Single Nucleotide Polymorphism Genotyping for Breeding and Genetics Applications in Chickpea and Pigeonpea using the BeadXpress Platform

Single nucleotide polymorphisms (SNPs) are ideal molecular markers due to their higher abundance. Although several types of genotyping platforms for assaying large number of SNPs are available, in cases such as marker-assisted selection, where few markers are required for genotyping a set of potential lines, highthroughput SNP genotyping platforms (e.g., iScan or Infinium) may not be cost effective. In this scenario, GoldenGate assays based on VeraCode technology using Illumina BeadXpress seems to be the most cost-effective platform. The objective of this study was to develop cost-effective SNP genotyping platforms in chickpea (Cicer arietinum L.) and pigeonpea (Cajanus cajan L.). Two sets of SNPs, one each for chickpea (96 SNPs) and pigeonpea (48 SNPs), were developed and tested by genotyping 288 diverse genotypes from respective reference sets. The SNPs selected for the oligo pool assays had high transferability to crop wild relative species. The mean polymorphism information content value of assayed SNP markers was 0.31 and 0.32 in chickpea and pigeonpea, respectively. No unique pattern was observed in the chickpea reference set whereas two major groups were observed in the case of the pigeonpea reference set. The Illumina BeadXpress platform assays developed for chickpea and pigeonpea are highly informative and cost effective for undertaking genetic studies in these legume species. Legumes play a critical role in food security for the people living in Asian and sub-Saharan African regions of the world. Chickpea and pigeonpea are among the most important legumes supplying protein to human diets, fodder for household animals, and manure to agricultural land. Global production of chickpea is approximately 11 million t and approximately 3.5 million t in case of pigeonpea (http://faostat.fao.org/site/567/default.aspx#ancor; accessed 11 Apr. 2013). As these crops are mainly grown in marginal environments and exposed to several biotic (mainly Fusarium wilt, sterility mosaic disease, Helicoverpa armigera, and Ascochyta blight) and abiotic stresses (drought, soil salinity, waterlogging, and cold), the productivity of these legumes is less than 1 t ha–1 (http:// faostat.fao.org/site/567/default.aspx#ancor; accessed 11 Apr. 2013), which is significantly lower than their potential yield (6 t ha–1 for chickpea and 2.5 t ha–1 for pigeonpea). The development of high yielding varieties that can tolerate abiotic and biotic stresses has been the area of focus for many researchers in the past. Plant breeders have been addressing these production constraints using conventional approaches. Genomics-assisted breeding (GAB) approaches have been very successful for developing superior varieties or parental lines of hybrids in many crops (Varshney et al., Published in The Plant Genome 6 doi: 10.3835/plantgenome2013.05.0017 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. M.I. Vales, current address: Oregon State Univ., Dep. of Crop and Soil Sciences, Corvallis, OR, 97331. O. Riera-Lizarazu, current address: Dow AgroSciences LLC, 2001 Country Club Rd., Pullman, WA 99163. R.K. Varshney, CGIAR Generation Challenge Programme (GCP), CIMMYT, Mexico DF, Mexico. Received 23 May 2013. *Corresponding author ([email protected]). Abbreviations: ADT, assay design tool; Cl, cluster; EST, expressed sequence tag; GAB, genomics-assisted breeding; KASPar, KBiosciences Competitive Allele-Specific polymerase chain reaction; MABC, marker-assisted backcrossing; MARS, markerassisted recurrent selection; MAS, marker-assisted selection; PIC, polymorphism information content; SNP, single nucleotide polymorphism; SSR, simple sequence repeat; TOG, tentative orthologous gene.