Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.) is one of the most important cereal crops in the world. There have been landmark achievements in rice improvement over the past 50 y, especially in the indica subspecies. A major breakthrough resulted from the independent development of a series of semidwarf varieties in China and by the International Rice Research Institute (IRRI) in the 1950s and 1960s, leading to the "green revolution" in rice. Since then, semidwarfness has been a basic characteristic for almost all modern varieties. Based on semidwarf varieties, improvement for other traits, such as abiotic stress resistance, broad-spectrum resistances to biotic stresses, and better grain quality, has also been achieved. Another major breakthrough stemmed from the exploitation of hybrid vigor in China (1), resulting in the largescale adoption of hybrid rice since the 1970s. Jointly, these breakthroughs have greatly increased rice productivity in the past several decades globally.Genomic studies in recent years have identified a large number of loci that were under selection during rice domestication (2). However, there has been very limited study to identify loci or genomic regions that have been under selection due to breeding. Next-generation sequencing technologies have enabled sequencing of a large number of rice accessions at relatively low cost, providing opportunities to inspect the genomic regions selected in the history of crop improvement. Meanwhile, genome-wide association studies (GWAS) have provided an effective approach to analyze the genetic architecture of complex traits and allow identification of candidate genes for further improvement of agronomically important traits (3,4).In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions, which revealed a large number of differentially selected regions associated with breeding efforts between two major subpopulations in indica. These selected regi...

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.

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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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Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WCR1 (WHITE-CORE RATE 1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica (TrJ) and wild rice O. rufipogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.

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