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.

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.

Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.

Maintaining rice yield and reducing nitrogen (N) input are two important targets in sustainable agriculture practices. The adoption of a nitrogen-saving variety (NSV) provides a unique opportunity to achieve this. However, limited options in NSV japonica rice and a lack of information on their responses to N reduction make management decisions difficult. This study aims to explore the responses of yield and nitrogen use efficiency (NUE) in NSV to N reduction. Two newly released NSVs and two popular general varieties (GVs) of japonica rice were field tested in Yangzhou, located at the lower reaches of Yangtze River of China, in two consecutive years. The results showed that for NSVs, with a 40–60% reduction in common practice N rate (300 Kg ha⁻¹), the rice yield could maintain a record average level (p < 0.05), whereas the yield for the GV would drop 20–30% (p < 0.05). This indicates that combining the practices of adoption of NSV and N reduction to 120–180 Kg N ha⁻¹ could balance the yield and N consumption. Moderate N reduction promotes the N accumulation and NUE, and it increases the number of tillers, the productive tiller percentage and the total amount of spikelets in the population, and increases the carbon and N metabolism of the population in the NSV. Compared with GV, NSV showed higher NUE and non-structural carbohydrate re-mobilization in the reduced N rate. The results showed that the practice of N reduction has to adopt NSV at the same time in order to maintain the grain yield level in rice.

Rice (Oryza sativa L.) bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) seriously threatens rice production. This disease can be controlled by cultivating lines with appropriate resistance genes. To discover new resistance loci, a natural population of 246 sequenced backbone varieties of indica rice was inoculated with Xoc in the field, and their disease level was evaluated. The population structure, distribution of resistance phenotypes, and effect of combinations of resistance genes were analyzed in a genome-wide association study. On the basis of single nucleotide polymorphism data and disease phenotypes at the seedling stage, seven resistance loci (qBls1.1, qBls4.1, qBls5.1, qBls7.1, qBls8.1, qBls9.1, and qBls12.1) were identified to determine the superior haplotype of the corresponding loci, which showed stronger BLS resistance. The effects of combining loci were analyzed. As the number of superior haplotypes increased, BLS resistance tended to increase, indicating that BLS resistance can be significantly improved by pyramiding multiple resistance loci in ideal germplasm. This study provides new resistance loci and genetic resources for breeding BLS-resistant rice varieties. These genetic resources will be useful for the fine mapping of resistance loci, gene cloning, and the breeding of BLS-resistant varieties in follow-up research.