Identification of QTLs for Domestication-Related Traits in Zombi Pea [Vigna vexillata (L.) A. Rich], a Lost Crop of Africa

Abstract

Zombi pea [Vigna vexillata (L.) A. Rich] is a legume crop found in Africa. Wild zombi pea is widely distributed throughout the tropical and subtropical regions, whereas domesticated zombi pea is rarely cultivated. Plant domestication is an evolutionary process in which the phenotypes of wild species, including seed dormancy, pod shattering, organ size, and architectural and phenological characteristics, undergo changes. The molecular mechanism underlying the domestication of zombi pea is relatively unknown. In this study, the genetic basis of the following 13 domesticationrelated traits was investigated in an F 2 population comprising 198 individuals derived from a cross between cultivated (var. macrosperma) and wild (var. vexillata) zombi pea accessions: seed dormancy, pod shattering, days-to-flowering, days-to-maturity, stem thickness, stem length, number of branches, leaf area, pod length, 100-seed weight, seed width, seed length, and seeds per pod. A genetic map containing 6,529 single nucleotide polymorphisms constructed for the F 2 population was used to identify quantitative trait loci (QTLs) for these traits. A total of 62 QTLs were identified for the 13 traits, with 1-11 QTLs per trait. The major QTLs for days-to-flowering, stem length, number of branches, pod length, 100-seed weight, seed length, and seeds per pod were clustered in linkage group 5. In contrast, the major QTLs for seed dormancy and pod shattering belonged to linkage groups 3 and 11, respectively. A comparative genomic analysis with the cowpea [Vigna unguiculata (L.) Walp.] genome used as the reference sequence (i.e., the genome of the legume species most closely related to zombi pea) enabled the identification of candidate genes for the major QTLs. Thus, we revealed the genomic regions associated with domestication-related traits and the candidate genes controlling these traits in zombi pea. The data presented herein may be useful for breeding new varieties of zombi pea and other Vigna species.

Transcriptome Analysis Reveals Key Pathways and Candidate Genes Controlling Seed Development and Size in Ricebean (Vigna umbellata)

“…In terms of pod development, seed size is a key determinant for the seed or grain yield in legume crops (Amkul et al, 2020). In ricebean, we found four candidate genes for seed size encoding: histidine kinase 2, delta sterol reductase, phosphate transporter (PHO1), and WRKY domain-containing protein (WRKY 40).…”

“…Hence, the higher expression of this gene in bold genotypes implies an increase in the number of seeds per pod that could result in the improvement of the ricebean yield. The Vigun05g126900 gene, encoding MALE STERILE 5, was selected as a candidate gene in zombie pea (Amkul et al, 2020). In a previous study on Arabidopsis, mutations to MALE STERILE 5 resulted in the development of "polyads" (i.e., tetrads with more than four pools of chromosomes following male meiosis) (Glover et al, 1998).…”

“…Out of the 57 candidate genes, 18 genes encode transcription factors like AP2/ERF, WRKY, and NAC, whereas the rest of the genes were involved in cellulose synthase and serine/threonine protein kinase. The candidate genes for pod shattering have also been identified in other legumes including Vigun02g095200 (cellulose synthase), Vigun03g306000 (NAC domain transcription factor), and zombi pea (Suanum et al, 2016;Lo et al, 2018;Takahashi et al, 2019;Amkul et al, 2020;Watcharatpong et al, 2020). In Sorghum propinquum, WRKY modulates the flower and seed development and lignin deposition, and it is also found to be involved in pod shattering (Tang et al, 2013).…”

“…The identification of pod shattering genes may reduce preharvest yield damages in ricebean, resulting in a more efficient yield. Thus, pod indehiscence may be a valuable trait during seed harvesting, making it a main concern during crop domestication (Amkul et al, 2020).…”

A Class II KNOX Gene, KNAT7-1, Regulates Physical Seed Dormancy in Mungbean [Vigna radiata (L.) Wilczek]

“…For example, the dormancy may provide the protection of pre-harvest sprouting. In the genus, Vigna that comprises 10 domesticated legume crops, there are not many studies reported on quantitative trait locus (QTL) mapping of domestication syndrome, including adzuki bean ( Isemura et al, 2007 ; Kaga et al, 2008 ), black gram ( Somta et al, 2020 ), cowpea ( Kongjaimun et al, 2012 ; Lo et al, 2018 ), mungbean ( Isemura et al, 2012 ), moth bean ( Yundaeng et al, 2019 ), and zombi pea ( Dachapak et al, 2018 ; Amkul et al, 2020 ). One to six QTLs controlled seed dormancy in these legume species.…”