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Development and integration of genome-wide polymorphic microsatellite markers onto a reference linkage map for constructing a high-density genetic map of chickpea

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Title Development and integration of genome-wide polymorphic microsatellite markers onto a reference linkage map for constructing a high-density genetic map of chickpea
 
Creator Khajuria, Yash Paul
Saxena, Maneesha S.
Gaur, Rashmi
Chattopadhyay, Debasis
Jain, Mukesh
Parida, Swarup K.
Bhatia, Sabhyata
 
Subject Chickpea
Microsatellite Markers
 
Description Accepted date: March 24, 2015
The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest number of new sequence-based robust microsatellite markers (634) which is an advancement over the previously documented (~300 markers) inter-specific genetic maps. This advanced high-density map will serve as a foundation for large-scale marker validation and genotyping applications, including identification and targeted mapping of trait-specific genes/QTLs (quantitative trait loci) with sub-optimal use of resources and labour in chickpea.
This study was funded by the National
Institute of Plant Genome Research, New Delhi and
the Department of Biotechnology, Ministry of Science
and Technology, Government of India.
 
Date 2016-01-06T09:55:49Z
2016-01-06T09:55:49Z
2015
 
Type Article
 
Identifier PLoS One, 10(5): e0125583
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/526
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125583
10.1371/journal.pone.0125583
 
Language en_US
 
Publisher PLOS