Single feature polymorphisms SFPs for drought tolerance in pigeonpea Cajanus spp.Report as inadecuate

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Functional and Integrative Genomics

, Volume 11, Issue 4, pp 651–657

First Online: 06 May 2011Received: 06 January 2011Revised: 13 April 2011Accepted: 17 April 2011


Single feature polymorphisms SFPs are microarray-based molecular markers that are detected by hybridization of DNA or cRNA to oligonucleotide probes. With an objective to identify the potential polymorphic markers for drought tolerance in pigeonpea Cajanus cajan L. Millspaugh, an important legume crop for the semi-arid tropics but deficient in genomic resources, Affymetrix Genome Arrays of soybean Glycine max, a closely related species of pigeonpea were used on cRNA of six parental genotypes of three mapping populations of pigeonpea segregating for agronomic traits like drought tolerance and pod borer Helicoverpa armigiera resistance. By using robustified projection pursuit method on 15 pair-wise comparisons for the six parental genotypes, 5,692 SFPs were identified. Number of SFPs varied from 780 ICPL 8755 × ICPL 227 to 854 ICPL 151 × ICPL 87 per parental combination of the mapping populations. Randomly selected 179 SFPs were used for validation by Sanger sequencing and good quality sequence data were obtained for 99 genes of which 75 genes showed sequence polymorphisms. While associating the sequence polymorphisms with SFPs detected, true positives were observed for 52.6% SFPs detected. In terms of parental combinations of the mapping populations, occurrence of true positives was 34.48% for ICPL 151 × ICPL 87, 41.86% for ICPL 8755 × ICPL 227, and 81.58% for ICP 28 × ICPW 94. In addition, a set of 139 candidate genes that may be associated with drought tolerance has been identified based on gene ontology analysis of the homologous pigeonpea genes to the soybean genes that detected SFPs between the parents of the mapping populations segregating for drought tolerance.

KeywordsSingle feature polymorphism Microarray Robustified projection pursuit Molecular markers Legumes Electronic supplementary materialThe online version of this article doi:10.1007-s10142-011-0227-2 contains supplementary material, which is available to authorized users.

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Author: Rachit K. Saxena - Xinping Cui - Vivek Thakur - Barbara Walter - Timothy J. Close - Rajeev K. Varshney


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