Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa)

Abstract

Seed dormancy in rice interrelates to the weedy characteristics shattering, awn, black hull color, and red pericarp color. A cross between the weedy strain SS18-2 and the breeding line EM93-1 was developed to investigate the genetic basis and adaptive significance of these interrelationships. These characteristics or their components differed in average degree of dominance from -0.8 to 1.5, in heritability from 0.5 to 0.96, and in their contribution to phenotypic or genotypic variation in dormancy by up to 25%. Five dormancy, four shattering, and three awn-length quantitative trait loci (QTLs) were detected in the BC1 population replicated in 2 years. Two QTLs for hull color were identified, and the SS18-2-derived and EM93-1-derived alleles increased the intensity of black, and red or yellow pigmentations, respectively. The only QTL for pericarp color co-located with the red pericarp gene Rc, with the SS18-2-derived allele increasing the intensity of black and red pigmentations. Four of the five dormancy QTLs were flanked or bracketed by one to four QTLs for the interrelated characteristics. The QTL organization pattern indicates the central role of seed dormancy in adaptive syndromes for non-domesticated plants, implies that the elimination of dormancy from cultivars could arise from the selections against multiple interrelated characteristics, and challenges the use of dormancy genes at these loci in breeding varieties for resistance to pre-harvest sprouting (PHS). However, another QTL (qSD12) provides candidate gene(s) for PHS resistance because it has a large effect in the population and it is independent of the loci for interrelated characteristics.

Caught Red-Handed:RcEncodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice

“…Red pericarp has long been used as marker for the cluster of domestication traits associated with weedy rice, including dormancy and shattering (Gu et al, 2005). Several studies have placed QTLs for dormancy and shattering in the pericentromeric region of chromosome 7, encompassing the Rc locus.…”

Was Asian Rice (Oryza sativa) Domesticated More Than Once?

“…The most detailed studies of dormancy have been conducted with an accession of wild-like weedy rice from Thailand (accession SS18-2) that exhibits hull-imposed dormancy [21][22][23][24][25][26]. The most important dormancy-related QTL in this Thai accession was located on chromosome 12, explaining about 50% of the phenotypic variance [22,24]. This chromosome 12 QTL may be the most important to study in relation to rice domestication because reduced dormancy must have been selected for early in the process of domestication.…”

Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication

“…The frequency of Ph is high in the indica type and low in the japonica type (Yu et al, 2008). In another study, using an F2 population developed from the cross between the weedy strain SS18-2 and the breeding line EM93-1, the two loci qHC4 and qHC7 that explained a major and a minor proportion of the phenotypic variation in black pigmentations on the hull were identified (Gu et al, 2005). But no candidate gene has been cloned for the transition from the black hull of the ancestral wild rice to the straw-white seed hull of cultivated rice, and the genetic basis for this kind of hull color alteration remains unknown.…”