Hideo Matsumura

The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes. Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domestication example, bitter gourd ( Momordica charantia ), an important Asian vegetable and medicinal plant of the family Cucurbitaceae. Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the separation of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progenitors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selection happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions. Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors.

To improve several agronomic traits in crisphead lettuce (Lactuca sativaL.) under high-temperature growth conditions, we investigated the correlation among those traits in multiple cultivars and performed genetic mapping of their causal genes. In a field cultivation test of Empire type (serrated leaf) and Salinas type (wavy leaf) cultivars, Empire type cultivars showed increased tipburn susceptibility and late bolting compared with Salinas type cultivars. We attempted genetic mapping of leaf shape and bolting time by ddRAD-seq using the F₂population derived from a cross between ‘VI185’ (Empire type) and ‘ShinanoGreen’ (Salinas type). These analyses suggested that both traits are controlled by a single locus in LG5. Genotyping of 51 commercial lettuce cultivars with a tightly linked marker (LG5_v8_252.743Mbp) at this locus showed an association between its genotype and the serrated leaf phenotype. By further fine mapping and transcriptome analysis, a gene encoding putative CIN-like TCP transcription factor was determined to be a candidate gene at this locus and was designated asLsTCP4. An insertion of retrotransposable element was found in the allele of ‘VI185’, and its transcript level in the leaves was lower than that in ‘ShinanoGreen’. Because shapes of leaf epidermal cells in ‘VI185’ were similar to those in the TCP family mutant ofArabidopsis thaliana, the leaf shape phenotype was likely caused by reduced expression ofLsTCP4. Furthermore, because it is known that the TCP family protein also controls flowering time via interaction with FT inA. thaliana, it was highly possible thatLsTCP4gave pleiotropic effects on both leaf shape and bolting time in lettuce.