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The seed-setting rate has a significant effect on grain yield in rice (Oryza sativa L.). Embryo sac development is essential for seed setting; however, the molecular mechanism underlying this process remains unclear. Here, we isolated defective embryo sac1 (des1), a rice mutant with a low seed-setting rate. Cytological examination showed degenerated embryo sacs and reduced fertilization capacity in des1. Map-based cloning revealed a nonsense mutation in OsDES1, a gene that encodes a putative nuclear envelope membrane protein (NEMP)-domain-containing protein that is preferentially expressed in pistils. The OsDES1 mutation disrupts the normal formation of functional megaspores, which ultimately results in a degenerated embryo sac in des1. Reciprocal crosses showed that fertilization is abnormal and that the female reproductive organ is defective in des1. OsDES1 interacts with LONELY GUY (LOG), a cytokinin-activating enzyme that acts in the final step of cytokinin synthesis; mutation of LOG led to defective female reproductive organ development. These results demonstrate that OsDES1 functions in determining the rice seed-setting rate by regulating embryo sac development and fertilization. Our study sheds light on the function of NEMP-type proteins in rice reproductive development.

Rice is one of the most important food crops in the world. To discover the genetic basis of yield components in super hybrid rice Nei2You No.6, 386 recombinant inbred sister lines (RISLs) were obtained for mapping quantitative trait loci (QTL) responsible for grain yield per plant, number of panicles per plant, grain number per panicle and 1000-grain weight. Using whole genome re-sequencing, a high-density linkage map consisting of 3203 Bin markers was constructed with total genetic coverage of 1951.1 cM and average density of 0.61 cM. A total of 43 yield-related QTL were mapped to all 12 chromosomes, and each explained 2.40–10.17% phenotypic variance, indicating that the medium and minor effect QTL are genetic basis for high yield of Nei2You No.6. With positive effect, 28 out of the 43 QTL are inherited from the maintainer line (Nei2B). Nine loci, qGYP-6b, qGNP-6c, qNP-7, qTGW-1a, qTGW-5, qTGW-7, qTGW-10b, qTGW-10c and qTGW-12 showed stable effects across multiple environments. Five of these nine QTL were co-located with previously reported QTL, and four novel locus, qNP-7, qGNP-6c, qTGW-7 and qTGW-12, were firstly identified in the present study. Subsequently, qNP-7, qTGW-7 and qTGW-12 were validated using corresponding paired sister lines which differed only in the target genome region. The recombinant inbred sister lines is an effective tool for mapping and confirming QTL of yield-associated traits. Newly detected QTL provide new resource for investigating genetics of yield components and will accelerate molecular breeding in rice.

Heading date is crucial for rice reproduction and the geographical expansion of cultivation. We fine-mapped qHD5 and identified LOC_Os05g03040, a gene that encodes an AP2 transcription factor, as the candidate gene of qHD5 in our previous study. In this article, using two near-isogenic lines NIL(BG1) and NIL(XLJ), which were derived from the progeny of the cross between BigGrain1 (BG1) and Xiaolijing (XLJ), we verified that LOC_Os05g03040 represses heading date in rice through genetic complementation and CRISPR/Cas9 gene-editing experiments. Complementary results showed that qHD5 is a semi-dominant gene and that the qHD5

Grain size is a key constituent of grain weight and appearance in rice. However, insufficient attention has been paid to the small-effect QTLs on grain size. In the present study, residual heterozygous populations were developed for mapping two genetically linked small-effect QTLs for grain size. After genotyping and phenotyping of five successive generations, qGS7.1 was dissected into three QTLs and two were selected for further analysis. qTGW7.2a was finally mapped into a 21.10-kb interval containing four annotated candidate genes. Transcript levels assay showed that the expression of candidates LOC_Os07g39490 and LOC_Os07g39500 were significantly reduced in the NIL- qTGW7.2a BG1 . Cytological observation indicated that qTGW7.2a regulated grain width through controlling cell expansion. Use the same strategy, qTGW7.2b was fine mapped into a 52.71-kb interval, showing a significant effect on grain length and width with opposite allelic directions but little on grain weight. Our study provides new genetic resources for yield improvement and fine-tunes of grain size in rice.

Grain size is a major determinant of grain weight, which is one of the components of rice yield. The objective o this study was to identify novel, and important quantitative trait loci (QTLs) for grain size and weight in rice. QTLs were mapped using a BC4F4 population including 192 backcross inbred lines (BILs) derived from a backcross between Xiaolijing (XLJ) and recombinant inbred lines (RILs). The mapping population was planted in both Lingshui (Hainan, 2015) and Fuyang (Zhejiang, 2016), with the short- and long-day conditions, respectively. A total of 10 QTLs for grain length, four for grain width, four for the ratio of grain length to width, and 11 for grain weight were detected in at least one environment and were distributed across 11 chromosomes. The phenotypic variance explained ranged from 6.76–25.68%, 14.30–34.03%, 5.28–26.50%, and 3.01–22.87% for grain length, grain width, the ratio of grain length to width, and thousand grain weight, respectively. Using the sequential residual heterozygotes (SeqRHs) method, qGS7.1, a QTL for grain size and weight, was mapped in a 3.2-Mb interval on chromosome 7. No QTLs about grain size and weight were reported in previous studies in this region, providing a good candidate for functional analysis and breeding utilization.

Tiller number is a crucial agronomic trait that directly affects the number of effective panicles and yield formation in rice. Here, we report a semi-dwarf and low tillering mutant Osdlt10 (dwarf and low tillering 10) that exhibited reduced tiller number, semi-dwarfism, increased grain width, low seed-setting rate, curled leaf tip and a series of abnormalities of agronomic traits. Phenotypic observations showed that Osdlt10 mutants had defects in tiller bud formation and grew slowly at the tillering stage. Map-based cloning revealed that LOC_Os10g41310 was the responsible gene for OsDLT10, which was subsequently demonstrated using the CRISPR/Cas9 system and a complementary experiment. Expression pattern analysis indicated that OsDLT10 was primarily expressed in the stem node, the basic part of axillary bud and leaf sheath, pulvinus. The hormone treatment investigation indicated that extremely high of exogenous auxin concentrations can inhibit the expression of OsDLT10. Endogenous auxin content decreased significantly at the base of stem node and axillary bud in Osdlt10 mutants. The results showed that OsDLT10 was related to auxin. qPCR analysis results further showed that the expression levels of auxin transport genes (PINs) and early response genes (IAAs) were significantly increased. The expression levels of WUS-like and FON1 were substantially decreased in the Osdlt10 mutants. These results revealed that OsDLT10 played a critical role in influencing tiller number, likely in association with hormone signals and the WUS-CLV pathway, to regulate axillary bud development in rice.

Grain shape is a key factor for yield and quality in rice. To investigate the genetic basis of grain shape in the high-yielding hybrid rice variety Nei2You No.6, a set of recombinant inbred sister lines (RISLs) were used to map quantitative trait loci (QTLs) determining grain length (GL), grain width (GW), and length-width ratio (LWR) in four environments. A total of 91 medium/minor-effect QTL were detected using a high-density genetic map consisting of 3203 Bin markers composed of single nucleotide polymorphisms, among which 64 QTL formed 15 clusters. Twelve of 15 clusters co-localized with QTL previously reported for grain shape/weight. Three new QTL were detected: qGL-7a, qGL-8, and qGL-11a. A QTL cluster, qLWR-12c/qGW-12, was detected across all four environments with phenotypic variation explained (PVE) ranging from 3.67% to 11.93%, which was subsequently validated in paired lines of F17 progeny and tightly linked marker assay in F10 generation. Subsequently, 17 candidate genes for qLWR-12c/qGW-12 were detected in the 431 Kb interval utilizing bulk segregant analysis (BSA). Among these, OsR498G1222170400, OsR498G1222171900, OsR498G1222185100, OsR498G1222173400, and OsR498G1222170500 were the best candidates, which lays the foundation for further cloning and will facilitate high-yield breeding in rice.

Background Rice is one of the most important food crops in the world. To determine the genetic basis of yield components in super rice Nei2You No.6, 387 recombinant inbred sister lines (RISLs) were obtained for mapping quantitative trait loci (QTL) responsible for yield-associated traits, such as 1000-grain weight (TGW), grain number per plant (GNP), number of panicles per plant (NP), and grain yield per plant (GYP). Results Using whole genome re-sequencing, a high-density linkage map consisting of 3203 bin markers was constructed with total genetic coverage of 1951.1 cM and an average density of 0.61 cM. As a result of the multi-environment test, 43 yield-related QTL were mapped to all 12 chromosomes, among which 28 inherited from Nei2B showed a positive effect on yield traits. Nine QTL, qTGW-1a, qTGW-5, qTGW-7, qTGW-10b, qTGW-10c, qTGW-12, qNP-7, qGNP-6c, and qGYP-6b, showed stable effects across multiple environments. Five of the nine QTL were co-located with previously reported QTL, and four novel loci, qTGW-7, qTGW-12, qGNP-6c, and qNP-7, were identified in the present study. Subsequently, qNP-7, qTGW-12, and qTGW-7 were validated using corresponding paired lines which differed only in the target region. Conclusions the RISL population is an effective tool for mapping and validating QTL of complex traits, for instance, yield-associated traits, and newly detected QTL provide new genetic resources for research of yield components and molecular breeding in rice.