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Milling quality directly affects production efficiency in rice, which is closely related to the brown rice recovery (BRR), the milled rice recovery (MRR) and the head milled rice recovery (HMRR). The present study investigated these three traits in 173 germplasms in two environments, finding abundant phenotypic variation. Three QTLs for BRR, two for MRR, and three for HMRR were identified in a genome-wide association study, five of these were identified in previously reported QTLs and three were newly identified. By combining the linkage disequilibrium (LD) analyses, the candidate gene LOC_Os05g08350 was identified. It had two haplotypes with significant differences and Hap 2 increased the BRR by 4.40%. The results of the qRT-PCR showed that the expression of LOC_Os05g08350 in small-BRR accessions was significantly higher than that in large-BRR accessions at Stages 4–5 of young panicle development, reaching the maximum value at Stage 5. The increase in thickness of the spikelet hulls of the accession carrying LOC_Os05g08350TT occurred due to an increase in the cell width and the cell numbers in cross-sections of spikelet hulls. These results help to further clarify the molecular genetic mechanism of milling-quality-related traits and provide genetic germplasm materials for high-quality breeding in rice. [ABSTRACT FROM AUTHOR]

The mining of favorable SNP loci and haplotypes is of great significance for the further cloning and molecular-assisted breeding of alkalinity-tolerance genes in rice. To improve the utilization rate of saline–alkaline lands and the yield of rice, we used the 1,322,884 SNPs obtained from the sequencing 173 of rice accessions in this study. Alkalinity-tolerance-related traits, including the germination energy (GE), germination rate (GR), seedling length (SL), root length (RL), relative alkaline damage rate (RADR) of the GERADR of the GR, RADR of the SL and RADR of the RL, were evaluated in 2019 and 2020 and revealed abundant phenotypes in the studied population. A genome-wide association analysis detected 10 quantitative trait loci (QTLs) related to alkalinity tolerance. In addition, a transcriptome sequencing analysis of the alkalinity-tolerant rice variety 'Yuedao 9' and the alkali-sensitive rice variety 'Tijin' under alkalinity stress and control conditions was performed. Three candidate genes that were predicted to be related to alkalinity tolerance in rice, namely LOC_Os06g06600, LOC_Os011g44680 and LOC_Os011g44600, were screened based on gene annotation, coding sequences and haplotype analysis. The results of this study provide important genetic information for the molecular improvement of rice. [ABSTRACT FROM AUTHOR]

Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline–alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (qGPR2) and SLR (qSLR9), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: LOC_Os02g40664, LOC_Os02g40810, and LOC_Os09g28310. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits with the 2,998,034 derived single nucleotide polymorphisms (SNPs) by using the best linear unbiased prediction (BLUP) values for each trait. The results revealed that 195 SNPs had significant associations with the six agronomic traits. Based on the genome-wide linkage disequilibrium (LD) blocks, candidate genes for the target traits were detected within 100 kb upstream and downstream of the relevant SNP loci. Results indicate that six quantitative trait loci (QTLs) significantly associated with six traits (qTGW4.1, qTGW4.2, qGL4.1, qGL12.1, qGL12.2, qGW2.1, qGW4.1, qGW6.1, qGW8.1, qGW8.2, qGW9.1, qGW11.1, qGLWR2.1, qGLWR2.2, qGLWR4.2, qPGWC5.1 and qDEC6.1) were identified for haplotype analysis. Among these QTLs, two (qTGW4.2 and qGW6.1), were overlapped with FLO19 and OsbZIP47, respectively, and the remaining four were novel QTLs. These candidate genes were further validated by haplotype block construction. [ABSTRACT FROM AUTHOR]

The shape of the rice flag leaf affects rice yield. Therefore, the detection of quantitative trait loci (QTLs) and alleles related to rice flag leaf shape is of great significance for rice yield improvement. Therefore, in 2019 and 2020, we carried out a genome-wide association study of flag leaf length (FLL), flag leaf width (FLW), flag leaf length–width ratio (FLR), and flag leaf area (FLA), considering 1.3 million single-nucleotide polymorphisms (SNPs) in 173 rice accessions, in order to investigate the effects of various genes on flag leaf shape. An abundance of phenotypic variation was found, with respect to the four flag leaf shape parameters of these accessions. We identified one significant SNP position associated with FLL and FLR on chromosome 5 and one significant SNP position associated with FLW on chromosome 2, which were detected in both of the two years of the study period through general linear model (GLM) and mixed linear model (MLM). Furthermore, three candidate genes—LOC_Os02g56760, LOC_Os05g34380, and LOC_Os05g34600—were found to possibly be significantly related to flag leaf shape in rice. Haplotype analysis indicated that LOC_Os05g34380 is highly associated with flag leaf length and flag leaf length–width ratio, LOC_Os05g34600 is highly associated with flag leaf length, and LOC_Os02g56760 is highly associated with flag leaf width. Our results provide important genetic information for the molecular improvement of rice flag leaf shape, laying the foundation for further cloning and molecular-assisted breeding of flag leaf genes. [ABSTRACT FROM AUTHOR]

Background: Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population. Results: The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg− 1, ranging from 0.22 mg.mg-1 to 0.93 mg.mg− 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg− 1 (RM7309–135 bp on chromosome 9) to 0.45 mg.mg− 1 (RM297–180 bp on chromosome 2). RM297–180 bp showed the largest phenotypic effect value (0.44 mg.mg− 1 in 2016 and 0.45 mg.mg− 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297–175 bp (0.43 mg.mg− 1 in 2016 and 0.44 mg.mg− 1 in 2017). Conclusion: Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future. [ABSTRACT FROM AUTHOR]

The efficiency of hybrid seed production can be improved by increasing the percentage of exserted stigma, which is closely related to the stigma length in rice. In the chromosome segment substitute line (CSSL) population derived from Nipponbare (recipient) and Kasalath (donor), a single CSSL (SSSL14) was found to show a longer stigma length than that of Nipponbare. The difference in stigma length between Nipponbare and SSSL14 was controlled by one locus (qSTL3). Using 7,917 individuals from the SSSL14/Nipponbare F2 population, the qSTL3 locus was delimited to a 19.8-kb region in the middle of the short arm of chromosome 3. Within the 19.8-kb chromosome region, three annotated genes (LOC_Os03g14850, LOC_Os03g14860 and LOC_Os03g14880) were found in the rice genome annotation database. According to gene sequence alignments in LOC_Os03g14850, a transition of G (Nipponbare) to A (Kasalath) was detected at the 474-bp site in CDS. The transition created a stop codon, leading to a deletion of 28 amino acids in the deduced peptide sequence in Kasalath. A T-DNA insertion mutant (05Z11CN28) of LOC_Os03g14850 showed a longer stigma length than that of wild type (Zhonghua 11), validating that LOC_Os03g14850 is the gene controlling stigma length. However, the Kasalath allele of LOC_Os03g14850 is unique because all of the alleles were the same as that of Nipponbare at the 474-bp site in the CDS of LOC_Os03g14850 among the investigated accessions with different stigma lengths. A gene-specific InDel marker LQ30 was developed for improving stigma length during rice hybrid breeding by marker-assisted selection. [ABSTRACT FROM AUTHOR]

Detecting quantity trait locus (QTLs) and elite alleles that are associated with grain-filling rate (GFR) in rice is essential for promoting the utilization of hybrid japonica rice and improving rice yield. Ninety-five varieties including 58 landraces and 37 elite varieties from the core germplasm collection were genotyped with 263 simple sequence repeat (SSR) markers. The GFR of the 95 varieties was evaluated at five stages, 7, 14, 21, 28 and 35 days after flowering (DAF) both in 2011 and 2012. We found abundant phenotypic and genetic diversity in the studied population. A population structure analysis identified seven subpopulations. A linkage disequilibrium (LD) analysis indicated that the levels of LD ranged from 60.3 cM to 84.8 cM and artificial selection had enhanced the LD. A time-course association analysis detected 31 marker-GFR associations involving 24 SSR markers located on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 11 and 12 of rice at five stages. The elite alleles for high GFR at each stage were detected. Fifteen excellent parental combinations were predicted, and the best parental combination ‘Nannongjing62401×Laolaihong’ could theoretically increase 4.086 mg grain-1 d-1 at the five stages. Our results demonstrate that the time-course association mapping for GFR in rice could detect elite alleles at different filling stages and that these elite alleles could be used to improve the GFR via pyramiding breeding. [ABSTRACT FROM AUTHOR]