Profiling the domestication hotspots for ear traits in two maize populations with teosinte gene introgression

Abstract Throughout the history of maize cultivation, ear-related traits have been domesticated. However, little is known about the domesticated genes involved in shaping the ear traits from those of the wild progenitor, teosinte, to those exhibited by modern maize. In this study, five ear traits (kernel row number [KRN], ear length [EL], kernel number per row [KNR], cob diameter [CD], and ear diameter [ED]) were investigated, and eight quantitative trait loci (QTL) hotspots were identified in two maize populations with teosinte gene introgression. We found remarkable enrichment of domesticated and ear-related domesticated genes in qCD1 , qCD7 , qCD13 , qED1 , qEL8 , qEL10 , qKNR11 , and qKRN6 , suggesting that these eight QTL are domestication hotspots involved in shaping the maize ear from teosinte to modern maize. By combining the QTL identified in this study with the results of the genome-wide association study (GWAS) of ear traits from two association panels, eight candidate domesticated genes related to KRN, KNR, CD, and ED were identified. Considering the expression patterns and sequence variations, Zm00001d025111 and Zm00001d033153, which encode WD40/YVTN and SMAD/FHA proteins, respectively, were proposed as positive regulators of KNR, whereas Zm00001d003083 and Zm00001d005866, which encode isocitrate dehydrogenase and protein disulfide isomerase, respectively, were proposed as negative regulators of KRN. This study presents a frame work for the genomic distribution of ear trait-related and domesticated loci. Several candidate genes with minor effects may be viable targets for further increases in the yield of modern maize.