Identification of Genomic Regions Associated with Differences in Flowering Time and Inflorescence Architecture between and .

Understanding the genetic basis of species differences in flowering time and inflorescence architecture can shed light on speciation and molecular breeding. shows rapid speciation, with about 100 species formed in the past few million years, and, meanwhile, possesses high ornamental values. Two largely sympatric and closely related species of this genus, and , differ markedly in flowering time and flower number per inflorescence. Here, we constructed an F2 population between and , and used extreme bulks for flowering time and flower number per inflorescence in this population to identify genomic regions underlying the two traits. We found high differentiation on nearly the whole chromosome 7 plus a few regions on other chromosomes between the two extreme bulks for flowering time. Large chromosomal inversions on chromosome 7 between the two species, which contain flowering-related genes, can explain recombinational suppression on the chromosome. We identified 1872 genes with one or more highly differentiated SNPs between the two bulks for flowering time, including , , , , , , , , , and , known to be related to flowering. We also identified 680 genes with one or more highly differentiated SNPs between the two bulks for flower number per inflorescence, including , and , knows to play important roles in inflorescence development. These large inversions on chromosome 7 prevent us from narrowing down the genomic region(s) associated with flowering time differences between the two species. Flower number per inflorescence in appears to be controlled by multiple genes, without any gene of major effect. Our study indicates that large chromosomal inversions can hamper the identification of the genetic basis of important traits, and the inflorescence architecture of species may have a complex genetic basis.