In silico mining of EST-SSRs in Arachis hypogaea L. and their utilization for genetic structure and diversity analysis in cultivars/breeding lines in Odisha, India

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• 作者：Sushree Sibanee Sardar ; Kedareswar Pradhan ; Ravi Prakash Shukla…
• 关键词：EST ; SSRs ; Repeat motif ; Arachis hypogaea ; Public domain
• 刊名：Molecular Breeding
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：36
• 期：4
• 全文大小：913 KB
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• 作者单位：Sushree Sibanee Sardar (1)
  Kedareswar Pradhan (1)
  Ravi Prakash Shukla (2)
  Ribha Saraswat (2)
  Anukool Srivastava (2)
  Satya Narayan Jena (2)
  Anath Bandhu Das (3)
  
  1. Department of Genetics and Plant Breeding, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, 751003, India
  2. Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
  3. Department of Botany, Utkal University, Vani Vihar, Bhubaneswar, Odisha, 751004, India
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Plant Sciences
  
• 出版者：Springer Netherlands
• ISSN：1572-9788

文摘

A total of 26,685 unutilized public domain expressed sequence tags (ESTs) of Arachis hypogaea L. were analyzed to give a total of 4442 EST-SSRs, in which 517 ESTs contained more than one simple sequence repeat (SSR). Of these EST-SSRs, 2542 were mononucleotide repeats (MNRs), 803 were dinucleotide repeats (DNRs), 1043 were trinucleotide repeats (TNRs), 40 were tetranucleotide repeats (TtNRs), six were pentanucleotide repeats (PNRs) and eight were hexanucleotide repeats (HNRs). Out of these 4442 EST-SSRs, only 1160 were found to be successful in non-redundant primer design; 1060 were simple SSRs, while the remaining 100 were compound forms. Among all the motifs, MNRs were abundant, followed by TNRs and DNRs. The AAG/CTT motif was the most abundant (~33 %) TNR, while AG/CT was the most abundant DNR. For redundancy and novelty, a stringent criterion deploying three different strategies was used and a total of 782 novel EST-SSRs were added to the public domain of peanut. These novel EST-SSR markers will be useful for qualitative and quantitative trait mapping, marker-assisted selection and genetic diversity studies in cultivated peanut as well as related Arachis species. A subset of 30 novel EST-SSRs was further randomly selected for validation and genotyping studies with eight well-known cultivars and 32 advanced breeding lines (ADBX lines, ADBY lines and ADBZ lines) from Odisha state, India. The number of polymorphic markers among accessions of A. hypogaea was low; however, a set of informative EST-SSR markers detected considerable levels of genetic variability in peanut cultivars and uncharacterized breeding lines collected from Odisha. The 30 newly developed EST-SSRs from Arachis spp. showed ~97 % amplification in Cicer arientinum and 93 % in pigeon pea. Thus, the EST-SSRs developed in this study will be a very useful asset for genetic analysis, comparative genome mapping, population genetic structure and phylogenetic inferences among wild and allied species of Arachis.