Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.

Rice is sensitive to cold and can be grown only in certain climate zones. Human selection of japonica rice has extended its growth zone to regions with lower temperature, while the molecular basis of this adaptation remains unknown. Here, we identify the quantitative trait locus COLD1 that confers chilling tolerance in japonica rice. Overexpression of COLD1(jap) significantly enhances chilling tolerance, whereas rice lines with deficiency or downregulation of COLD1(jap) are sensitive to cold. COLD1 encodes a regulator of G-protein signaling that localizes on plasma membrane and endoplasmic reticulum (ER). It interacts with the G-protein α subunit to activate the Ca(2+) channel for sensing low temperature and to accelerate G-protein GTPase activity. We further identify that a SNP in COLD1, SNP2, originated from Chinese Oryza rufipogon, is responsible for the ability of COLD(jap/ind) to confer chilling tolerance, supporting the importance of COLD1 in plant adaptation.

nature biotechnology advance online publication l e t t e r sThe brown planthopper (BPH) is the most destructive pest of rice (Oryza sativa) and a substantial threat to rice production, causing losses of billions of dollars annually 1,2 . Breeding of resistant cultivars is currently hampered by the rapid breakdown of BPH resistance 2 . Thus, there is an urgent need to identify more effective BPH-resistance genes. Here, we report molecular cloning and characterization of Bph3, a locus in rice identified more than 30 years ago that confers resistance to BPH. We show that Bph3 is a cluster of three genes encoding plasma membrane-localized lectin receptor kinases (OsLecRK1-OsLecRK3). Introgression of Bph3 into susceptible rice varieties by transgenic or marker-assisted selection strategies significantly enhanced resistance to both the BPH and the white back planthopper. Our results suggest that these lectin receptor kinase genes function together to confer broad-spectrum and durable insect resistance and provide a resource for molecular breeding of insect-resistant rice cultivars.BPH (Nilaparvata lugens Stål, Hemiptera, Delphacidae) is a monophagous, phloem-sucking herbivore. It sucks the sap from the rice phloem using its stylet, and causes direct damage to rice plants. BPH can also cause indirect damage to rice plants through the transmission of viruses including the rice ragged stunt virus and grassy stunt virus 2 . Repeated overapplication of pesticides for BPH management has heavily polluted the environment 3 . Breeding of resistant cultivars is the most cost-effective and environmentally responsible strategy for BPH management but developing insect resistant cultivars by traditional breeding approaches is extremely difficult and time consuming owing to a paucity of knowledge about BPH resistance genes and germplasm.To date, 28 BPH resistance loci have been identified from cultivated and wild species of Oryza 2,4,5 . Only two of these resistance genes, Bph14 and Bph26 have been cloned to date 6,7 . In addition, BPH resistance of IR26 and IR36, two widely cultivated rice varieties that harbor the BPH resistance loci Bph1 and bph2, respectively, was quickly broken down in just a few years owing to the rapid adaptation of the BPH 8 . Thus, there is still an urgent need to identify new types of resistance genes and germplasm for developing efficient approaches to breed broad-spectrum and durable BPH-resistant rice cultivars. Notably, the Bph3 locus, originally identified in the Sri Lankan indica cultivar Rathu Heenati 9 , displayed resistance to four BPH biotypes (BPH biotypes refer to specific populations of BPH classified according to their virulence on different BPH resistance genes) 2,10 . Furthermore, rice varieties harboring Bph3 deployed more than 30 years ago in the Philippines are still resistant to BPH 8 . However, the molecular basis of this broad-spectrum and durable resistance of Bph3 against BPH remains unknown.We observed that Bph3-containing Rathu Heenati infested with BPH of mixed biotypes (biotype ...