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Title of Journal: Theor Appl Genet

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Abbravation: Theoretical and Applied Genetics

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Springer-Verlag

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DOI

10.1007/bf01474728

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1432-2242

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ESTderived genic molecular markers development a

Authors: Shalu Choudhary Rashmi Gaur Shefali Gupta Sabhyata Bhatia
Publish Date: 2012/02/03
Volume: 124, Issue: 8, Pages: 1449-1462
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Abstract

Wellsaturated linkage maps especially those based on expressed sequence tag ESTderived genic molecular markers GMMs are a prerequisite for molecular breeding This is especially true in important legumes such as chickpea where few simple sequence repeats SSR and even fewer GMMbased maps have been developed Therefore in this study 2496 ESTs were generated from chickpea seeds and utilized for the development of 487 novel ESTderived functional markers which included 125 ESTSSRs 151 intron targeted primers ITPs 109 expressed sequence tag polymorphisms ESTPs and 102 single nucleotide polymorphisms SNPs Whereas ESTSSRs ITPs and ESTPs were developed by in silico analysis of the developed EST sequences SNPs were identified by allele resequencing and their genotyping was performed using the Illumina GoldenGate Assay Parental polymorphism was analyzed between C arietinum ICC4958 and C reticulatum PI489777 parents of the reference chickpea mapping population using a total of 872 markers 487 new genebased markers developed in this study along with 385 previously published markers of which 318 365 were found to be polymorphic and were used for genotyping The genotypic data were integrated with the previously published data of 108 markers and an advanced linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 14977 cM The average marker density was 368 cM and the average number of markers per LG was 508 Among the mapped markers 303 new genomic locations were defined that included 177 genebased and 126 gSSRs genomic SSRs thereby producing the most advanced generich map of chickpea solely based on codominant markersThis research was supported by the National Institute of Plant Genome Research NIPGR New Delhi India and also by the Department of Biotechnology DBT Government of India by means of a project grant BT/PR9658/AGR/02/470/2007 We are thankful to Dr Fred Muehlbauer Washington State University USA for providing the interspecific chickpea mapping population and genotypic data of published STMS markers The fellowships provided to SC by University Grants Commission UGC India and SG by Council for Scientific and Industrial Research CSIR India is gratefully acknowledged

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