Domestication and association analysis of Hd1 in Chinese mini-core collections of rice

Abstract

Hd1 is one of the major photoperiod genes with high degree of polymorphisms and contributes to rice (Oryza sativa L.) flowering in different light conditions. Ninety-two rice landraces and 111 accessions of common wild rice (O. rufipogon Griff.) from the mini-core collections in China were selected and sequenced to analyze the domestication process and association of Hd1 with rice flowering. Association analysis revealed that three insertions and two deletions in the coding region of Hd1 are highly correlated with flowering time in the short-day condition. Phylogenetic analysis suggested that the polymorphisms of Hd1 in wild rice are related to the distributions. Haplotype analysis indicated that Hd1 in most O. sativa L. ssp. indica Kato and O. sativa L. ssp. japonica Kato landraces evolved from different O. rufipogon groups containing functional Hd1 and that most aus varieties were domesticated from O. rufipogon containing the long-insertions Hd1, suggesting multiple origins of Hd1. Moreover, O. rufipogon which contained the long-insertions Hd1 could only be found in Southern China, implying that Southern China might be one of the domestication centers of O. sativa. This study provides much significant information to aid further understanding of the domestication process of Hd1.

Nonfunctional alleles of long‐day suppressor genes independently regulate flowering time

“…The sequences of Hd1 , DTH8 , Ghd7 and OsPRR37 (Table S3) were collected from five studies reported by Wei et al (), Fujino et al (), Wei et al (), Lu et al () and Koo et al (). To ensure the samples covering all distribution areas and rice subgroups, we further sequenced 5, 8, 7 and 14 accessions for Hd1 , DTH8 , Ghd7 and OsPRR37, respectively.…”

“…All accessions were sequenced by ABI3730XL automatic sequencer (Applied Biosystems). Since heterozygous individuals may exist for a small number of cultivars (Wei et al ), PCR fragments of heterozygous samples were cloned into EASY vectors (Transgen, China) and three cloned DNA fragments were sequenced for each individual. Taq errors occur randomly so polymorphisms shared by more than two clones are unlikely to be artificial (Eyre et al ; Zheng and Ge ).…”

“…In this study, we classified haplotypes as functional or nonfunctional based on previous studies (Wei et al ; Fujino et al ; Lu et al ; Koo et al ; Wei et al ). The correlation between the functional and nonfunctional of these alleles and flowering time was examined by the Spearman Correlation Coefficient Test.…”

“…Interestingly, many studies have found that the flower suppressor genes under LD conditions in rice are important for rice to extend to high latitude (Komiya et al ; Xue et al ). For example, molecular and association analysis revealed that natural variation in Hd1 alleles contributes to variation in flowering time and plays an important role in the regional adaptation of rice (Komiya et al ; Wei et al ). Allelic variation at the Ghd7 locus increases grain yield by adapting to long growing seasons and plays a key role in the adaptability of cultivated rice on a global scale (Xue et al ; Lu et al ).…”

Haplotype diversity analysis of bacterial leaf blight resistance gene <i>Xa21</i> in rice

“…The non-synonymous mutations that occur in the CDS will lead to creating diversity at the protein level (Lu et al, 2012). Based on these non-synonymous mutations it is possible to identify functional protein-types owing to the fact that mutations at functional domains could lead to a conformational change of the protein resulting altered functionality (Lu et al, 2012;Wei et al, 2014;Li et al, 2015). In the current study, based on 14 such sites with nonsynonymous mutations (10 SNPs and 4 InDel sites) within the CDS, nine protein-types XA21-1 to XA21-9) were identified ( Figure 2).…”