Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The...Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The SGT3 promoter haplotype with(TA)10exhibits signifcantly higher transcriptional activity,correlating with high SGAs content,while the(TA)13haplotype is linked to low SGAs in natural germplasms.展开更多
Embryo size is a critical trait determining not only grain yield but also the nutrition of the maize kernel.Up to the present,only a few genes have been characterized affecting the maize embryo/kernel ratio.Here,we id...Embryo size is a critical trait determining not only grain yield but also the nutrition of the maize kernel.Up to the present,only a few genes have been characterized affecting the maize embryo/kernel ratio.Here,we identify 63 genes significantly associated with maize embryo/kernel weight ratio using a genome-wide association study(GWAS).The peak GWAS signal shows that the natural variation in Zea mays COMPACT PLANT2(CT2),encoding the heterotrimeric G proteinαsubunit,is significantly associated with the Embryo/Kernel Weight Ratio(EKWR).Further analyses show that a missense mutation of CT2 increases its enzyme activity and associates with EKWR.The function of CT2 on affecting embryo/kernel weight ratio is further validated by the characterization of two ct2 mutants,for which EKWR is significantly decreased.Subsequently,the key downstream genes of CT2 are identified by combining the differential expression analysis of the ct2 mutant and quantitative trait transcript analysis in the GWAS population.In addition,the allele frequency spectrum shows that CT2 was under selective pressure during maize domestication.This study provides important genetic insights into the natural variation of maize embryo/kernel weight ratio,which could be applied in future maize breeding programs to improve grain yield and nutritional content.展开更多
As an essential crop that provides vegetable oil and protein,soybean(Glycine max(L.)Merr.)is widely planted all over the world.However,the scarcity of water resources worldwide has seriously impacted on the quality an...As an essential crop that provides vegetable oil and protein,soybean(Glycine max(L.)Merr.)is widely planted all over the world.However,the scarcity of water resources worldwide has seriously impacted on the quality and yield of soybean.To address this,exploring excellent genes for improving drought resistance in soybean is crucial.In this study,we identified natural variations of GmFNSII-2(flavone synthase II)significantly affect the drought resistance of soybeans.Through sequence analysis of GmFNSII-2 in 632 cultivated and 44 wild soybeans nine haplotypes were identified.The full-length allele GmFNSII-2^(C),but not the truncated allele GmFNSII-2^(A) possessing a nonsense nucleotide variation,increased enzyme activity.Further research found that GmDREB3,known to increase soybean drought resistance,bound to the promoter region of GmFNSII-2^(C).GmDREB3 positively regulated the expression of GmFNSII-2^(C),increased flavone synthase abundance and improved the drought resistance.Furthermore,a singlebase mutation in the GmFNSII-2^(C) promoter generated an additional drought response element(CCCCT),which had stronger interaction strength with GmDREB3 and increased its transcriptional activity under drought conditions.The frequency of drought-resistant soybean varieties with Hap 1(Pro:GmFNSII-2^(C))has increased,suggesting that this haplotype may be selected during soybean breeding.In summary,GmFNSII-2^(C) could be used for molecular breeding of drought-tolerant soybean.展开更多
Seed vigor is a crucial trait for the direct seeding of rice.Here we examined the genetic regulation of seed vigor traits in rice,including germination index(GI)and germination potential(GP),using a genome-wide associ...Seed vigor is a crucial trait for the direct seeding of rice.Here we examined the genetic regulation of seed vigor traits in rice,including germination index(GI)and germination potential(GP),using a genome-wide association study approach.One major quantitative trait locus,qGI6/qGP6,was identified simultaneously for both GI and GP.The candidate gene encoding the cytochrome c oxidase subunit 5B(OsCOX5B)was validated for qGI6/qGP6.The disruption of OsCOX5B caused the vigor traits to be significantly lower in Oscox5b mutants than in the japonica Nipponbare wild type(WT).Gene co-expression analysis revealed that OsCOX5B influences seed vigor mainly by modulating the tricarboxylic acid cycle process.The glucose levels were significantly higher while the pyruvic acid and adenosine triphosphate levels were significantly lower in Oscox5b mutants than in WT during seed germination.The elite haplotype of OsCOX5B facilitates seed vigor by increasing its expression during seed germination.Thus,we propose that OsCOX5B is a potential target for the breeding of rice varieties with enhanced seed vigor for direct seeding.展开更多
Rice has a large number of nitrate or peptide transporter family(NPF) genes, but the effects of most members on rice growth and development are unknown. We report that Os NPF5.16, a nitrate transporter gene with natur...Rice has a large number of nitrate or peptide transporter family(NPF) genes, but the effects of most members on rice growth and development are unknown. We report that Os NPF5.16, a nitrate transporter gene with natural variation in its promoter sequence, is essential for rice growth and yield. The promoter sequence showed various differences between indica and japonica cultivars, and higher expression of Os NPF5.16 was found in indica cultivars with higher plant weight and more tillers than japonica cultivars.Os NPF5.16 was highly expressed in roots, tiller basal parts, and leaf sheaths, and its protein was localized on the plasma membrane. In c RNA-injected Xenopus laevis oocytes, Os NPF5.16 transport of nitrate at high nitrate concentration depended on p H. Overexpression of Os NPF5.16 increased nitrate content and total nitrogen content in leaf sheath as well as biomass and tiller bud length in rice. Elevated expression of Os NPF5.16 increased rice tiller number and grain yield by regulating cytokinin levels. Inhibition of Os NPF5.16 expression showed the opposite effects. Regulating Os NPF5.16 expression has potential for improving rice grain yield.展开更多
The resistance in tomato plants to bacterial speck caused by Pseudomonas syringae pv. tomato is triggered by the interactions between the plant resistance protein Pto and the pathogen avirulence proteins AvrPto or Avr...The resistance in tomato plants to bacterial speck caused by Pseudomonas syringae pv. tomato is triggered by the interactions between the plant resistance protein Pto and the pathogen avirulence proteins AvrPto or AvrPtoB. Fen is a gene encoding closely related functional protein kinases as the Pto gene. To investigate the status of resistance to the pathogen and natural variation of Pto and Fen genes in tomato, 67 lines including 29 growing in China were subject to disease resistance evaluation and fenthion-sensitivity test. Alleles of Pto and Fen were amplified from genomic DNA of 25 tomato lines using polymerase chain reaction （PCR） and sequences were determined by sequencing the PCR products. The results indicated that none of the 29 cultivars/hybrids growing in China were resistant to bacterial speck race 0 strain DC3000. Seven of eight tomato lines resistant to DC3000 were also fenthion-sensitive. Analysis of deduced amino acid sequences identified three novel residue substitutions between Pto and pto, and one new substitution identified between Fen and fen. A PCR-based marker was developed and successfully used to select plants with resistance to DC3000.展开更多
Many attentions have been previously focused to identify the multiple biochemical components related to tea quality and health benefits,however, the natural variation of biochemical components present in tea germplasm...Many attentions have been previously focused to identify the multiple biochemical components related to tea quality and health benefits,however, the natural variation of biochemical components present in tea germplasm has not been adequately evaluated. In this study, the main biochemical components, leaf morphological and yield characteristics were evaluated for four rounds of tea leaves in a panel of 87 elite tea cultivars suitable for black, green, or oolong tea. Significant variations were observed among the tea cultivars, as well as seasonal differences in the levels of the free amino acid(FAA), caffeine(CAF), tea polyphenols(TP), water extract(WE) and TP to FAA ratio(TP/FAA). Results showed that the average levels of FAA showed a seasonal change, with the highest level of 4.0% in the 1st spring tea in the cultivars suitable for green tea and the lowest of 3.2% in summer tea in the cultivars suitable for black tea. The average CAF content was highest 3.2% in the cultivars suitable for oolong tea in the 1st spring and the lowest 2.5% in the cultivars suitable for green tea in summer. Limited seasonal and varietal variations were noticed in the average levels of WE among the three categories of tea. In addition, significant natural variation of the morphological characteristics, bud length varying from 2.5 cm to 8.7 cm, bud density from 190.3 buds · m-2to 1 730.3 buds · m-2, mature leaves biomass from 128.4 kg · hm-2to 2 888.4 kg · hm-2, and yield component traits of 100 buds(one bud with two leaves) dry weight from 3.7 g to37.7 g, tea yield/round from 444.6 kg · hm-2to 905.3 kg · hm-2, were observed. The aim of our evaluation was not only to identify the advantages of seasonal and clonal variations but also to provide a new viewpoint for their further application. Representative accessions were selected from the germplasm to promote the establishment of an inherent biochemical constituent expressing the quality of black, green, and oolong tea. The findings might be utilized to establish early selection criteria to enhance the tea breeding and production program.展开更多
Water is a major limiting factor for food production and many countries fail to produce sufficient food for their population due to severe water scarcity （Jury and Vaux, 2005）. Rice is the main staple food worldwide...Water is a major limiting factor for food production and many countries fail to produce sufficient food for their population due to severe water scarcity （Jury and Vaux, 2005）. Rice is the main staple food worldwide. More than 50% of rice in the world is rain-fed and drought causes severe reduction in rice grain yield in rain-fed environments （Venuprasad et al., 2007; Zhang, 2007; Sandhu et al., 2014）. Therefore, enhancing drought resistance （DR） of rice is important for food security. However, DR is a complex trait, which is controlled by a large number of loci with small effect and is also affected by different genetic background, genotype-by-environment interaction and other stresses such as heat （Hu and Xiong, 2014）.展开更多
Potato(Solanum tuberosum)was domesticated 8000–10000 years ago from wild species in the Andes.Due to its adaptation potential to diverse climates,its cultivation spread globally.Today,potato is the fourth most import...Potato(Solanum tuberosum)was domesticated 8000–10000 years ago from wild species in the Andes.Due to its adaptation potential to diverse climates,its cultivation spread globally.Today,potato is the fourth most important staple crop worldwide in terms of production quantity and plays a critical role in food security,especially since its production and consumption constantly increase in developing countries(FAOSTAT Database 2022,https://www.fao.org/statistics/en).展开更多
Spikelets are the basic unit of the inflorescence in crops, consisting of one or more florets, playing a key role in determining yield. During cereal flower development, the spikelet meristem (SM) arises from the infl...Spikelets are the basic unit of the inflorescence in crops, consisting of one or more florets, playing a key role in determining yield. During cereal flower development, the spikelet meristem (SM) arises from the inflorescence meristem or branch meristem, and subsequently gives rise to the floret meristem (FM) (Xie et al., 2023). The multi-ovary or multi-floret spikelet phenomenon is commonly observed in certain cereal germplasms (Zhu et al., 2019;Ren et al., 2020;Selva et al., 2023), demonstrating the potential for enhancing grain yield through the production of a larger number of grains. A typical sorghum spikelet produces a single fertile floret, resulting in a single-grain spikelet morphology. However, the multiple-grain spikelet (MGS) sorghum germplasm, first documented in 1936, contains more than half of the double-grain spikelets per panicle and exhibits an unusual spikelet architecture in which two mature grains are produced within a single spikelet (Karper and Stephens, 1936). Despite this, the genetic basis underlying this trait has remained unclear.展开更多
Improving the methionine (Met) content in maize kernels is of key importance to the animal feed industry;however, the genetic and molecular mechanisms governing maize kernel Met content remain largely unexplored. In t...Improving the methionine (Met) content in maize kernels is of key importance to the animal feed industry;however, the genetic and molecular mechanisms governing maize kernel Met content remain largely unexplored. In this study, we leveraged a panel consisting of 348 diverse inbred maize lines to explore the genetic and molecular mechanisms that control kernel Met levels. A genome-wide association study followed by transcriptomic analysis identified the deSUMOylating isopeptidase gene ZmDeSI2. Further biochemical experiments revealed that ZmDeSI2 directly reduces the SUMOylation and accumulation of the sulfite reductase ZmSIR, thereby repressing Met accumulation. Natural variants in the ZmDeSI2 promoter region were found to serve as key determinants of the expression of this gene, predominantly due to the absence or presence of a ZmWRKY105 transcription factor binding site. The elite ZmDeSI2^(Hap2) haplotype without this binding site in the ZmDeSI2 promoter was associated with a 1.36-fold increase in Met levels in the kernels of modified near-isogenic lines generated through marker-assisted breeding. Taken together, these results provide new insights into the molecular processes that control Met biosynthesis, highlighting an elite natural variant suitable for application in maize breeding for Met biofortification.展开更多
Maize(Zea mays)is one of the most important crops in the world,but its yield and quality are seriously affected by diverse diseases.Identifying broad-spectrum resistance genes is crucial for developing effective strat...Maize(Zea mays)is one of the most important crops in the world,but its yield and quality are seriously affected by diverse diseases.Identifying broad-spectrum resistance genes is crucial for developing effective strategies to control the disease in maize.In a genome-wide study in maize,we identified a G-type lectin receptor kinase ZmLecRK1,as a new resistance protein against Pythium aphanidermatum,one of the causal pathogens of stalk rot in maize.Genetic analysis showed that the specific ZmLecRK1 allele can confer resistance to multiple pathogens in maize.The cell death and disease resistance phenotype mediated by the resistant variant of ZmLecRK1 requires the co-receptor ZmBAK1.A naturally occurring A404S variant in the extracellular domain of ZmLecRK1 determines the ZmLecRK1-ZmBAK1 interaction and the formation of ZmLecRK1-related protein complexes.Interestingly,the ZmLecRK1 susceptible variant was found to possess the amino acid S404 that is present in the ancestral variants of ZmLecRK1 and conserved among the majority of grass species,while the resistance variant of ZmLecRK1 with A404 is only present in a few maize inbred lines.Substitution of S by A at position 404 in ZmLecRK1-like proteins of sorghum and rice greatly enhances their ability to induce cell death.Further transcriptomic analysis reveals that ZmLecRK1 likely regulates gene expression related to the pathways in cell wall organization or biogenesis in response to pathogen infection.Taken together,these results suggest that the ZmLecRK1 resistance variant enhances its binding affinity to the co-receptor ZmBAK1,thereby enhancing the formation of active complexes for defense in maize.Our work highlights the biotechnological potential for generating disease-resistant crops by precisely modulating the activity of ZmLecRK1 and its homologs through targeted base editing.展开更多
Grain yield is determined mainly by grain number and grain weight.In this study,we identified and characterized MORE GRAINS1(MOG1),a gene associated with grain number and grain weight in rice(Oryza sativa L.),through ...Grain yield is determined mainly by grain number and grain weight.In this study,we identified and characterized MORE GRAINS1(MOG1),a gene associated with grain number and grain weight in rice(Oryza sativa L.),through map-based cloning.Overexpression of MOG1 increased grain yield by 18.6%-22.3%under field conditions.We determined that MOG1,a bHLH transcription factor,interacts with OsbHLH107 and directly activates the expression of LONELY GUY(LOG),which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1(EXPLA1),positively regulating grain number per panicle and grain weight.Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation,leading to functional differences.Haplotype analysis revealed that Hap-HNW,which results in a greater number and heavier grains,has undergone strong selection but has been poorly utilized in modern lowland rice breeding.In summary,the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway,thereby increasing grain number and grain weight.These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.展开更多
Maize(Zea mays)is highly susceptible to waterlogging stress,which reduces both the yield and quality of this important crop.However,the molecular mechanism governing waterlogging tolerance is poorly understood.In this...Maize(Zea mays)is highly susceptible to waterlogging stress,which reduces both the yield and quality of this important crop.However,the molecular mechanism governing waterlogging tolerance is poorly understood.In this study,we identify a waterlogging-and ethylene-inducible gene ZmEREB179 that encodes an ethylene response factor(ERF)localized in the nucleus.Overexpression of ZmEREB179 in maize increases the sensitivity to waterlogging stress.Conversely,the zmereb179 knockout mutants are more tolerant to waterlogging,suggesting that ZmEREB179 functions as a negative regulator of waterlogging tolerance.A transcriptome analysis of the ZmEREB179-overexpressing plants reveals that the ERF-type transcription factor modulates the expression of various stress-related genes,including ZmEREB180.We find that ZmEREB179 directly targets the ZmEREB180 promoter and represses its expression.Notably,the analysis of a panel of 220 maize inbred lines reveals that genetic variations in the ZmEREB179 promoter(Hap2)are highly associated with waterlogging resistance.The functional association of Hap2 with waterlogging resistance is tightly co-segregated in two F2 segregating populations,highlighting its potential applications in breeding programs.Our findings shed light on the involvement of the transcriptional cascade of ERF genes in regulating plant-waterlogging tolerance.展开更多
Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using ...Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using whole- genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 （OsPRR37; hereafter PRR37） is respon- sible for the Early heading7-2 （EH7-2）/Heading date2 （Hd2） QTL which was identified from a cross of late-heading rice ＇Milyang23 （M23）＇ and early-heading rice ＇H143＇. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT （CONSTANS, CO-like, and TOC1） domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day condi- tions, and are adapted to the northernmost regions of rice cultivation, up to 53~ N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and GhdT/ Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.展开更多
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 hig...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 ｜Q domains, which interacts with the rice calmodulin protein, OsCaMl-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, GSE5DELl＋IN1, and GSESDEL~ in cultivated rice were identified based on the deletion/insertion type in its pro- moter region. We demonstrated that a 950-bp deletion （DELl） in indica varieties carrying the GSE5DELl＋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 acces- sions 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.展开更多
Flavonoids constitute a major group of plant phenolic compounds.While extensively studied in Arabidopsis,profiling and naturally occurring variation of these compounds in rice（Oryza sativa）,the monocot model plant,a...Flavonoids constitute a major group of plant phenolic compounds.While extensively studied in Arabidopsis,profiling and naturally occurring variation of these compounds in rice（Oryza sativa）,the monocot model plant,are less reported.Using a collection of rice germplasm,comprehensive profiling and natural variation of flavonoids were presented in this report.Application of a widely targeted metabolomics method facilitated the simultaneous identification and quantification of more than 90 flavonoids using liquid chromatography tandem mass spectrometry（LC-MS/MS）.Comparing flavonoid contents in various tissues during different developmental stages revealed tissue-specific accumulation of most flavonoids.Further investigation indicated that flavone mono-C-glycosides,malonylated flavonoid O-hexosides,and some flavonoid O-glycosides accumulated at significantly higher levels in indica than in japonica,while the opposite was observed for aromatic acylated flavone C-hexosyl-O-hexosides.In contrast to the highly differential accumulation between the two subspecies,relatively small variations within subspecies were detected for most flavonoids.Besides,an association analysis between flavonoid accumulation and its biosynthetic gene sequence polymorphisms disclosed that natural variation of flavonoids was probably caused by sequence polymorphisms in the coding region of flavonoid biosynthetic genes.Our work paves the way for future dissection of biosynthesis and regulation of flavonoid pathway in rice.展开更多
Japonica/geng and indica/xian are two major rice(Oryza sativa)subspecies with multiple divergent traits,but how these traits are related and interact within each subspecies remains elusive.Brassinosteroids(BRs)are a c...Japonica/geng and indica/xian are two major rice(Oryza sativa)subspecies with multiple divergent traits,but how these traits are related and interact within each subspecies remains elusive.Brassinosteroids(BRs)are a class of steroid phytohormones that modulate many important agronomic traits in rice.Here,using different physiological assays,we revealed that japonica rice exhibits an overall lower BR sensitivity than indica.Extensive screening of BR signaling genes led to the identification of a set of genes distributed throughout the primary BR signaling pathway with divergent polymorphisms.Among these,we demonstrate that the C38/T variant in BR Signaling Kinase2(OsBSK2),causing the amino acid change P13L,plays a central role in mediating differential BR signaling in japonica and indica rice.OsBSK2in indica plays a greater role in BR signaling than OsB SK2in japonica by affecting the auto-binding and protein accumulation of OsBSK2.Finally,we determined that OsBSK2 is involved in a number of divergent traits in japonica relative to indica rice,including grain shape,tiller number,cold adaptation,and nitrogen-use efficiency.Our study suggests that the natural variation in OsB SK2 plays a key role in the divergence of BR signaling,which underlies multiple divergent traits between japonica and indica.展开更多
Histone modifications affect gene expression, but the mechanism and biological consequence of natural variation in histone modifications remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modif...Histone modifications affect gene expression, but the mechanism and biological consequence of natural variation in histone modifications remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modification and transcriptome for Col, C24 and their F1 hybrid. A total of 1,828 genomic regions showing variation in H3K27me3 modification between Col and C24 were identified, most of which were associated with genic regions. Natural variation of H3K27me3 modification between parents could result in aUelic bias of H3K27me3 in hybrids. Furthermore, we found that H3K27me3 variation between Col and C24 was negatively correlated with gene expression differences between two accessions, espe- cially with those arising from the cis-effect. Importantly, mutation of CLF, an Arabidopsis methyltransferase for H3K27,altered gene expression patterns between the parents. Together, these data provide insights into natural variation of histone modifications and their association with gene expression differences between Arabidopsis ecotypes.展开更多
The Pto protein kinase from Solanum pimpinellifolium interacts with Pseudomonas syringae effectors AvrPto or AvrPtoB to activate effector-triggered immunity. The previously solved crystal structures of the AvrPto-Pto ...The Pto protein kinase from Solanum pimpinellifolium interacts with Pseudomonas syringae effectors AvrPto or AvrPtoB to activate effector-triggered immunity. The previously solved crystal structures of the AvrPto-Pto and AvrPtoB-Pto complexes revealed that Pro binds each effector through both a shared and a unique interface. Hera we use natural variation in wild species of tomato to further investigate Pto recognition of these two effectors. One species, Solanum chmielewskU, was found to have many accessions that recognize only AvrPtoB. The Pto ortholog from one of these accessions was responsible for recognition of AvrPtoB and it differed from Solanum pimpinellifolium Pto by only 14 amino acids, including two in the AvrPto-specific interface, glutamate-49/glycine-51. Converting these two residues to those in Pro （histidine-49/valine-51） did not restore recognition of AvrPto. Subsequent experiments revealed that a single substitution of a histidine-to-aspartate at position 193 in Pto, which is not near the AvrPto- specific interface, was sufficient for conferring recognRion of AvrPto in plant cells. The reciprocal substi- tution of aspartate-to-histidine-193 in Pto abolished AvrPto recognition, confirming the importance of this residue. Our results reveal new aspects about effector recognition by Pto and demonstrate the value of using natural variation to understand the interaction between resistance proteins and pathogen effectors.展开更多
基金financially supported by the Guangdong Major Project of Basic and Applied Basic Research,China(2021B0301030004)the National Natural Science Foundation of China(32360757,U2202206 and 32361143517)the Yunnan Fundamental Research Projects,China(202201AT070037,202501AS070012)。
文摘Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The SGT3 promoter haplotype with(TA)10exhibits signifcantly higher transcriptional activity,correlating with high SGAs content,while the(TA)13haplotype is linked to low SGAs in natural germplasms.
基金supported by National Key Research and Development Program of China(2023YFF1000400)National Natural Science Foundation of China(32101693)+2 种基金Key Research and Development Program of Shaanxi(2021ZDLNY01-06)Agricultural Science and Technology Innovation Program of CAAS(CAAS-ZDRW202004)supported by Hatch project(1019088).
文摘Embryo size is a critical trait determining not only grain yield but also the nutrition of the maize kernel.Up to the present,only a few genes have been characterized affecting the maize embryo/kernel ratio.Here,we identify 63 genes significantly associated with maize embryo/kernel weight ratio using a genome-wide association study(GWAS).The peak GWAS signal shows that the natural variation in Zea mays COMPACT PLANT2(CT2),encoding the heterotrimeric G proteinαsubunit,is significantly associated with the Embryo/Kernel Weight Ratio(EKWR).Further analyses show that a missense mutation of CT2 increases its enzyme activity and associates with EKWR.The function of CT2 on affecting embryo/kernel weight ratio is further validated by the characterization of two ct2 mutants,for which EKWR is significantly decreased.Subsequently,the key downstream genes of CT2 are identified by combining the differential expression analysis of the ct2 mutant and quantitative trait transcript analysis in the GWAS population.In addition,the allele frequency spectrum shows that CT2 was under selective pressure during maize domestication.This study provides important genetic insights into the natural variation of maize embryo/kernel weight ratio,which could be applied in future maize breeding programs to improve grain yield and nutritional content.
基金supported by grants from the National Key Research and Development Program of China(2023YFF1000404,2022YFF10001501)the National Natural Science Foundation of China(32171971)。
文摘As an essential crop that provides vegetable oil and protein,soybean(Glycine max(L.)Merr.)is widely planted all over the world.However,the scarcity of water resources worldwide has seriously impacted on the quality and yield of soybean.To address this,exploring excellent genes for improving drought resistance in soybean is crucial.In this study,we identified natural variations of GmFNSII-2(flavone synthase II)significantly affect the drought resistance of soybeans.Through sequence analysis of GmFNSII-2 in 632 cultivated and 44 wild soybeans nine haplotypes were identified.The full-length allele GmFNSII-2^(C),but not the truncated allele GmFNSII-2^(A) possessing a nonsense nucleotide variation,increased enzyme activity.Further research found that GmDREB3,known to increase soybean drought resistance,bound to the promoter region of GmFNSII-2^(C).GmDREB3 positively regulated the expression of GmFNSII-2^(C),increased flavone synthase abundance and improved the drought resistance.Furthermore,a singlebase mutation in the GmFNSII-2^(C) promoter generated an additional drought response element(CCCCT),which had stronger interaction strength with GmDREB3 and increased its transcriptional activity under drought conditions.The frequency of drought-resistant soybean varieties with Hap 1(Pro:GmFNSII-2^(C))has increased,suggesting that this haplotype may be selected during soybean breeding.In summary,GmFNSII-2^(C) could be used for molecular breeding of drought-tolerant soybean.
基金supported by the Hainan Province Science and Technology Special Fund,China(ZDYF2023XDNY086)the Project of Sanya Yazhou Bay Science and Technology City,China(SCKJ-JYRC-2022-87)+2 种基金the Natural Science Foundation of Guangdong Province,China(2023A1515012052 and 2023A1515012092)the Guangzhou Science and Technology Plan Project,China(2023A04J1452 and 2023A04J0749)the Double First-class Discipline Promotion Project,China(2021B10564001).
文摘Seed vigor is a crucial trait for the direct seeding of rice.Here we examined the genetic regulation of seed vigor traits in rice,including germination index(GI)and germination potential(GP),using a genome-wide association study approach.One major quantitative trait locus,qGI6/qGP6,was identified simultaneously for both GI and GP.The candidate gene encoding the cytochrome c oxidase subunit 5B(OsCOX5B)was validated for qGI6/qGP6.The disruption of OsCOX5B caused the vigor traits to be significantly lower in Oscox5b mutants than in the japonica Nipponbare wild type(WT).Gene co-expression analysis revealed that OsCOX5B influences seed vigor mainly by modulating the tricarboxylic acid cycle process.The glucose levels were significantly higher while the pyruvic acid and adenosine triphosphate levels were significantly lower in Oscox5b mutants than in WT during seed germination.The elite haplotype of OsCOX5B facilitates seed vigor by increasing its expression during seed germination.Thus,we propose that OsCOX5B is a potential target for the breeding of rice varieties with enhanced seed vigor for direct seeding.
基金supported by the National Key Research and Development Program(2016YFD0100700)the Wuhan Science and Technology Project(2020020601012259)+4 种基金Hubei Natural Science Foundation(2020CFB117)the National Natural Science Foundation of China(31301250)the Talent Project from Guizhou Education Department(Qian jiao he KY zi(2021)024)the Key Cultivation Project of Guizhou University(201903)the Talent Project from Thousands of Innovative and Entrepreneurial in Guizhou Province。
文摘Rice has a large number of nitrate or peptide transporter family(NPF) genes, but the effects of most members on rice growth and development are unknown. We report that Os NPF5.16, a nitrate transporter gene with natural variation in its promoter sequence, is essential for rice growth and yield. The promoter sequence showed various differences between indica and japonica cultivars, and higher expression of Os NPF5.16 was found in indica cultivars with higher plant weight and more tillers than japonica cultivars.Os NPF5.16 was highly expressed in roots, tiller basal parts, and leaf sheaths, and its protein was localized on the plasma membrane. In c RNA-injected Xenopus laevis oocytes, Os NPF5.16 transport of nitrate at high nitrate concentration depended on p H. Overexpression of Os NPF5.16 increased nitrate content and total nitrogen content in leaf sheath as well as biomass and tiller bud length in rice. Elevated expression of Os NPF5.16 increased rice tiller number and grain yield by regulating cytokinin levels. Inhibition of Os NPF5.16 expression showed the opposite effects. Regulating Os NPF5.16 expression has potential for improving rice grain yield.
基金supported by the National High Technology Research and Development Program of China (2006AA10Z1A6)the Program for New Century Excellent Talents in University, China (NCET-08-0531)
文摘The resistance in tomato plants to bacterial speck caused by Pseudomonas syringae pv. tomato is triggered by the interactions between the plant resistance protein Pto and the pathogen avirulence proteins AvrPto or AvrPtoB. Fen is a gene encoding closely related functional protein kinases as the Pto gene. To investigate the status of resistance to the pathogen and natural variation of Pto and Fen genes in tomato, 67 lines including 29 growing in China were subject to disease resistance evaluation and fenthion-sensitivity test. Alleles of Pto and Fen were amplified from genomic DNA of 25 tomato lines using polymerase chain reaction （PCR） and sequences were determined by sequencing the PCR products. The results indicated that none of the 29 cultivars/hybrids growing in China were resistant to bacterial speck race 0 strain DC3000. Seven of eight tomato lines resistant to DC3000 were also fenthion-sensitive. Analysis of deduced amino acid sequences identified three novel residue substitutions between Pto and pto, and one new substitution identified between Fen and fen. A PCR-based marker was developed and successfully used to select plants with resistance to DC3000.
基金jointly supported by the National Key Research and Development Program of China (Grant No. 2021YFD1000401)the National Natural Science Foundation of China (Grant No.32070376)+1 种基金the Program of Horticultural Crop Germplasm Resources in Hubei Province (Grant No. 2021DFE016)the Key Technology of Safety Production to Improve Tea Quality and Efficiency in Three Gorges Reservoir Area。
文摘Many attentions have been previously focused to identify the multiple biochemical components related to tea quality and health benefits,however, the natural variation of biochemical components present in tea germplasm has not been adequately evaluated. In this study, the main biochemical components, leaf morphological and yield characteristics were evaluated for four rounds of tea leaves in a panel of 87 elite tea cultivars suitable for black, green, or oolong tea. Significant variations were observed among the tea cultivars, as well as seasonal differences in the levels of the free amino acid(FAA), caffeine(CAF), tea polyphenols(TP), water extract(WE) and TP to FAA ratio(TP/FAA). Results showed that the average levels of FAA showed a seasonal change, with the highest level of 4.0% in the 1st spring tea in the cultivars suitable for green tea and the lowest of 3.2% in summer tea in the cultivars suitable for black tea. The average CAF content was highest 3.2% in the cultivars suitable for oolong tea in the 1st spring and the lowest 2.5% in the cultivars suitable for green tea in summer. Limited seasonal and varietal variations were noticed in the average levels of WE among the three categories of tea. In addition, significant natural variation of the morphological characteristics, bud length varying from 2.5 cm to 8.7 cm, bud density from 190.3 buds · m-2to 1 730.3 buds · m-2, mature leaves biomass from 128.4 kg · hm-2to 2 888.4 kg · hm-2, and yield component traits of 100 buds(one bud with two leaves) dry weight from 3.7 g to37.7 g, tea yield/round from 444.6 kg · hm-2to 905.3 kg · hm-2, were observed. The aim of our evaluation was not only to identify the advantages of seasonal and clonal variations but also to provide a new viewpoint for their further application. Representative accessions were selected from the germplasm to promote the establishment of an inherent biochemical constituent expressing the quality of black, green, and oolong tea. The findings might be utilized to establish early selection criteria to enhance the tea breeding and production program.
基金supported by grants from the National Program for Basic Research of China(No.2012CB114305)the National Program on High Technology Development(No. 2012AA10A303)the Oversea Graduate Program from Ministry of Education to K.Songyikhangsuthor
文摘Water is a major limiting factor for food production and many countries fail to produce sufficient food for their population due to severe water scarcity （Jury and Vaux, 2005）. Rice is the main staple food worldwide. More than 50% of rice in the world is rain-fed and drought causes severe reduction in rice grain yield in rain-fed environments （Venuprasad et al., 2007; Zhang, 2007; Sandhu et al., 2014）. Therefore, enhancing drought resistance （DR） of rice is important for food security. However, DR is a complex trait, which is controlled by a large number of loci with small effect and is also affected by different genetic background, genotype-by-environment interaction and other stresses such as heat （Hu and Xiong, 2014）.
基金supported by the Federal Ministery of Agriculture,Food and Regional Identity/Fachagentur Nachwachsende Rohstoffe,Grant Number:2222NR078Athe Federal Ministry of Research,Technology and Space/Projekttrager Julich,Grant Number 031B1550B.
文摘Potato(Solanum tuberosum)was domesticated 8000–10000 years ago from wild species in the Andes.Due to its adaptation potential to diverse climates,its cultivation spread globally.Today,potato is the fourth most important staple crop worldwide in terms of production quantity and plays a critical role in food security,especially since its production and consumption constantly increase in developing countries(FAOSTAT Database 2022,https://www.fao.org/statistics/en).
基金funded by the National Natural Science Foundation of China(32241038,32472124,32241045,32241042,and 32201780)the National High-Level Personnel of Special Support Program(2024WRQB003)+5 种基金the Shenzhen Science and Technology Program(JCYJ20240813151204006)the National Key R&D Program of China(2022YFD1500503,2023YFD1200700,and 2023YFD1200704)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA0440302)the ShenZhen Postdoctoral Funding Project(77000*42100029)the Fundamental Research Fund for the Central Universities(77000-12240011)a joint research project from Shanxi Xinghuacun Fenjiu Distillery Co.Ltd.
文摘Spikelets are the basic unit of the inflorescence in crops, consisting of one or more florets, playing a key role in determining yield. During cereal flower development, the spikelet meristem (SM) arises from the inflorescence meristem or branch meristem, and subsequently gives rise to the floret meristem (FM) (Xie et al., 2023). The multi-ovary or multi-floret spikelet phenomenon is commonly observed in certain cereal germplasms (Zhu et al., 2019;Ren et al., 2020;Selva et al., 2023), demonstrating the potential for enhancing grain yield through the production of a larger number of grains. A typical sorghum spikelet produces a single fertile floret, resulting in a single-grain spikelet morphology. However, the multiple-grain spikelet (MGS) sorghum germplasm, first documented in 1936, contains more than half of the double-grain spikelets per panicle and exhibits an unusual spikelet architecture in which two mature grains are produced within a single spikelet (Karper and Stephens, 1936). Despite this, the genetic basis underlying this trait has remained unclear.
文摘Improving the methionine (Met) content in maize kernels is of key importance to the animal feed industry;however, the genetic and molecular mechanisms governing maize kernel Met content remain largely unexplored. In this study, we leveraged a panel consisting of 348 diverse inbred maize lines to explore the genetic and molecular mechanisms that control kernel Met levels. A genome-wide association study followed by transcriptomic analysis identified the deSUMOylating isopeptidase gene ZmDeSI2. Further biochemical experiments revealed that ZmDeSI2 directly reduces the SUMOylation and accumulation of the sulfite reductase ZmSIR, thereby repressing Met accumulation. Natural variants in the ZmDeSI2 promoter region were found to serve as key determinants of the expression of this gene, predominantly due to the absence or presence of a ZmWRKY105 transcription factor binding site. The elite ZmDeSI2^(Hap2) haplotype without this binding site in the ZmDeSI2 promoter was associated with a 1.36-fold increase in Met levels in the kernels of modified near-isogenic lines generated through marker-assisted breeding. Taken together, these results provide new insights into the molecular processes that control Met biosynthesis, highlighting an elite natural variant suitable for application in maize breeding for Met biofortification.
基金supported by Biological Breeding-National Science and Technology Major Project(no.2023ZD04070,W.Z.)the National Key Research and Development Program,Ministry of Science and Technology of China(no.2022YFD1201802,W.Z.)+1 种基金the National Natural Science Foundation of China(no.32472499,W.Z.)the Pinduoduo-China Agricultural University Research Fund(no.PC2023A01005,Y.-L.P.).
文摘Maize(Zea mays)is one of the most important crops in the world,but its yield and quality are seriously affected by diverse diseases.Identifying broad-spectrum resistance genes is crucial for developing effective strategies to control the disease in maize.In a genome-wide study in maize,we identified a G-type lectin receptor kinase ZmLecRK1,as a new resistance protein against Pythium aphanidermatum,one of the causal pathogens of stalk rot in maize.Genetic analysis showed that the specific ZmLecRK1 allele can confer resistance to multiple pathogens in maize.The cell death and disease resistance phenotype mediated by the resistant variant of ZmLecRK1 requires the co-receptor ZmBAK1.A naturally occurring A404S variant in the extracellular domain of ZmLecRK1 determines the ZmLecRK1-ZmBAK1 interaction and the formation of ZmLecRK1-related protein complexes.Interestingly,the ZmLecRK1 susceptible variant was found to possess the amino acid S404 that is present in the ancestral variants of ZmLecRK1 and conserved among the majority of grass species,while the resistance variant of ZmLecRK1 with A404 is only present in a few maize inbred lines.Substitution of S by A at position 404 in ZmLecRK1-like proteins of sorghum and rice greatly enhances their ability to induce cell death.Further transcriptomic analysis reveals that ZmLecRK1 likely regulates gene expression related to the pathways in cell wall organization or biogenesis in response to pathogen infection.Taken together,these results suggest that the ZmLecRK1 resistance variant enhances its binding affinity to the co-receptor ZmBAK1,thereby enhancing the formation of active complexes for defense in maize.Our work highlights the biotechnological potential for generating disease-resistant crops by precisely modulating the activity of ZmLecRK1 and its homologs through targeted base editing.
基金supported by grants from the STI2030 Major Projects(2023ZD0406803)Agro ST Project(NK2022050103)+5 种基金the National Natural Science Foundation of China(32372094,32272123,and 32072036)the Modern Agricultural Industry Technology System Projects of Henan,China(HARS-22-03-G3)the Key R&D projects of Henan(231111110500)the Key Laboratory of Functional Agriculture,Guizhou Province([2023]007)the Key Laboratory of Molecular Breeding for Grain and Oil crops,Guizhou Province([2023]008)the China Postdoctoral Science Foundation(2021M701108).
文摘Grain yield is determined mainly by grain number and grain weight.In this study,we identified and characterized MORE GRAINS1(MOG1),a gene associated with grain number and grain weight in rice(Oryza sativa L.),through map-based cloning.Overexpression of MOG1 increased grain yield by 18.6%-22.3%under field conditions.We determined that MOG1,a bHLH transcription factor,interacts with OsbHLH107 and directly activates the expression of LONELY GUY(LOG),which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1(EXPLA1),positively regulating grain number per panicle and grain weight.Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation,leading to functional differences.Haplotype analysis revealed that Hap-HNW,which results in a greater number and heavier grains,has undergone strong selection but has been poorly utilized in modern lowland rice breeding.In summary,the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway,thereby increasing grain number and grain weight.These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.
基金supported by the science and technology major program of Hubei Province(2022ABA001)the National Key Research and Development Program of Shandong Province(2022CXPT014)the Knowledge Innovation Program of Wuhan-Shugung Project(2023020201020413).
文摘Maize(Zea mays)is highly susceptible to waterlogging stress,which reduces both the yield and quality of this important crop.However,the molecular mechanism governing waterlogging tolerance is poorly understood.In this study,we identify a waterlogging-and ethylene-inducible gene ZmEREB179 that encodes an ethylene response factor(ERF)localized in the nucleus.Overexpression of ZmEREB179 in maize increases the sensitivity to waterlogging stress.Conversely,the zmereb179 knockout mutants are more tolerant to waterlogging,suggesting that ZmEREB179 functions as a negative regulator of waterlogging tolerance.A transcriptome analysis of the ZmEREB179-overexpressing plants reveals that the ERF-type transcription factor modulates the expression of various stress-related genes,including ZmEREB180.We find that ZmEREB179 directly targets the ZmEREB180 promoter and represses its expression.Notably,the analysis of a panel of 220 maize inbred lines reveals that genetic variations in the ZmEREB179 promoter(Hap2)are highly associated with waterlogging resistance.The functional association of Hap2 with waterlogging resistance is tightly co-segregated in two F2 segregating populations,highlighting its potential applications in breeding programs.Our findings shed light on the involvement of the transcriptional cascade of ERF genes in regulating plant-waterlogging tolerance.
文摘Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using whole- genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 （OsPRR37; hereafter PRR37） is respon- sible for the Early heading7-2 （EH7-2）/Heading date2 （Hd2） QTL which was identified from a cross of late-heading rice ＇Milyang23 （M23）＇ and early-heading rice ＇H143＇. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT （CONSTANS, CO-like, and TOC1） domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day condi- tions, and are adapted to the northernmost regions of rice cultivation, up to 53~ N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and GhdT/ Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.
文摘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 ｜Q domains, which interacts with the rice calmodulin protein, OsCaMl-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, GSE5DELl＋IN1, and GSESDEL~ in cultivated rice were identified based on the deletion/insertion type in its pro- moter region. We demonstrated that a 950-bp deletion （DELl） in indica varieties carrying the GSE5DELl＋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 acces- sions 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.
基金supported by the Major State Basic Research Development Program of China(2013CB127001)the National High Technology R&D Program of China(2012AA10A304)+1 种基金the National Natural Science Foundation of China(31070267)the Program for New Century Excellent Talents in University of Ministry of Education in China(NCET-09-0401)
文摘Flavonoids constitute a major group of plant phenolic compounds.While extensively studied in Arabidopsis,profiling and naturally occurring variation of these compounds in rice（Oryza sativa）,the monocot model plant,are less reported.Using a collection of rice germplasm,comprehensive profiling and natural variation of flavonoids were presented in this report.Application of a widely targeted metabolomics method facilitated the simultaneous identification and quantification of more than 90 flavonoids using liquid chromatography tandem mass spectrometry（LC-MS/MS）.Comparing flavonoid contents in various tissues during different developmental stages revealed tissue-specific accumulation of most flavonoids.Further investigation indicated that flavone mono-C-glycosides,malonylated flavonoid O-hexosides,and some flavonoid O-glycosides accumulated at significantly higher levels in indica than in japonica,while the opposite was observed for aromatic acylated flavone C-hexosyl-O-hexosides.In contrast to the highly differential accumulation between the two subspecies,relatively small variations within subspecies were detected for most flavonoids.Besides,an association analysis between flavonoid accumulation and its biosynthetic gene sequence polymorphisms disclosed that natural variation of flavonoids was probably caused by sequence polymorphisms in the coding region of flavonoid biosynthetic genes.Our work paves the way for future dissection of biosynthesis and regulation of flavonoid pathway in rice.
基金supported by the Central Public-interest Scientific Institution Basal Research Fund(grant nos.S2022ZD02,Y2020XK16)the National Natural Science Foundation(grant nos.U21A20208,31871587,31900177,31901534)+1 种基金Hainan Yazhou Bay Seed Laboratory(grant no.B21HJ0215)supported by the China Postdoctoral Science Foundation(grant nos.2019M650917,2020T130709)。
文摘Japonica/geng and indica/xian are two major rice(Oryza sativa)subspecies with multiple divergent traits,but how these traits are related and interact within each subspecies remains elusive.Brassinosteroids(BRs)are a class of steroid phytohormones that modulate many important agronomic traits in rice.Here,using different physiological assays,we revealed that japonica rice exhibits an overall lower BR sensitivity than indica.Extensive screening of BR signaling genes led to the identification of a set of genes distributed throughout the primary BR signaling pathway with divergent polymorphisms.Among these,we demonstrate that the C38/T variant in BR Signaling Kinase2(OsBSK2),causing the amino acid change P13L,plays a central role in mediating differential BR signaling in japonica and indica rice.OsBSK2in indica plays a greater role in BR signaling than OsB SK2in japonica by affecting the auto-binding and protein accumulation of OsBSK2.Finally,we determined that OsBSK2 is involved in a number of divergent traits in japonica relative to indica rice,including grain shape,tiller number,cold adaptation,and nitrogen-use efficiency.Our study suggests that the natural variation in OsB SK2 plays a key role in the divergence of BR signaling,which underlies multiple divergent traits between japonica and indica.
基金supported by grants from the National Basic Research Program of China(973Program:2012CB910900)the National Natural Science Foundation of China(31330048)+1 种基金Peking-Tsinghua Center for Life Sciences(to X.W.D)State Key Laboratory of Protein and Plant Gene Research
文摘Histone modifications affect gene expression, but the mechanism and biological consequence of natural variation in histone modifications remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modification and transcriptome for Col, C24 and their F1 hybrid. A total of 1,828 genomic regions showing variation in H3K27me3 modification between Col and C24 were identified, most of which were associated with genic regions. Natural variation of H3K27me3 modification between parents could result in aUelic bias of H3K27me3 in hybrids. Furthermore, we found that H3K27me3 variation between Col and C24 was negatively correlated with gene expression differences between two accessions, espe- cially with those arising from the cis-effect. Importantly, mutation of CLF, an Arabidopsis methyltransferase for H3K27,altered gene expression patterns between the parents. Together, these data provide insights into natural variation of histone modifications and their association with gene expression differences between Arabidopsis ecotypes.
基金This research was supported, in part, by National Science Foundation grant IOS-1025642 （G,B.M.）,
文摘The Pto protein kinase from Solanum pimpinellifolium interacts with Pseudomonas syringae effectors AvrPto or AvrPtoB to activate effector-triggered immunity. The previously solved crystal structures of the AvrPto-Pto and AvrPtoB-Pto complexes revealed that Pro binds each effector through both a shared and a unique interface. Hera we use natural variation in wild species of tomato to further investigate Pto recognition of these two effectors. One species, Solanum chmielewskU, was found to have many accessions that recognize only AvrPtoB. The Pto ortholog from one of these accessions was responsible for recognition of AvrPtoB and it differed from Solanum pimpinellifolium Pto by only 14 amino acids, including two in the AvrPto-specific interface, glutamate-49/glycine-51. Converting these two residues to those in Pro （histidine-49/valine-51） did not restore recognition of AvrPto. Subsequent experiments revealed that a single substitution of a histidine-to-aspartate at position 193 in Pto, which is not near the AvrPto- specific interface, was sufficient for conferring recognRion of AvrPto in plant cells. The reciprocal substi- tution of aspartate-to-histidine-193 in Pto abolished AvrPto recognition, confirming the importance of this residue. Our results reveal new aspects about effector recognition by Pto and demonstrate the value of using natural variation to understand the interaction between resistance proteins and pathogen effectors.
