Background Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties. Results In this study, a recombinant inbred line (RIL) population derived from a cross between YZX and 02428 exhibited obvious coleoptile phenotypic differences. Mapping analysis using a high-density bin map indicated that a total of 25 loci were detected across two cropping seasons, including 10 previously detected loci and a total of 13 stable loci. Analysis of the 13 stable loci demonstrated that the more elite alleles that were pyramided in an individual, the higher the values of these traits were in the two cropping seasons. Furthermore, some anaerobic germination-tolerant recombinant inbred lines, namely G9, G10, G16, and G151, were identified. A total of 84 differentially expressed genes were obtained from the 13 stable loci via genome-wide expression analysis of the two parents at three key periods. Among them, Os06g0110200, Os07g0638300, Os07g0638400, Os09g0532900, Os09g0531701 and Os12g0539751 constitute the best candidates associated with anaerobic germination. Conclusions Both the anaerobic germination-tolerant recombinant inbred lines and the loci identified in this study will provide new genetic resources for improving the anaerobic germination tolerance of rice using molecular breeding strategies, as well as will broaden our understanding of the genetic control of germination tolerance under anaerobic conditions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5741-y) contains supplementary material, which is available to authorized users.

No abstract

Background: Seed germination and young seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice. Previous studies have focused on the identification of QTLs. However, there are few studies on the metabolome or transcriptome of germination and young seedling growth in rice. Results: Here, an indica rice and a japonica rice were used as materials, and the transcripts and metabolites were detected during the germination and young seedling growth periods on a large scale by using RNA sequencing and a widely targeted metabolomics method, respectively. Fourteen shared transcripts and 15 shared metabolites that were continuously differentially expressed in the two materials were identified and may be essential for seed germination and young seedling growth. Enrichment analysis of differentially expressed genes in transcriptome expression profiles at different stages indicated that cell wall metabolism, lipid metabolism, nucleotide degradation, amino acid, etc., were enriched at 0-2 days, and most of the results are consistent with those of previous reports. Specifically, phenylpropanoid biosynthesis and glutathione metabolism were continuously enriched during the seed germination and young seedling growth stages. Next, KO enrichment analysis was conducted by using the differentially expressed genes of the two materials at 2, 3 and 4 days. Fourteen pathways were enriched. Additionally, 44 differentially expressed metabolites at 2, 3 and 4 days were identified. These metabolites may be responsible for the differences in germination and young seedling growth between the two materials. Further attention was focused on the ascorbate-glutathione pathway, and it was found that differences in ROS-scavenging abilities mediated by some APX, GPX and GST genes may be directly involved in mediating differences in the germination and young seedling growth speed of the two materials. Conclusions: In summary, these results may enhance the understanding of the overall mechanism of seed germination and young seedling growth, and the outcome of this study is expected to facilitate rice breeding for direct seeding.

No abstract

Utilization of R (resistance) genes to develop resistant cultivars is an effective strategy to combat against rice blast disease. In this study, R genes Pi46 and Pita in a resistant accession H4 were introgressed into an elite restorer line Hang-Hui-179 (HH179) using the marker-assisted backcross breeding (MABB) procedure. As a result, three improved lines (e.g., R1791 carrying Pi46 alone, R1792 carrying Pita alone and R1793 carrying both Pi46 and Pita) were developed. The three improved lines had significant genetic similarities with the recurrent parent HH179. Thus, they and HH179 could be recognized as near isogenic lines (NILs). The resistance spectrum of the three improved lines, which was tested at seedling stage, reached 91.1, 64.7 and 97.1%, respectively. This was markedly broader than that of HH179 (23.5%). Interestingly, R1793 showed resistance to panicle blast but neither R1791 nor R1792 exhibited resistance at two natural blast nurseries. The results implied that the stacking of Pi46 and Pita resulted in enhanced resistance, which was unachievable by either R gene alone. Further comparison indicated that the three improved lines were similar to HH179 in multiple agronomic traits; including plant height, tillers per plant, panicle length, spikelet fertility, and 1 000-grain weight. Thus, the three improved lines with different R genes can be used as new sources of resistance for developing variety. There is a complementary effect between the two R genes Pi46 and Pita.

No abstract

No abstract

A rice (Oryza sativa L.) mutant, named m3, was isolated from a population of the M2 generation derived from an indica accession, BBS, where the seeds of BBS were treated with carbon ion irradiation at a dosage of 100 Gy to produce mutants. The m3 mutant is primarily characterized by the production of abnormal wilted leaves by appearance on the main stem, and additional tillers at the 9‐leaf stage. This abnormal leaf‐wilt phenotype is temporary, persisting only to the 13‐leaf stage, after which subsequent new leaves on the main stem and tiller appear normal. The phenotypic change of m3 during the 9‐ and 13‐leaf growth stages was further confirmed at physiological and biochemical levels. Additionally, compared with the wild type (WT, BBS), the heading date of m3 was noticeably delayed. The numbers of grains per panicle were lower by 32.44% than that of the WT. Moreover, plant height, width of flag leaf, panicle weight per plant, panicle length, and seed‐setting rate of m3 were considerably lower than those of the WT. Our genetic analysis revealed that the mutant phenotype of m3 was controlled by a single recessive gene, designated m3(g). We used recessive F2 individuals and mapped the m3(g) locus to a 3824‐kb region near the centromere of chromosome 11. We also performed a MutMap approach to refine the m3(g) locus to a 1030‐kb region comprising 115 genes, but six genes show nonsynonymous mutations. This study provides essential information for the cloning of the m3(g) gene and demonstrates that the MutMap approach is powerful enough to map a target gene that is located in centromeric regions.