Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.) uri icon

abstract

  • 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 8755xICPL 227) to 854 (ICPL 151xICPL 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 151xICPL 87, 41.86% for ICPL 8755xICPL 227, and 81.58% for ICP 28xICPW 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.
  • Single feature polymorphisms (SFPs) aremicroarray-based molecular markers that are detected byhybridization of DNA or cRNA to oligonucleotide probes.With an objective to identify the potential polymorphicmarkers for drought tolerance in pigeonpea (Cajanus cajan(L.) Millspaugh), an important legume crop for the semiaridtropics but deficient in genomic resources, AffymetrixGenome Arrays of soybean (Glycine max), a closely relatedspecies of pigeonpea were used on cRNA of six parentalgenotypes of three mapping populations of pigeonpeasegregating for agronomic traits like drought tolerance andpod borer (Helicoverpa armigiera) resistance. By usingrobustified projection pursuit method on 15 pair-wisecomparisons for the six parental genotypes, 5,692 SFPswere identified. Number of SFPs varied from 780 (ICPL8755×ICPL 227) to 854 (ICPL 151×ICPL 87) per parentalcombination of the mapping populations. Randomly selected179 SFPs were used for validation by Sanger sequencingand good quality sequence data were obtained for 99 genes of which 75 genes showed sequence polymorphisms. Whileassociating the sequence polymorphisms with SFPsdetected, true positives were observed for 52.6% SFPsdetected. In terms of parental combinations of the mappingpopulations, occurrence of true positives was 34.48% forICPL 151×ICPL 87, 41.86% for ICPL 8755×ICPL 227,and 81.58% for ICP 28×ICPW 94. In addition, a set of 139candidate genes that may be associated with droughttolerance has been identified based on gene ontologyanalysis of the homologous pigeonpea genes to the soybeangenes that detected SFPs between the parents of themapping populations segregating for drought tolerance

publication date

  • 2011
  • 2011
  • 2011