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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 XLJ and qHD5 BG1 alleles are both functional. The homozygous mutant line generated from knocking out qHD5 XLJ in NIL(XLJ) headed earlier than NIL(XLJ) under both short-day and long-day conditions. In addition, the homozygous mutant line of qHD5 BG1 in NIL(BG1) also headed slightly earlier than NIL(BG1). All of these results show that qHD5 represses the heading date in rice. Transient expression showed that the qHD5 protein localizes to the nucleus. Transactivation activity assays showed that the C-terminus is the critical site that affects self-activation in qHD5 XLJ. qRT-PCR analysis revealed that qHD5 represses flowering by down-regulating Ehd2. qHD5 may have been selected during indica rice domestication. • qHD5 is a semi-dominant gene that represses heading date in rice. • qHD5 XLJ and qHD5 BG1 alleles are both functional and the repression function of qHD5XLJ is stronger than that of the qHD5BG1 allele. • qHD5 represses heading by down-regulating Ehd2. [ABSTRACT FROM AUTHOR]

Drought poses a significant constraint on rice production, and, in this study, we have discovered a novel drought-sensitive mutant, designated as dsm3, arising from the progenies of indica rice variety Zhonghui8015 treated with ethyl methane sulphonate (EMS). Under drought stress conditions, dsm3 exhibited characteristic withered leaf tips, accompanied by increased levels of malondialdehyde (MDA) and H2O2, a reduced net photosynthetic rate (Pn), and decreased activity of peroxidase (POD) and superoxide dismutase (SOD). Genetic analysis revealed that the withered leaf tip phenotype was governed by a single recessive gene, designated as Osdsm3. To begin with, Osdsm3 was initially mapped to the short arm of chromosome 1 through a cross involving dsm3 and 02428. Subsequently, utilizing a population of 2591 F2 individuals, we narrowed down the location of Osdsm3 to a 78 Kb interval, encompassing 13 open reading frames (ORFs). Sequencing analysis unveiled a mutation (1275G → A) in the exon of the candidate gene (LOC_Os01g10680), leading to premature translation termination. Moreover, a quantitative RT-PCR assay demonstrated a high expression of OsDSM3 in the panicle and sheath, with a significant upregulation of drought-stress-related genes under drought conditions. Phylogenetic analyses indicated that Osdsm3 shares evolutionary homology with UNE1, an intracellular transport protein found in Arabidopsis thaliana. Subcellular studies further confirmed that OsDSM3 resides in the cytoplasm. In conclusion, the forthcoming cloning of Osdsm3 holds promise for delving deeper into the molecular mechanisms governing rice drought resistance. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

• OsDLT10 affects the formation and outgrowth of axillary buds. • OsDLT10 is specifically expressed in stem nodes. • Local auxin content are extremely reduced after mutation. • IAA treatment of high concentration can inhibit the expression level of OsDLT10. 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. [ABSTRACT FROM AUTHOR]