Mapping of identity by descent reveals genes shaping morphology and biological traits in the cultivated lettuce varieties during the long-term crossbreeding.

The domestication of lettuce (Lactuca sativa L.) has resulted in its unique leaf morphology, making it one of the most widely consumed vegetable crops worldwide. The development of sequencing technology provides the opportunity to thoroughly investigate how the genomic variants contribute to the distinct morphology and biological traits of various major cultivated lettuce varieties such as Butterhead, Crisphead and Cos, which remains largely unknown. First, we present the phylogeny of the cultivated lettuce varieties and population structure of the sequenced represented cultivated lettuce varieties. We then utilized the method of relative Identity by descent (rIBD) to map the genomic regions and genes that show evidence of shared ancestry and selection in the pair-wised comparisons of these varieties. The average rIBD scores of 0.063, 0.093 and 0.187 were observed between Butterhead and Cos, Butterhead and Crisphead, Crisphead and Cos, respectively, and we further employed the Fixation index and integrated haplotype score method to validate whether these genomic regions are also under selection. We have identified candidate significant genes such as WOX2, GT5, RZ1B, ATPK2 and HIRA which play key roles in seed development, anthocyanins 3-O-glucosyltransferase activity and the accumulation of anthocyanin pigment, tolerance to cold stress, plant disease resistance and tolerance to heavy metal cadmium and leaf development during long-term cross-breeding and selection. Our relative identity by descent mapping reveals critical functional genes under selection shaping morphology and biological traits in the cultivated lettuce varieties throughout long-term crossbreeding.