Development of genome-wide SSR markers in horsegram and their use for genetic diversity and cross-transferability analysis |
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Authors: | Rahul Kaldate Maneet Rana Vikas Sharma Hideki Hirakawa Rahul Kumar Gagandeep Singh Rakesh Kumar Chahota Sachiko N. Isobe Tilak Raj Sharma |
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Affiliation: | 1.Department of Agricultural Biotechnology,CSK Himachal Pradesh Agricultural University,Palampur,India;2.Division of Crop Improvement,ICAR-Indian Grassland & Fodder Research Institute,Jhansi,India;3.Department of Botany,Punjabi University Patiala,Punjab,India;4.Kazusa DNA Research Institute,Kisarazu, Chiba,Japan;5.Department of Agriculture,DAV University Jalandhar,Punjab,India;6.Biotechnology Division,CSIR-Institute of Himalayan Bioresource Technology,Palampur,India;7.ICAR-Indian Institute of Agricultural Biotechnology,Ranchi,India |
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Abstract: | 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. |
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