Grain size is a major determinant of grain yield and quality in rice (Oryza sativa), and was therefore an important selective target during domestication and breeding (Fitzgerald et al., 2009) (Takano- Kai et al., 2009). In the past few decades, a dozen grain size-related QTLs/genes have been cloned (Huang et al., 2013;Zuo and Li, 2014). Pyramiding grain size QTLs to breed high-yielding and high-quality rice varieties has proved to be a great success. For example, by pyramiding the nonfunctional alleles gs3 and gw8 in line HJX74, Wang et al. (2012) converted a line with short and wide grains into one with slender grains and substantially improved grain quality. By pyramiding the GW7 allele from TFA and gs3, Wang et al. (2015) developed new high-yielding indica hybrid rice varieties with simultaneously improved yield and grain quality. Thus, it is of considerable importance to identify more grain size QTLs to facilitate further improvement in rice yield and quality.
Stigma exsertion, a key determinant of the rice mating system, greatly contributes to the application of heterosis in rice. Although a few quantitative trait loci associated with stigma exsertion have been fine mapped or cloned, the underlying genetic architecture remains unclear. We performed a genome-wide association study on stigma exsertion and related floral traits using 6.5 million SNPs characterized in 533 diverse accessions of Oryza sativa. We identified 23 genomic loci that are significantly associated with stigma exsertion and related traits, three of which are co-localized with three major grain size genes GS3, GW5, and GW2. Further analyses indicated that these three genes affected the stigma exsertion by controlling the size and shape of the spikelet and stigma. Combinations of GS3 and GW5 largely defined the levels of stigma exsertion and related traits. Selections of these two genes resulted in specific distributions of floral traits among subpopulations of O. sativa. The low stigma exsertion combination gw5GS3 existed in half of the cultivated rice varieties; therefore, introducing the GW5gs3 combination into male sterile lines is of high potential for improving the seed production of hybrid rice.
Appearance and taste are important factors in rice (Oryza sativa) grain quality. Here, we investigated the taste scores and related eating-quality traits of 533 diverse cultivars to assess the relationships between-and genetic basis of-rice taste and eating-quality. A genome-wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy (Wx) allele, Wx la , which combined two mutations from Wx b and Wx in , exhibited a unique phenotype. Reduced This article is protected by copyright. All rights reserved. Accepted Article GBSSI activity conferred Wx la rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wx la was derived from intragenic recombination. In fact, the recombination rate at the Wx locus was estimated to be 3.34 kb/cM, which was about 75-fold higher than the genome-wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice.
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