Modulation of histone acetylation enables fully mechanized hybrid rice breeding.

Hybrid rice has achieved high grain yield and greatly contributes to food security, but the manual-labour-intensive hybrid seed production process limits fully mechanized hybrid rice breeding. For next-generation hybrid seed production, the use of small-grain male sterile lines to mechanically separate small hybrid seeds from mixed harvest is promising. However, it is difficult to find ideal grain-size genes for breeding ideal small-grain male sterile lines without penalties in the number of hybrid seeds and hybrid rice yield. Here we report that the use of small-grain alleles of the ideal grain-size gene GSE3 in male sterile lines enables fully mechanized hybrid seed production and dramatically increases hybrid seed number in three-line and two-line hybrid rice systems. The GSE3 gene encodes a histone acetyltransferase that binds histones and influences histone acetylation levels. GSE3 is recruited by the transcription factor GS2 to the promoters of their co-regulated grain-size genes and influences the histone acetylation status of their co-regulated genes. Field trials demonstrate that genome editing of GSE3 can be used to immediately improve current elite male sterile lines of hybrid rice for fully mechanized hybrid rice breeding, providing a new perspective for mechanized hybrid breeding in other crops.

An endoplasmic reticulum-associated degradation-related E2-E3 enzyme pair controls grain size and weight through the brassinosteroid signaling pathway in rice.

Grain size is an important agronomic trait, but our knowledge about grain size determination in crops is still limited. Endoplasmic reticulum (ER)-associated degradation (ERAD) is a special ubiquitin proteasome system that is involved in degrading misfolded or incompletely folded proteins in the ER. Here, we report that SMALL GRAIN 3 (SMG3) and DECREASED GRAIN SIZE 1 (DGS1), an ERAD-related E2-E3 enzyme pair, regulate grain size and weight through the brassinosteroid (BR) signaling pathway in rice (Oryza sativa). SMG3 encodes a homolog of Arabidopsis (Arabidopsis thaliana) UBIQUITIN CONJUGATING ENZYME 32, which is a conserved ERAD-associated E2 ubiquitin conjugating enzyme. SMG3 interacts with another grain size regulator, DGS1. Loss of function of SMG3 or DGS1 results in small grains, while overexpression of SMG3 or DGS1 leads to long grains. Further analyses showed that DGS1 is an active E3 ubiquitin ligase and colocates with SMG3 in the ER. SMG3 and DGS1 are involved in BR signaling. DGS1 ubiquitinates the BR receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1) and affects its accumulation. Genetic analysis suggests that SMG3, DGS1, and BRI1 act together to regulate grain size and weight. In summary, our findings identify an ERAD-related E2-E3 pair that regulates grain size and weight, which gives insight into the function of ERAD in grain size control and BR signaling.

A natural allele of OsMS1 responds to temperature changes and confers thermosensitive genic male sterility.

Changes in ambient temperature influence crop fertility and production. Understanding of how crops sense and respond to temperature is thus crucial for sustainable agriculture. The thermosensitive genic male-sterile (TGMS) lines are widely used for hybrid rice breeding and also provide a good system to investigate the mechanisms underlying temperature sensing and responses in crops. Here, we show that OsMS1 is a histone binding protein, and its natural allele OsMS1wenmin1 confers thermosensitive male sterility in rice. OsMS1 is primarily localized in nuclei, while OsMS1wenmin1 is localized in nuclei and cytoplasm. Temperature regulates the abundances of OsMS1 and OsMS1wenmin1 proteins. The high temperature causes more reduction of OsMS1wenmin1 than OsMS1 in nuclei. OsMS1 associates with the transcription factor TDR to regulate expression of downstream genes in a temperature-dependent manner. Thus, our findings uncover a thermosensitive mechanism that could be useful for hybrid crop breeding.

The GW2-WG1-OsbZIP47 pathway controls grain size and weight in rice.

Regulation of seed size is a key strategy for improving crop yield and is also a basic biological question. However, the molecular mechanisms by which plants determine their seed size remain elusive. Here, we report that the GW2-WG1-OsbZIP47 regulatory module controls grain width and weight in rice. WG1, which encodes a glutaredoxin protein, promotes grain growth by increasing cell proliferation. Interestingly, WG1 interacts with the transcription factor OsbZIP47 and represses its transcriptional activity by associating with the transcriptional co-repressor ASP1, indicating that WG1 may act as an adaptor protein to recruit the transcriptional co-repressor. In contrary, OsbZIP47 restricts grain growth by decreasing cell proliferation. Further studies reveal that the E3 ubiquitin ligase GW2 ubiquitinates WG1 and targets it for degradation. Genetic analyses confirm that GW2, WG1, and OsbZIP47 function in a common pathway to control grain growth. Taken together, our findings reveal a genetic and molecular framework for the control of grain size and weight by the GW2-WG1-OsbZIP47 regulatory module, providing new targets for improving seed size and weight in crops.

The LARGE2-APO1/APO2 regulatory module controls panicle size and grain number in rice.

Panicle size and grain number are important agronomic traits and influence grain yield in rice (Oryza sativa), but the molecular and genetic mechanisms underlying panicle size and grain number control remain largely unknown in crops. Here we report that LARGE2 encodes a HECT-domain E3 ubiquitin ligase OsUPL2 and regulates panicle size and grain number in rice. The loss of function large2 mutants produce large panicles with increased grain number, wide grains and leaves, and thick culms. LARGE2 regulates panicle size and grain number by repressing meristematic activity. LARGE2 is highly expressed in young panicles and grains. Biochemical analyses show that LARGE2 physically associates with ABERRANT PANICLE ORGANIZATION1 (APO1) and APO2, two positive regulators of panicle size and grain number, and modulates their stabilities. Genetic analyses support that LARGE2 functions with APO1 and APO2 in a common pathway to regulate panicle size and grain number. These findings reveal a novel genetic and molecular mechanism of the LARGE2-APO1/APO2 module-mediated control of panicle size and grain number in rice, suggesting that this module is a promising target for improving panicle size and grain number in crops.

Control of Grain Size and Weight by the GSK2-LARGE1/OML4 Pathway in Rice.

Regulation of grain size is crucial for improving crop yield and is also a basic aspect in developmental biology. However, the genetic and molecular mechanisms underlying grain size control in crops remain largely unknown despite their central importance. Here, we report that the MEI2-LIKE PROTEIN4 (OML4) encoded by the LARGE1 gene is phosphorylated by GLYCOGEN SYNTHASE KINASE2 (GSK2) and negatively controls grain size and weight in rice (Oryza sativa). Loss of function of OML4 leads to large and heavy grains, while overexpression of OML4 causes small and light grains. OML4 regulates grain size by restricting cell expansion in the spikelet hull. OML4 is expressed in developing panicles and grains, and the GFP-OML4 fusion protein is localized in the nuclei. Biochemical analyses show that the GSK2 physically interacts with OML4 and phosphorylates it, thereby possibly influencing the stability of OML4. Genetic analyses support that GSK2 and OML4 act, at least in part, in a common pathway to control grain size in rice. These results reveal the genetic and molecular mechanism of a GSK2-OML4 regulatory module in grain size control, suggesting that this pathway is a suitable target for improving seed size and weight in crops.

A mitogen-activated protein kinase phosphatase influences grain size and weight in rice.

Grain size and weight are directly associated with grain yield in crops. However, the molecular mechanisms that set final grain size and weight remain largely unknown. Here, we characterize two large grain mutants, large grain8-1 (large8-1) and large grain8-2 (large8-2). LARGE8 encodes the mitogen-activated protein kinase phosphatase1 (OsMKP1). Loss of function mutations in OsMKP1 results in large grains, while overexpression of OsMKP1 leads to small grains. OsMKP1 determines grain size by restricting cell proliferation in grain hulls. OsMKP1 directly interacts with and deactivates the mitogen-activated protein kinase 6 (OsMAPK6). Taken together, we identify OsMKP1 as a crucial factor that influences grain size by deactivating OsMAPK6, indicating that the reversible phosphorylation of OsMAPK6 plays important roles in determining grain size in rice.

Control of Grain Size and Weight by the OsMKKK10-OsMKK4-OsMAPK6 Signaling Pathway in Rice.

Grain size is one of the key agronomic traits that determine grain yield in crops. However, the mechanisms underlying grain size control in crops remain elusive. Here we demonstrate that the OsMKKK10-OsMKK4-OsMAPK6 signaling pathway positively regulates grain size and weight in rice. In rice, loss of OsMKKK10 function results in small and light grains, short panicles, and semi-dwarf plants, while overexpression of constitutively active OsMKKK10 (CA-OsMKKK10) results in large and heavy grains, long panicles, and tall plants. OsMKKK10 interacts with and phosphorylates OsMKK4. We identified an OsMKK4 gain-of-function mutant (large11-1D) that produces large and heavy grains. OsMKK4A227T encoded by the large11-1D allele has stronger kinase activity than OsMKK4. Plants overexpressing a constitutively active form of OsMKK4 (OsMKK4-DD) also produce large grains. Further biochemical and genetic analyses revealed that OsMKKK10, OsMKK4, and OsMAPK6 function in a common pathway to control grain size. Taken together, our study establishes an important genetic and molecular framework for OsMKKK10-OsMKK4-OsMAPK6 cascade-mediated control of grain size and weight in rice.

WIDE AND THICK GRAIN 1, which encodes an otubain-like protease with deubiquitination activity, influences grain size and shape in rice.

Grain size and shape are two crucial traits that influence grain yield and grain appearance in rice. Although several factors that affect grain size have been described in rice, the molecular mechanisms underlying the determination of grain size and shape are still elusive. In this study we report that WIDE AND THICK GRAIN 1 (WTG1) functions as an important factor determining grain size and shape in rice. The wtg1-1 mutant exhibits wide, thick, short and heavy grains and also shows an increased number of grains per panicle. WTG1 determines grain size and shape mainly by influencing cell expansion. WTG1 encodes an otubain-like protease, which shares similarity with human OTUB1. Biochemical analyses indicate that WTG1 is a functional deubiquitinating enzyme, and the mutant protein (wtg1-1) loses this deubiquitinating activity. WTG1 is expressed in developing grains and panicles, and the GFP-WTG1 fusion protein is present in the nucleus and cytoplasm. Overexpression of WTG1 results in narrow, thin, long grains due to narrow and long cells, further supporting the role of WTG1 in determining grain size and shape. Thus, our findings identify the otubain-like protease WTG1 to be an important factor that determines grain size and shape, suggesting that WTG1 has the potential to improve grain size and shape in rice.

Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice.

The utilization of natural genetic variation greatly contributes to improvement of important agronomic traits in crops. Understanding the genetic basis for natural variation of grain size can help breeders develop high-yield rice varieties. In this study, we identify a previously unrecognized gene, named GSE5, in the qSW5/GW5 locus controlling rice grain size by combining the genome-wide association study with functional analyses. GSE5 encodes a plasma membrane-associated protein with IQ domains, which interacts with the rice calmodulin protein, OsCaM1-1. We found that loss of GSE5 function caused wide and heavy grains, while overexpression of GSE5 resulted in narrow grains. We showed that GSE5 regulates grain size predominantly by influencing cell proliferation in spikelet hulls. Three major haplotypes of GSE5 (GSE5, GSE5DEL1+IN1, and GSE5DEL2) in cultivated rice were identified based on the deletion/insertion type in its promoter region. We demonstrated that a 950-bp deletion (DEL1) in indica varieties carrying the GSE5DEL1+IN1 haplotype and a 1212-bp deletion (DEL2) in japonica varieties carrying the GSE5DEL2 haplotype associated with decreased expression of GSE5, resulting in wide grains. Further analyses indicate that wild rice accessions contain all three haplotypes of GSE5, suggesting that the GSE5 haplotypes present in cultivated rice are likely to have originated from different wild rice accessions during rice domestication. Taken together, our results indicate that the previously unrecognized GSE5 gene in the qSW5/GW5 locus, which is widely utilized by rice breeders, controls grain size, and reveal that natural variation in the promoter region of GSE5 contributes to grain size diversity in rice.

SMALL GRAIN 11 Controls Grain Size, Grain Number and Grain Yield in Rice.

BACKGROUND: Grain size is one of key agronomic traits that determine grain yield in rice. Several regulators of grain size have been identified in rice, but the mechanisms that determine grain size and yield remain largely unknown. RESULTS: Here we characterize a small grain (smg11) mutant in rice, which exhibits small grains, dense panicles and the increased number of grains per panicle. Cloning and sequence analyses of the SMG11 gene reveal that smg11 is a new allele of DWARF2 (D2), which encodes a cytochrome P450 (CYP90D2) involved in brassinosteroid biosynthetic pathway. Overexpression of D2/SMG11 increases grain size and grain weight of wild-type plants. Overexpression of D2/SMG11 at a suitable level also significantly increases grain yield in rice. Cellular analyses indicate that D2/SMG11 controls grain size by promoting cell expansion. Further results reveal that D2/SMG11 influences expression of several known grain size genes involved in the regulation of cell expansion, revealing a novel link between D2/SMG11 and known grain size genes. CONCLUSIONS: SMG11 controls grain size by promoting cell expansion in grain hulls. SMG11 regulates cell expansion, at least in part, by influencing expression of several grain size genes involved in the regulation of cell expansion. The smg11 is a new allele of DWARF2/D2. The suitable expression of SMG11 increases grain size, grain weight and grain yield. Our findings reveal the functions of D2/SMG11 in grain size and grain yield, suggesting that the suitable expression of D2/SMG11 is a promising approach to improve grain yield in rice.

Sucrose metabolism gene families and their biological functions.

Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.

Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice.

An increase in grain yield is crucial for modern agriculture(1). Grain size is one of the key components of grain yield in rice and is regulated by quantitative trait loci (QTLs)(2,3). Exploring new QTLs for grain size will help breeders develop elite rice varieties with higher yields(3,4). Here, we report a new semi-dominant QTL for grain size and weight (GS2) in rice, which encodes the transcription factor OsGRF4 (GROWTH-REGULATING FACTOR 4) and is regulated by OsmiR396. We demonstrate that a 2 bp substitution mutation in GS2 perturbs OsmiR396-directed regulation of GS2, resulting in large and heavy grains and increased grain yield. Further results reveal that GS2 interacts with the transcription coactivitors OsGIF1/2/3, and overexpression of OsGIF1 increases grain size and weight. Thus, our findings define the regulatory mechanism of GS2, OsGIFs and OsmiR396 in grain size and weight control, suggesting this pathway could be used to increase yields in crops.

SMALL GRAIN 1, which encodes a mitogen-activated protein kinase kinase 4, influences grain size in rice.

Although grain size is one of the most important components of grain yield, little information is known about the mechanisms that determine final grain size in crops. Here we characterize rice small grain1 (smg1) mutants, which exhibit small and light grains, dense and erect panicles and comparatively slightly shorter plants. The short grain and panicle phenotypes of smg1 mutants are caused by a defect in cell proliferation. The smg1 mutations were identified, using a map-based cloning approach, in mitogen-activated protein kinase kinase 4 (OsMKK4). Relatively higher expression of OsMKK4/SMG1 was detected in younger organs than in older ones, consistent with its role in cell proliferation. Green fluorescent protein (GFP)-OsMKK4/SMG1 fusion proteins appear to be distributed ubiquitously in plant cells. Further results revealed that OsMKK4 influenced brassinosteroid (BR) responses and the expression of BR-related genes. Thus, our findings have identified OsMKK4 as a factor for grain size, and suggest a possible link between the MAPK pathways and BRs in grain growth.

Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on sorghum.

Plant bZIP transcription factors play crucial roles in multiple biological processes. However, little is known about the sorghum bZIP gene family although the sorghum genome has been completely sequenced. In this study, we have carried out a genome-wide identification and characterization of this gene family in sorghum. Our data show that the genome encodes at least 92 bZIP transcription factors. These bZIP genes have been expanded mainly by segmental duplication. Such an expansion mechanism has also been observed in rice, arabidopsis and many other plant organisms, suggesting a common expansion mode of this gene family in plants. Further investigation shows that most of the bZIP members have been present in the most recent common ancestor of sorghum and rice and the major expansion would occur before the sorghum-rice split era. Although these bZIP genes have been duplicated with a long history, they exhibited limited functional divergence as shown by nonsynonymous substitutions (Ka)/synonymous substitutions (Ks) analyses. Their retention was mainly due to the high percentages of expression divergence. Our data also showed that this gene family might play a role in multiple developmental stages and tissues and might be regarded as important regulators of various abiotic stresses and sugar signaling.