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Development of EST‐derived SSR markers in pea ( Pisum sativum ) and their potential utility for genetic mapping and transferability
Author(s) -
Mishra Raghvendra K.,
Gangadhar Baniekal H.,
Nookaraju Akula,
Kumar Sushil,
Park Se W.
Publication year - 2012
Publication title -
plant breeding
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.583
H-Index - 71
eISSN - 1439-0523
pISSN - 0179-9541
DOI - 10.1111/j.1439-0523.2011.01926.x
Subject(s) - biology , transferability , microsatellite , expressed sequence tag , genetics , sativum , locus (genetics) , primer (cosmetics) , dinucleotide repeat , gene mapping , quantitative trait locus , genetic marker , amplicon , allele , botany , gene , polymerase chain reaction , complementary dna , chromosome , statistics , mathematics , chemistry , organic chemistry , logit
With 1 figure and 3 tablesAbstract Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) are important resources for gene discovery and mapping. In this study, we developed EST‐based SSR (eSSRs) markers and assessed their ability in mapping and transferability. A total of 10 800 unigenes were detected from 18 522 pea EST sequences (December 2009). Screening of 10 800 unigenes by MISA (MIcroSAtellite) revealed 2612 (14.1%) eSSRs in 2395 (12.9%) SSR‐containing ESTs from which 577 (24.1%) primer pairs were designed. The most abundant repeat motif identified in eSSR was mononucleotide (85.2%), followed by trinucleotide (10.6%) and dinucleotide (2.8%). Among 108 randomly selected primer pairs, 40 were assessed for mapping and 68 to test cross‐species transferability in six leguminous species. Out of 40 primer pairs, 85% produced amplicons, 60% showed polymorphism and 47.5% were mapped. Furthermore, 68 primer pairs revealed high rate of transferability (48–85%) in leguminous species. High levels of polymorphism, reproducibility, presence of alleles (3.8/locus) and transferability revealed the potential use of these eSSR markers in molecular mapping, quantitative trait loci (QTL) analysis and comparative mapping in pea and other legumes.