in India and across the globe. Horsegram is tolerant to many biotic and abiotic stresses and considered a potential future food legume. Despite being a multiutility crop, insufficient genomic information is available in this species, which is otherwise required for genetic improvement. Hence, in the present work we used next-generation sequencing (NGS) technology for genome-wide development and characterization of novel simple sequence repeat (SSR) markers in horsegram. In all, 2458 SSR primer pairs were designed from NGS data and 117 SSRs were characterized in 48 diverse lines of horsegram. Cross-transferability of these markers was also checked in nine related legume species. The polymorphic SSRs revealed high diversity measures such as mean values of expected heterozygosity (He; 0.54), observed heterozygosity (Ho; 0.64), and polymorphism information content (PIC; 0.46). Analysis of molecular variance (AMOVA) revealed high degree of genetic variance within the populations. Dendrogram based on Jaccard’s similarity coefficient and principal component analysis (PCA) revealed two groups in the analyzed accessions. This observation was further confirmed by Bayesian genetic STRUCTURE analysis. The SSR markers developed herein can be used in diverse genetic analysis including association mapping in this crop and also in related legume crops with limited marker resources. Hence, this new SSR dataset can be useful for molecular breeding research in this underutilized pulse crop. In addition, genetic diversity estimates of analyzed germplasm can be important for devising future breeding programmes in horsegram.
ISSN:1380-3743
1572-9788
DOI:10.1007/s11032-017-0701-1