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.

Background: The low grain water content (GWC) at harvest is a prerequisite to mechanical harvesting in maize, or otherwise would cause massive broken kernels and increase drying costs. The GWC at harvest in turn depends on GWC at the physiological maturity (PM) stage and grain dehydration rate (GDR). Both GWC and GDR are very complex traits, governed by multiple quantitative trait loci (QTL) and easily influenced by environmental conditions. So far, a number of experiments have been conducted to reveal numbers of GWC and GDR QTL, however, very few QTL have been confirmed, and no QTL has been fine-mapped or even been cloned.Results: We demonstrated that GWCs after PM were positively correlated with GWC at PM, whereas negatively with GDRs after PM. With a recombinant inbred line (RIL) population, we identified totally 31 QTL related to GWC and 17 QTL related to GDR in three field trials. Seven GWC QTL were consistently detected in at least two of the three field trials, each of which could explain 6.92–24.78% of the total GWC variation. Similarly, one GDR QTL was consistently detected, accounting for 9.44–14.46% of the total GDR variation. Three major GWC QTL were found to overlap with three GDR QTL in bins 1.05/06, 2.06/07, and 3.05, respectively. One of the consistent GWC QTL, namelyqGwc1.1, was fine-mapped from a 27.22 Mb to a 2.05 Mb region by using recombinant-derived progeny test. TheqGwc1.1acted in a semi-dominant manner to reduce GWC by 1.49–3.31%.Conclusions: A number of consistent GWC and GDR QTL have been identified, and one of them, QTL-qGwc1.1, was successfully refined into a 2.05 Mb region. Hence, it is realistic to clone the genes underlying the GWC and GDR QTL and to make use of them in breeding of maize varieties with low GWC at harvest.

Doubled haploid (DH) lines produced via in vivo haploid induction have become indispensable in maize research and practical breeding, so it is important to understand traits characteristics in DH and its corresponding haploids which derived from each DH lines. In this study, a DH population derived from Zheng58 × Chang7-2 and a haploid population, were developed, genotyped and evaluated to investigate genetic architecture of eight stalk traits, especially rind penetrometer resistance (RPR) and in vitro dry matter digestion (IVDMD), which affecting maize stalk lodging-resistance and feeding values, respectively. Phenotypic correlation coefficients ranged from 0.38 to 0.69 between the two populations for eight stalk traits. Heritability values of all stalk traits ranged from 0.49 to 0.81 in the DH population, and 0.58 to 0.89 in the haploid population. Quantitative trait loci (QTL) mapping study showed that a total of 47 QTL for all traits accounting for genetic variations ranging from 1.6 to 36.5 % were detected in two populations. One or more QTL sharing common region for each trait were detected between two different ploidy populations. Potential candidate genes predicated from the four QTL support intervals for RPR and IVDMD were indirectly or directly involved with cellulose and lignin biosynthesis, which participated in cell wall formation. The increased expression levels of lignin and cellulose synthesis key genes in the haploid situation illustrated that dosage compensation may account for genome dosage effect in our study. The current investigation extended understanding about the genetic basis of stalk traits and correlations between DH and its haploid populations, which showed consistence and difference between them in phenotype, QTL characters, and gene expression. The higher heritabilities and partly higher QTL detection power were presented in haploid population than in DH population. All of which described above could lay a preliminary foundation for genetic architecture study with haploid population and may benefit selection in haploid-stage to reduce cost in DH breeding.

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.

Rice is the primary source of food for more than half of the global population. Accordingly, improving the cold tolerance of rice is vital for ensuring food security. In this study, a new cold tolerance-related QTL in rice (qPSR7-2) was detected on chromosome 7 following a genome-wide association study involving 173 japonica rice germplasm resources. The fine mapping of this locus identified Os07g0541800 as a candidate gene associated with qPSR7-2. This gene encodes a cysteine-rich receptor-like kinase. The functional verification of Os07g0541800 involving transgenic plants indicated that qPSR7-2 positively regulates rice cold tolerance at the seedling stage. The examination of the cold tolerance of 984 germplasm resources from the 3000 Rice Genomes Project at the seedling stage and their respective haplotypes at qPSR7-2 revealed that the proportion of favorable haplotypes in germplasm resources increased as the latitude increased. More than 90% of the rice varieties cultivated in Europe and Japan appear to carry qPSR7-2, implying that qPSR7-2 may mediate the acclimation of rice to low-temperature stress. The findings of this study will further clarify the molecular networks regulating rice cold tolerance, while also providing researchers and breeders with new genetic resources and information relevant for developing cold-tolerant rice varieties.