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...

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice (Oryza sativa) and the extent of variations explored is very limited. We conducted a genome-wide association study (GWAS) using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down-regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 (NAL1) corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5' UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding.

The photoprotective processes conferred by nonphotochemical quenching (NPQ) serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice (Oryza sativa), and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS) for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified. To check the validity of the GWAS signals, three F2 mapping populations with parents selected from the association panel were constructed and assayed. All QTLs detected in mapping populations could correspond to at least one GWAS signal, indicating the GWAS results were quite reliable. OsPsbS1 was repeatedly detected and explained more than 40% of the variation in the whole association population in two years, and demonstrated to be a common major QTL in all three mapping populations derived from inter-group crosses. We revealed 43 single nucleotide polymorphisms (SNPs) and 7 insertions and deletions (InDels) within a 6,997-bp DNA fragment of OsPsbS1, but found no non-synonymous SNPs or InDels in the coding region, indicating the PsbS1 protein sequence is highly conserved. Haplotypes with the 2,674-bp insertion in the promoter region exhibited significantly higher NPQ values and higher expression levels of OsPsbS1. The OsPsbS1 RNAi plants and CRISPR/Cas9 mutants exhibited drastically decreased NPQ values. OsPsbS1 had specific and high-level expression in green tissues of rice. However, we didn't find significant function for OsPsbS2, the other rice PsbS homologue. Manipulation of the significant loci or candidate genes identified may enhance photoprotection and improve photosynthesis and yield in rice.

Rice (Oryza sativa L.) is considered as one of the most important food crops all over the world. Because of the improvement of the actual living standards, there is more and more demand for improved grain quality. Although, the grain quality is a very complex quantitative trait in rice, it has great scientific significance and practical application value for the improvement of the quality of rice grain using high and up to date techniques. Here, we focus on the new advances in the application of the genetic improvement of grain quality by high throughput sequencing, genomic editing, near infrared spectroscopy, scanning electron microscopy, and other new techniques. Simultaneously, the application prospects of these high and up to date techniques have also been expected in the genetic improvement of rice quality. Thus, this will provide important information for genetic improvement of grain quality in rice breeding.

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Black rice is the main member of the special rice family, and it is also a rare grain and oil crop resource in China. Black rice has special medicinal components and high nutritional value. In recent years, the research on the nutritional value and application of black rice has become an important direction, and a series of important progress has been made. In this paper, the nutrition and its influencing factors of black rice, the main ways to improve eating quality, the health care and medical functions of black rice were reviewed. Meanwhile, the application prospect of black rice has also been prospected. Therefore, this review will provide an important theoretical basis for genetic improvement and breeding of new varieties of black rice.

Background: Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations. Results: In this study, two F 1 populations with CMS-WA and CMS-HL background respectively were developed using 337 XI and aus accessions being paternal parents. Genome-wide association studies on three fertility-related traits of the two populations for two consecutive years revealed that both fertility restoration of CMS-WA and CMS-HL were controlled by a major locus and several minor loci respectively. The major locus for fertility restoration of CMS-WA was co-located with Rf4, and that for fertility restoration of CMS-HL was co-located with Rf5, which are cloned major restorer of fertility (Rf) genes. Furthermore, haplotype analysis of Rf4, Rf5 and Rf6, the three cloned major Rf genes, were conducted using the 337 paternal accessions. Four main haplotypes were identified for Rf4, and displayed different subgroup preferences. Two main haplotypes were identified for Rf5, and the functional type was carried by the majority of paternal accessions. In addition, eight haplotypes were identified for Rf6. Conclusions: Haplotype analysis of three Rf genes, Rf4, Rf5 and Rf6, could provide valuable sequence variations that can be utilized in marker-aided selection of corresponding genes in rice breeding. Meanwhile, fertility evaluation of 337 accessions under the background of CMS could provide material resources for development of maintainer lines and restorers.

Rice is one of the most important food crops in the world, and about half of the world’s population uses it as the main food source. China’s annual rice output accounts for about 34% of the world’s annual rice output, ranking first in the world, thus China is known as the "Rice Kingdom". Rice has high nutritional value, providing the human body with 35% of the total energy intake and about 28% of the required protein. Therefore, the nutritional value of rice is directly related to human nutrition and health. In this paper, the three aspects of rice nutrition and human health, factors affecting rice nutritional quality and genetic improvement of nutritional quality of rice are reviewed. The new challenges of rice nutrition quality were analyzed, and the prospect of improving rice nutritional quality was prospected. The results provide theoretical basis for genetic improvement of rice nutrition quality and cultivation of new high-quality rice varieties in the future.