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

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Relation http://oar.icrisat.org/4198/
http://dx.doi.org/10.1007/s10142-011-0227-2
 
Title Single feature polymorphisms (SFPs) for drought tolerance
in pigeonpea (Cajanus spp.)
 
Creator Saxena, R K
Cui, X
Thakur, V
Walter, B
Close, T J
Varshney, R K
 
Subject Pigeonpea
 
Description 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 semiarid
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.
 
Publisher Springer Verlag
 
Date 2011
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/4198/1/FunctIntegrGenomics_11_651-657_2011.pdf
Saxena, R K and Cui, X and Thakur, V and Walter, B and Close, T J and Varshney, R K (2011) Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.). Functional & Integrative Genomics, 11 (4). pp. 651-657.