Rice (Oryza sativa) grain shape is a key determinant of grain yield and market values. Facilitated by advancements in genomics and various molecular markers, more than 400 quantitative trait loci ...(QTLs) associated with rice grain traits have been identified. In this review, we examine the genetic bases of rice grain shape, focusing on the protein products of 13 genes that have been cloned and the chromosome locations of 15 QTLs that have been fine mapped. Although more genes affecting grain traits are likely to be cloned in the near future, characterizing their functions at the biochemical level and applying these molecular data to rice breeding programs will be a more challenging task.
Leaf angle is an important agronomic trait in rice (
Oryza sativa
L.). It affects both the efficiency of sunlight capture and nitrogen reservoirs. The erect leaf phenotype is suited for high-density ...planting and thus increasing crop yields. Many genes regulate leaf angle by affecting leaf structure, such as the lamina joint, mechanical tissues, and the midrib. Signaling of brassinosteroids (BR), auxin (IAA), and gibberellins (GA) plays important roles in the regulation of lamina joint bending in rice. In addition, the biosynthesis and signaling of BR are known to have dominant effects on leaf angle development. In this review, we summarize the factors and genes associated with the development of leaf angle in rice, outline the regulatory mechanisms based on the signaling of BR, IAA, and GA, and discuss the contribution of crosstalk between BR and IAA or GA in the formation of leaf angle. Promising lines of research in the transgenic engineering of rice leaf angle to increase grain yield are proposed.
Grain shape is controlled by quantitative trait loci (QTLs) in rice (Oryza sativa L.). A rice mutant (JF178) with long and large grains has been used in a breeding program for over a decade, but its ...genetic basis has been unclear. Here, a semi-dominant QTL, designated Large Grain Size 1 (LGS1), was cloned and the potential molecular mechanism of LGS1 function was studied. Near-isogenic lines (NILs) and a map-based approach were employed to clone the LGS1 locus. LGS1 encodes the OsGRF4 transcription factor and contains a 2 bp missense mutation in the coding region that coincides with the putative pairing site of miRNA396. The LGS1 transcript levels in the mutant line were found to be higher than the lgs1 transcript levels in the control plants, suggesting that the mutation might disrupt the pairing of the LGS1 mRNA with miR396. In addition to producing larger grains, LGS1 also enhanced cold tolerance at the seedling stage and increased the survival rate of seedlings after cold stress treatment. These findings indicate that the mutation in LGS1 appears to disturb the GRF4-miR396 stress response network and results in the development of enlarged grains and enhancement of cold tolerance in rice.
Chalkiness is one of several major restricting factors for the improvement of rice quality. Although many chalkiness-related quantitative trait loci have been mapped, only a small number of genes ...have been cloned to date. In this study, the candidate gene
of a major quantitative trait locus (QTL) for rice chalkiness,
, was identified by map-based cloning. Phenotyping and haplotype analysis of
transgenic line,
mutant, and 69 rice varieties further confirmed that
had the pleiotropic effects and regulated both chalkiness and grain shape. Genetic analysis showed
was a dominant gene for grain length and a semi-dominant gene for grain width and chalkiness. The DNA interval closely linked to
was introgressed to Zhenshan 97B (ZB) based on molecular marker-assisted selection, and the improved ZB showed lower chalkiness and longer but smaller grains, which showed that
played an important role in breeding rice varieties with high yield and good quality. Transcriptomics, proteomics, and qRT-PCR analyses showed that thirty-nine genes associated with carbon and protein metabolism are regulated by
to affect the formation of chalkiness, including some newly discovered genes, such as
,
,
,
,
,
, etc. The low-chalkiness lines showed higher amino sugar and nucleotide sugar metabolism at 10 days after pollination (DAP), lower carbohydrate metabolism at 15 DAP, and lower protein metabolism at 10 and 15 DAP. With heat shock at 34/30°C, rice chalkiness increased significantly;
and
were upregulated at 6 and 12 DAP, respectively, and
was downregulated at 12 DAP. Our results identified the function and pleiotropic effects of
dissected its genetic characteristics and the expression profiles of the genes affecting the chalkiness formation, and provided a theoretical basis and application value to harmoniously pursue high yield and good quality in rice production.
Strigolactones (SLs) are recently identified plant hormones that inhibit shoot branching and control various aspects of plant growth, development and interaction with parasites. Previous studies have ...shown that plant D10 protein is a carotenoid cleavage dioxygenase that functions in SL biosynthesis. In this work, we used an allelic SL-deficient d10 mutant XJC of rice (Oryza sativa L. spp. indica) to investigate proteins that were responsive to SL treatment. When grown in darkness, d10 mutant seedlings exhibited elongated mesocotyl that could be rescued by exogenous application of SLs. Soluble protein extracts were prepared from d10 mutant seedlings grown in darkness in the presence of GR24, a synthetic SL analog. Soluble proteins were separated on two-dimensional gels and subjected to proteomic analysis. Proteins that were expressed differentially and phosphoproteins whose phosphorylation status changed in response to GR24 treatment were identified. Eight proteins were found to be induced or down-regulated by GR24, and a different set of 8 phosphoproteins were shown to change their phosphorylation intensities in the dark-grown d10 seedlings in response to GR24 treatment. Analysis of these proteins revealed that they are important enzymes of the carbohydrate and amino acid metabolic pathways and key components of the cellular energy generation machinery. These proteins may represent potential targets of the SL signaling pathway. This study provides new insight into the complex and negative regulatory mechanism by which SLs control shoot branching and plant development.
The LGS1 (Large grain size 1) gene, also known as GS2/GL2/OsGRF4, is involved in regulating grain size and quality in rice, but the mechanism governing grain size has not been elucidated. We ...performed transcriptomic, proteomic, and phosphoproteomic analyses of young rice panicles in Samba (a wild-type cultivar with extra-small grain) and NIL-LGS1 (a nearly isogenic line of LGS1 with large grain in the Samba genetic background) at three developmental stages (4–6) to identify internal dynamic functional networks determining grain size that are mediated by LGS1. Differentially expressed proteins formed seven highly functionally correlated clusters. The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice. In stage 5, 16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated, and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein–protein interaction networks. Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development. Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level, and this analysis also suggested a regulatory mechanism, regulation of protein translation levels, in the biological process that extends from transcript to protein to the development of grain. Functional analysis suggested that biological processes including MAPK signaling, calcium signaling, cell proliferation, cell wall, energy metabolism, hormone pathway, and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length. Thus, LGS1-mediated regulation of grain size is affected by dynamic transcriptional, posttranscriptional, translational and posttranslational changes.
Grain weight is an important characteristic of grain shape and a key contributing factor to the grain yield in rice. Here, we report that gw2.1, a new allele of the Grain Width and Weight 2 (GW2) ...gene, regulates grain size and grain weight. A single nucleotide substitution in the coding sequence (CDS) of gw2.1 resulted in the change of glutamate to lysine (E128K) in GW2.1 protein. Complementation tests and GW2 overexpression experiments demonstrated that the missense mutation in gw2.1 was responsible for the phenotype of enlarged grain size in the mutant line jf42. The large grain trait of the near-isogenic line NIL-gw2.1 was found to result from increased cell proliferation during flower development. Meanwhile, NIL-gw2.1 was shown to increase grain yield without compromising the grain quality. The GW2 protein was localized to the cell nucleus and membrane, and interacted with CHB705, a subunit of the chromatin remodeling complex. Finally, the F1 hybrids from crosses of NIL-gw2.1 with 7 cytoplasmic male-sterile lines exhibited large grains and desirable grain appearance. Thus, gw2.1 is a promising allele that could be applied to improve grain yield and grain appearance in rice.
The datasets generated and/or analyzed in the study are available from the corresponding author on reasonable request.
•gw2.1 was a new GW2 allele that influences grain size and grain weight.•NIL-gw2.1 exhibits a larger grain size and increased grain weight without reducing rice appearance quality.•gw2.1 affects glume shape by regulating cell proliferation.•GW2 is located in the cell nucleus and membrane and interacts with CHB705.•The application of gw2.1 improves grain yield and appearance quality in hybrid rice combinations.
Main conclusion
The
zqdm1
identified from a rice mutant is a novel allele of
BRD2
and is responsible for regulating rice plant height, grain size and appearance, which has possibilities on improving ...rice quality.
Plant height is an important agronomic trait related to rice yield, and grain size directly determines grain yield in rice (
Oryza sativa
L.). With the development of molecular biotechnology and genome sequencing technology, more and more key genes associated with plant height and grain size have been cloned and identified in recent years. This study identified the
zqdm1
gene from a mutant with reduced plant height and grain size. The
zqdm1
gene was revealed to be a new allele of
BRASSINOSTEROID DEFICIENT DWARF 2
(
BRD2
), encoding a FAD-linked oxidoreductase protein involved in the brassinosteroid (BR) biosynthesis pathway, and regulates plant height by reducing cell number of longitudinal sections of the internode and regulates grain size by altering cell expansion. A 369-bp DNA fragment was found inserted at the first exon, resulting in protein-coding termination. This mutation has not been discovered in previous studies. Complementation tests have confirmed that 369-bp insertion in
BRD2
was responsible for the plant height and grain size changing in the
zqdm1
mutant. Over-expression of
BRD2
driven by different promoters into
indica
rice variety Jiafuzhan (JFZ) results in slender grains, suggesting its function on regulating grain shape. In summary, the current study has identified a new
BRD2
allele, which facilitated the further research on the molecular mechanism of this gene on regulating growth and development.
To identify potential protein markers associated with tillering in rice, a d10 allelic mutant (JHCA) with a high-tillering dwarf phenotype and a wild-type cultivar (GLA4) with normal numbers of ...tillers were used to produce a hybrid (F1), and 2-DE (two-dimensional electrophoresis) analysis was conducted in seedling leaf sheaths and roots of the rice hybrid and its parents. A total of 61 protein spots representing qualitative or quantitative polymorphisms were detected. Among them, 38 spots were successfully identified as 23 different proteins by MALDI-TOF/MS. The identified proteins were further divided into P/As (presence/absence variations), PSs (position shift variations) and qVs (quantitative variations). Most of the identified polymorphic proteins exhibited tissue-specific expression. Two spot families, identified as a putative vitamin B12-independent methionine synthase and a putative phosphoglycerate mutase were found. The profiles of expression abundance of three iso-spots in each spot family showed a reciprocal relationship between the two parents.
ABSTRACT Grain shape in rice is a key determinant of grain appearance, yield and market value, and thus has been widely studied. Rice mutant lines with long-grain phenotypes were previously isolated ...from an M2 population derived from mutagenized mature pollen grains that were treated with gamma-ray irradiation for a cultivar Ma85. To understand the genetic basis underlying the long-grain trait, two mutant lines, JF171 and JF178, were crossed with the short-grain parents JF222 and Samba, generating three F2 populations. Molecular marker-based genetic analysis was employed to detect the major QTLs that affected grain length, grain width, length-to-width ratio and grain weight. Based on the data obtained for the three populations, a joint major QTL for grain length was mapped to a 4.7 Mb region between the SSR makers RM263 and RM318 on the long arm of chromosome 2. The results suggested that the two independent mutations contained in JF171 and JF178 are likely due to alterations in the same genetic region. Furthermore, we developed a BC2F2 population using JF178 and Samba and narrowed the region to 0.6 Mb. The results of the current study will be helpful to reveal the genetic basis of the above long-grain mutant lines. In general, our results provide solid genetic data to identify the unknown gene that affects grain length by map-based cloning and practice marker-assisted breeding for long-grain rice cultivars.
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