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Elucidating the genetic basis of natural variation in grain size and weight among rice varieties can help breeders develop high-yielding varieties. We identified a novel gene, GW3a (Grain Weight 3a) (LOC_Os03g27350), that affects rice grain size and weight. gw3a mutants showed higher total starch content and dry matter accumulation than the wild type (WT), Nipponbare, suggesting that GW3a negatively regulates grain size and weight. Moreover, our study found that GW3a interacted with OsATG8 by cleaving it, suggesting that GW3a may be involved in the assembly of autophagosomes and starch degradation in plants. The haplotype analysis of GW3a showed functional differences between indica and japonica rice. Taken together, we conclude that GW3a is expressed in the autophagosome pathway regulating starch metabolism in rice, affecting yield-related traits, such as grain size, grain weight and thousand grain weight (TGW). Our findings also shed new light on autophagy-mediated yield trait regulation, proposing a possible strategy for the genetic improvement of high-yield germplasm in rice. [ABSTRACT FROM AUTHOR]

Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a bacterial disease affecting rice production in Asia and Africa, whose severity is expected to increase with climate change. Identification of new quantitative-trait loci (QTL) or resistance genes for BLS resistance is essential for developing resistant rice. A genome-wide association study to identify QTL associated with BLS resistance was conducted using phenotypic and genotypic data from 429 rice accessions. Of 47 QTL identified, 45 were novel and two co-localized with previously reported QTL or genes conferring BLS resistance. qBLS6.2 on chromosome 6 explained the greatest phenotypic variation. Combined analysis of differential expression and annotations of predicted genes near qBLS6.2 based on haplotype and disease phenotype identified OsBLS6.2 (LOC_Os06g02960) as a candidate gene for qBLS6.2. OsBLS6.2 knockout plants showed higher resistance to Xoc than wild-type plants. Many other candidate genes for resistance to Xoc were identified. [ABSTRACT FROM AUTHOR]

Grain size influences the yield and quality of rice (Oryza sativa L.), and grain length is one of the component traits of grain size. In this study, a near-isogenic line LB3 with long grain size was constructed using japonica rice cultivar 02428, with short grain size, as the recipient parent and indica rice cultivar ZYX, with long grain size, as the donor parent, by multi-generation backcrossing and selfing. BSA-seq was used for preliminary QTL mapping and InDel markers were developed to fine map the locus. The major QTL, tentatively named qGL10, for grain length was located in a 128.45 kb region of chromosome 10. Combined with haplotype analysis of rice varieties, expression pattern analysis of candidate genes suggested LOC_Os10g39130 (OsMADS56) as a candidate gene. Sequence alignment of OsMADS56 in 02428 and LB3 revealed that there were 15 SNPs in the promoter region and four in the coding region. Further haplotype analysis suggested that SNP9 (G/A) located in the TGTCACA motif might account for the different expression levels of OsMADS56 in 02428 and LB3. These results lay a foundation for the application of qGL10 in molecular breeding of new rice varieties. [ABSTRACT FROM AUTHOR]

The relationship between parental genetic differences and the quality and yield of japonica hybrid rice strongly influences japonica hybrid rice breeding. In this study, 137 parental lines of japonica hybrid rice were genotyped using 8K rice SNP-Chips to characterize their genetic diversity, population structure, and indica-genotype proportion. The genetic diversity of total parental lines averaged 0.264, with values of 0.287 for restorer lines and 0.148 for the sterile lines. The introduction of indica lineage increased the genetic diversity of restorer lines relative to that of sterile lines. By model-based population structure analysis, the 137 lines were divided into 14 groups. According to the grouping results, eight restorer lines and five sterile lines were selected from different groups for cross breeding, yielding 40 japonica hybrid rice combinations (F1). Investigation of the yield and quality of these combinations showed that highyield combinations could be obtained by increasing parental genetic distance to 0.8-0.9, a result accomplished largely by the introduction of indica genomic components of restorer lines. To further improve grain quality, the genetic distance between parents should be reduced to 0.4-0.5, suggesting an indicagenotype proportion of 30%-40% for restorer lines. This study may provide a reference for breeding of japonica hybrid rice. [ABSTRACT FROM AUTHOR]

Pod shattering causes severe yield loss in rapeseed (Brassica napus L.) under modern agricultural practice. Identification of highly shatter-resistant germplasm is desirable for the development of rapeseed cultivars for mechanical harvesting. In the present study, an elite line OR88 with strong shatter resistance and a lignified-layer bridge (LLB) structure was identified. The LLB structure was unique to OR88 and co-segregated with high pod-shatter resistance. The LLB structure is differentiated at stage 12 of gynoecium development without any gynoecium defects. Genetic analysis showed that LLB is controlled by a single recessive gene. By BSA-Seq and map-based cloning, the resistance gene location was delimited to a 0.688 Mb region on chromosome C09. Transcriptome analysis suggested BnTCP8.C09 as the gene responsible for LLB. The expression of BnTCP.C09 was strongly downregulated in OR88, suppressing cell proliferation in the pod valve margin. KASP markers linked to the candidate gene were developed. This pod shatter-resistant line could be used in rapeseed breeding programs by direct transfer of the gene with the assistance of the DNA markers. [ABSTRACT FROM AUTHOR]