Genome-wide association study reveals novel genomic regions for flowering time and growth habit in cowpea (Vigna unguiculata [L.] Walp).

BACKGROUND: Cowpea is one of the most important legume crops in the world. Flowering time (FT) and growth habit (GH) are fundamentally important in determining cowpea yield. However, the genetic basis of nature variation in FT and GH has been seldom explored. RESULTS: In this study, we evaluated the FT and GH of a genetic diversity panel of 344 cowpea accessions within two experimental replications in 2022 Spring and 2023 Autumn, respectively. We investigated their phenotypic variation and the distribution in three cowpea subpopulations. The FT varied from 53 to 70 days and 30-65 days in 2022 spring and 2023 autumn, respectively. Prostrate type accounted for 92% (315 accessions) and the erect type only made up 4% (14 accessions). We identified 6 genomic regions significantly associated with FT and 14 regions controlling GH through genome-wide association study, respectively. Haplotype analysis confirmed the correlation between different haplotypes and the corresponding phenotypes. We also found the pyramiding effect of the favorable alleles on FT and GH. In addition, six candidate genes were regarded as the likely candidate genes for 6 significant regions, which may involve in the hormone signaling, transcription factor and various metabolic pathways. CONCLUSIONS: These results enhanced our understanding of genetic mechanism of FT and GH, and facilitate the development of new varieties with correct flowering time and ideal growth habit.