Identification of QTL controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp)

Abstract

Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine traits. Based on annotations of the cowpea reference genome, genes within these regions are reported. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programs.

The genome of cowpea (Vigna unguiculata [L.] Walp.)

“…Crop domestication typically involved size increases of specific organs harvested by humans (Doebley et al ., ). Recently, a genomic region related to increased organ size in cowpea was identified on Vu08 using a recombinant inbred line (RIL) population derived from a domesticated × wild cross (Lo et al ., ). This region contains a cluster of QTLs for pod length, seed size, leaf length and leaf width ( CPodl8 , CSw8 , CLl8 , CLw8 ).…”

“…This suggests that the reference genome orientation of this region is rare among landraces and that its frequency has been increased among breeding lines. Also, a complete lack of recombination across this region is reflected in the genetic map derived from a cultivated × wild cross (Lo et al ., ; IT99K‐573‐1‐1 × TVNu‐1158; Figure S10), which indicates that the wild parent has the opposite orientation of the cultivated accession. Because this cultivated parent has the same haplotype as the reference genome, and thus presumably also the same orientation, the lack of recombination across this region suggests that the opposite‐to‐reference orientation is the ancestral (wild) type while the reference orientation carries an inversion.…”

“…() and Lo et al . (). The remaining three genetic maps were generated as part of this study after genotyping three additional RIL populations with the Cowpea iSelect Consortium Array (Muñoz‐Amatriaín et al ., ).…”

“…A highly fragmented draft assembly and BAC sequence assemblies of IT97K‐499‐35 were previously generated (Muñoz‐Amatriaín et al ., ). Although these resources enabled progress on cowpea genetics (Yao et al ., ; Carvalho et al ., ; Misra et al ., ; Huynh et al ., ; Lo et al ., ), they lacked the contiguity and completeness required for accurate genome annotation, detailed investigation of candidate genes or thorough genome comparisons. Here, we re‐estimated the genome size of V. unguiculata and produced a genome assembly using single‐molecule real‐time sequencing combined with optical and genetic mapping.…”

Pod indehiscence is a domestication and aridity resilience trait in common bean

“…Association mapping revealed several other dehiscence‐related QTLs across the gene pools and races of common bean (Table ). Our ADP association mapping identified significant Pv03 SNPs in an interval that is syntenic with a region controlling dehiscence in cowpea (Lo et al ., ). NAC family and C2H2‐type zinc finger transcription factors are found in this region (Table ) and members of these families affect PD in soybean (Dong et al ., ) and rapeseed (Tao et al ., ), respectively.…”