Open Access Research article

Identification of candidate genes and molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp]

Marti Pottorff1, Philip A Roberts2, Timothy J Close1*, Stefano Lonardi3, Steve Wanamaker1 and Jeffrey D Ehlers14*

Author Affiliations

1 Department of Botany & Plant Sciences, University of California Riverside, Riverside, CA, USA

2 Department of Nematology, University of California Riverside, Riverside, CA, USA

3 Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA

4 Bill & Melinda Gates Foundation, Seattle, Washington, USA

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BMC Genomics 2014, 15:328  doi:10.1186/1471-2164-15-328

Published: 1 May 2014



Heat-induced browning (Hbs) of seed coats is caused by high temperatures which discolors the seed coats of many legumes, affecting the visual appearance and quality of seeds. The genetic determinants underlying Hbs in cowpea are unknown.


We identified three QTL associated with the heat-induced browning of seed coats trait, Hbs-1, Hbs-2 and Hbs-3, using cowpea RIL populations IT93K-503-1 (Hbs positive) x CB46 (hbs negative) and IT84S-2246 (Hbs positive) x TVu14676 (hbs negative). Hbs-1 was identified in both populations, accounting for 28.3% -77.3% of the phenotypic variation. SNP markers 1_0032 and 1_1128 co-segregated with the trait. Within the syntenic regions of Hbs-1 in soybean, Medicago and common bean, several ethylene forming enzymes, ethylene responsive element binding factors and an ACC oxidase 2 were observed. Hbs-1 was identified in a BAC clone in contig 217 of the cowpea physical map, where ethylene forming enzymes were present. Hbs-2 was identified in the IT93K-503-1 x CB46 population and accounted for of 9.5 to 12.3% of the phenotypic variance. Hbs-3 was identified in the IT84S-2246 x TVu14676 population and accounted for 6.2 to 6.8% of the phenotypic variance. SNP marker 1_0640 co-segregated with the heat-induced browning phenotype. Hbs-3 was positioned on BAC clones in contig512 of the cowpea physical map, where several ACC synthase 1 genes were present.


The identification of loci determining heat-induced browning of seed coats and co-segregating molecular markers will enable transfer of hbs alleles into cowpea varieties, contributing to higher quality seeds.

Cowpea; Synteny; Legumes; Genomics; Marker-assisted selection; Heat-stress; Seed coat discoloration; Candidate genes; Ethylene