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Discovery of single feature polymorphisms in Pigeonpea using soybean genome arrays

Varshney, R.K.ORCID: 0000-0002-4562-9131 and Saxena, R.K. (2010) Discovery of single feature polymorphisms in Pigeonpea using soybean genome arrays. In: Plant & Animal Genome Conference XVIII, 9 - 13 Jan. 2010, San Diego, CA.


A Pigeonpea is an important food legume crop of tropical and sub-tropical regions of the world, especially in India and Africa. High density genetic linkage maps are perquisite for marker assisted breeding but are not available for pigeonpea. In this study, we have used soybean genome arrays for detecting single-feature polymorphisms (SFPs) in six pigeonpea parental lines of three mapping populations (ICPL 151× ICPL 87, ICPL 8755× ICPL 227 and ICP 28× ICPW 94) which are segregating for a number of agronomic important traits such as drought and Helicoverpa resistance. SFPs are individual oligos that constitute gene specific probes on an expression array which can behave as polymorphic markers. SFP detection is based on calculating hybridization intensity differences between samples for probes on the chip and reproducible differences reflect indel and/or SNP polymorphisms in the sequences of the probes. Robustified projection pursuit (RPP) has been used for statistical analysis using RNA as a surrogate for DNA. A total of 1,355 potential SFPs were detected across these six genotypes. In terms of parental polymorphism a varied level was detected for instance 627 SFPs in ICPL 151× ICPL 87, 580 SFPs in ICPL 8755× ICPL 227 and only 177 SFPs in ICP 28× ICPW 94. These SFPs should be useful, after validation, to integrate in the existing genetic map of pigeonpea. Such genetic maps should be useful to pigeonpea community for aligning them with that of soybean and cowpea which will facilitate transfer ofgenome information from soybean and cowpea in pigeonpea improvement.

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