Background: Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resources is considered to be an efficient approach to dissect the genetic basis of the complex traits. Central China is one of the main regions where thejaponicarice is produced. However, dozens of high-yield rice varieties in this region still exist with low quality or susceptibility to blast disease, severely limiting their application in rice production.Results: Here, we re-sequence 200japonicarice varieties grown in central China over the past 30 years and analyze the genetic structure of these cultivars using 2.4 million polymorphic SNP markers. Genome-wide association mapping and selection scans indicate that strong selection for high-yield and taste quality associated with low-amylose content may have led to the loss of resistance to the rice blast fungusMagnaporthe oryzae. By extensive bioinformatic analyses of yield components, resistance to rice blast, and taste quality, we identify several superior alleles for these traits in the population. Based on this information, we successfully introduce excellent taste quality and blast-resistant alleles into the background of two high-yield cultivars and develop two elite lines, XY99 and JXY1, with excellent taste, high yield, and broad-spectrum of blast resistance.Conclusions: This is the first large-scale genomic landscape analysis ofjaponicarice varieties grown in central China and we demonstrate a balancing of multiple agronomic traits by genomic-based strategy.

Cold stress is a major factor limiting rice (Oryza sativa L.) production worldwide, especially at the seedling and booting stages. Identification of genes associated with cold tolerance (CT) in rice is important for sustainable food production. Here, we report the results of a genome-wide association study (GWAS) to identify the genetic loci associated with CT by using a 1,033-accession diversity panel. We identified five CT-related genetic loci at the booting stage. Accessions carrying multiple cold-tolerant alleles displayed a higher seed setting rate than did accessions that had no cold-tolerant alleles or carried a single allele. At the seedling stage, eight genetic loci related to CT have been identified. Among these, LOC_Os10g34840 was identified as the candidate gene for the qPSR10 genetic locus that is associated with CT in rice seedlings. A single-nucleotide polymorphism (SNP), SNP2G, at position 343 in LOC_Os10g34840 is responsible for conferring cold tolerance at the seedling stage in rice. Further analysis of the haplotype network revealed that SNP2G was present in 80.08% of the temperate japonica accessions but only 3.8% of the indica ones. We used marker-assisted selection to construct a series of BC4F3 near-isogenic lines possessing the cold-tolerance allele SNP2G. When subjected to cold stress, plants carrying SNP2G survived better as seedlings and showed higher grain weight than plants with carrying the SNP2A allele. The CT-related loci identified here and the functional verification of LOC_Os10g34840 will provide genetic resources for breeding cold-tolerant varieties and for studying the molecular basis of cold tolerance in rice.

This study reports the creation of herbicide-resistant rice lines via CRISPR-Cas9-mediated editing of the 3' UTR of OsHPPD. Resistance index calculations revealed that two resistant lines, TS8-2^#-10 and TS8-8^#-6, exhibited 4.8-fold and 3.7-fold greater resistance to HPPD-inhibiting herbicides compared with the wild type, YG3012.

Summary: The genetic improvement of rice eating and cooking quality (ECQ) is an important goal in rice breeding. It is important to understand the genetic regulation of ECQ at the genomic level for effective breeding to improve ECQ. However, the mechanisms underlying the improvement of ECQ of indica and japonica cultivars in southern China remain unclear. In this study, 290 rice cultivars (155 indica and 135 japonica cultivars) bred in southern China in the past 30 years were collected. Physicochemical indicators, namely, apparent amylose content (AAC), protein content (PC), lipid content and taste value, were measured and correlation analysis was performed. A decrease in AAC and PC was a crucial factor for the ECQ improvement of the rice cultivars in southern China. Genome‐wide association analysis and selective domestication analysis preliminarily clarified that the comprehensive utilization of major and minor genes was an important genetic basis for improvement of ECQ. An elite allele, RAmy1A^A, with potential application in breeding to improve starch viscosity characteristics and ECQ, was mined. The Wx^b/OsmtSSB1L^T/OsDML4^G/RPBF^T/Du3^T and Wx^b/OsEro1^T/Glup3^G/OsNAC25^G/OsBEIIb^C/RAmy1A^A/FLO12^A gene modules, neither of which have been widely used, are proposed as the optimal allele combinations for ECQ improvement of indica and japonica cultivars in southern China. The results clarify the genetic regulation of rice ECQ improvement in southern China and provide novel genetic resources and breeding strategies for ECQ improvement in rice.