Multiple introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L.

Abstract

Flowering time is a major determinant for the local adaptation of crops. Hd1 is a key flowering-time gene in rice and is orthologous to the Arabidopsis CONSTANS gene. To elucidate the role of Hd1 in selection, we examined the Hd1 alleles of 60 landraces of Asian cultivated rice (Oryza sativa L.) originating from all regions of Asia, which comprised three cultivar groups, indica, japonica, and aus. The identified alleles were classified into four allele groups. The functional Hd1 alleles in allele groups I and II corresponded to indica and japonica, respectively. Non-functional alleles in these groups were not clearly associated with cultivar groups or locations. Allele groups III and IV corresponded to the aus cultivar group. The ancestry of each cultivar group was identified by the coalescent approach for Hd1 molecular evolution using the haplotype patterns of 14 regions over the 1.1 Mb chromosomal region surrounding Hd1 and the pSINE patterns of two loci, 1.4 and 4.4 Mb apart from Hd1. The haplotype patterns clearly revealed that Hd1 allele migration was caused by multiple and complex introgression events between cultivar groups. The Hd1 haplotypes among dozens of accessions of the wild species O. rufipogon were strongly divergent and only two of the haplotype clusters in O. rufipogon were closely related to those in cultivated rice. This strongly suggested that multiple introgression events have played an important role in the shaping and diversification of adaptation in addition to primary selection steps at the beginning of domestication.

Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

“…5 and 6). In crop domestication and breeding, it is not uncommon to independently select alleles of the same gene, which results in allelic heterogeneity of agronomically important genes 41,53,54 . This suggests that gene-based association analysis is important for GWAS of agronomic traits.…”

“…The peak was located close to Hd1 (ref. 40), which contributes to genetic diversity in heading date in the rice breeding program 41,42 . Thus, we hypothesized that the causal gene of the significant peak was Hd1.…”

“…In the population we used, there were eleven haplotypes for Hd1 (haplotypes A-K), which included the null and intermediate alleles previously reported 41 (Supplementary Figs. 16 and 17).…”

Origin of rice (Oryza sativa L.) domestication genes

“…Absence of these alleles in wild populations would indicate that the mutations indeed emerged during domestication. Allelic uniformity in cultivated rice would then imply either a single origin of O. sativa , or spread of the domestication alleles among different groups of O. sativa by introgressive hybridization, as has been suggested (Sweeney et al 2007; Fujino et al 2010; Hua et al 2015; Oikawa et al 2015; Si et al 2016). However, if the association between the mutations and the phenotype is not strict in O. rufipogon , and the “domestication alleles” are found in wild populations—as is the case with sh4 and prog1 —then it is more difficult to make conclusions about the origin of those alleles in different cultivated groups.…”

Diversification of the plant-specific hybrid glycine-rich protein (HyGRP) genes in cereals

“…PCR, electrophoresis, and sequencing were performed as described previously (Fujino et al, 2004, 2005, 2010). The 1128-bp Os10g0554800 region was sequenced, including the 364-bp 5′ upstream region, 504-bp coding region, and 260-bp 3′ downstream region.…”