The improvement of soybean seed carotenoid contents is very important due to the beneficial role of carotenoids in human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthes...The improvement of soybean seed carotenoid contents is very important due to the beneficial role of carotenoids in human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthesis remains largely unknown. In the present study, we employed next generation sequencing-based bulked-segregant analysis to identify new genomic regions governing seed carotenoids in 1,551 natural soybean accessions. The genomic DNA samples of individual plants with extreme phenotypes were pooled to form two bulks with high(50 accessions) and low(50 accessions) carotenoid contents for Illumina sequencing. A total of 125.09 Gb of clean bases and 89.82% of Q30 were obtained, and the average alignment efficiency was 99.45% with an average coverage depth of 62.20× and 99.75% genome coverage. Based on the G prime statistic algorithm(G') method analysis, 16 candidate genomic loci with a total length 20.41 Mb were found to be related to the trait. Of these loci, the most significant regions displaying the highest elevated G' values were found in chromosome 06 at a position of 18.53–22.67 Mb, and chromosome 19 at genomic region intervals of 8.36–10.94, 12.06–13.79 and 18.45–20.26 Mb. These regions were then used to identify the key candidate genes. In these regions, 250 predicted genes were found and analyzed to obtain 90 significantly enriched(P<0.05) Gene Ontology(GO) terms. Based on ANNOVAR analysis, 50 genes with non-synonymous and stopgained mutations were preferentially selected as potential candidate genes. Of those 50 genes, following their gene annotation functions and high significant haplotype variations in various environments,five genes were identified as the most promising candidate genes regulating soybean seed carotenoid accumulation, and they should be investigated in further functional validation studies. Collectively, understanding the genetic basis of carotenoid pigments and identifying genes underpinning carotenoid accumulation via a bulked-segregant analysis-based sequencing(BSA-seq) approach provide new insights for exploring future molecular breeding efforts to produce soybean cultivars with high carotenoid content.展开更多
Pre-harvest sprouting(PHS)or vivipary is a major problem affecting cereal quality and grain quantity and is primarily linked to the dysregulation of abscisic acid(ABA)biosynthesis in plants.Therefore,elucidating the m...Pre-harvest sprouting(PHS)or vivipary is a major problem affecting cereal quality and grain quantity and is primarily linked to the dysregulation of abscisic acid(ABA)biosynthesis in plants.Therefore,elucidating the molecular mechanisms governing seed dormancy is crucial for developing strategies to improve crop productivity.In this study,we identified a novel viviparous maize mutant,viviparous-like 5(vp-like5),which exhibits precocious germination in developing seeds.Through map-based cloning,we discovered that ZmCNX6,which encodes a small subunit of molybdopterin synthase essential for molybdenum cofactor(MoCo)biosynthesis,is the causal gene responsible for the vp-like5 phenotype.Biochemical assays have demonstrated significantly reduced activities of MoCo-dependent enzymes,including aldehyde oxidase(AO),xanthine dehydrogenase(XDH),and nitrate reductase(NR),in vplike5.AO is essential for the ABA biosynthesis,and the observed ABA deficiency in vp-like5 likely drives the viviparous phenotype.Expression analysis showed that ZmCNX6 was stably expressed during seed development,indicating its significant role in seed development.Furthermore,overexpression of ZmCNX6 not only enhanced the activities of MoCo-dependent enzymes but also improved drought tolerance in maize.Collectively,our study revealed ZmCNX6 as a multifunctional hub coordinating MoCo metabolism,ABA-dependent dormancy regulation,and abiotic stress responses,offering a potential target for simultaneously mitigating vivipary and improving drought resistance in maize.展开更多
Despite its negative impacts on plant functioning,climate change benefits plants at the cellular level.For example,the stimulation of C3 photosynthesis by elevated CO_(2)can increase N2 fixation by 73%and grain yield ...Despite its negative impacts on plant functioning,climate change benefits plants at the cellular level.For example,the stimulation of C3 photosynthesis by elevated CO_(2)can increase N2 fixation by 73%and grain yield by 10%–11%.The global elevated atmospheric CO_(2)concentration has already decreased the nitrogen content in C3 crop species and C3 woody vegetation by 14%and 21%,respectively,regardless of added nitrogen fertilizer.^(15)N-feeding experiments have shown that,after 19 h under elevated CO_(2),the^(15)N concentration in the stems,roots plus rhizomes,and whole plants of Scirpus olneyi(S.olneyi)decreased by 51%,63%,and 74%,respectively.Moreover,S.olneyi showed reduced NH_(4)^(+)assimilation under elevated CO_(2),which decreased the amino acid contents in the stems by 25.6%for glycine and 65.0%for serine,and that in the roots plus rhizomes by 2%for gamma-aminobutyric acid(GABA)and 80%for glutamate.Wheat grain protein has also been found to decrease by 7.4%under elevated CO_(2)due to reductions in threonine,valine,iso-leucine,leucine,and phenylalanine.The mineral nutrient contents in grains of rice and maize were similarly found to decrease under high CO_(2)by 1.0%and 7.1%for phosphorus,7.8%and 2.1%for sulfur,5.2%and 5.8%for iron,3.3%and 5.2%for zinc,10.6%and 9.9%for copper,and 7.5%and 4.2%for manganese,respectively.In general,mineral concentrations in C3 plants are predicted to decrease by 8%under elevated CO_(2),while total non-structural carbohydrates(mainly starch and sugars)are expected to increase.These decreases in grain protein,amino acids,and mineral nutrients could double the incidence of global protein-calorie malnutrition and micronutrient deficiency—especially in Africa,where agricultural soils are inherently low in nutrient elements.Additionally,the increase in total non-structural carbohydrates(mainly starch and sugars)in cereal crops could elevate diabetes incidence due to heavy reliance on starchy diets.The negative effects of elevated CO_(2)on rice,maize,and wheat—the world's three major staple crops—suggest an increase in global food insecurity with rising atmospheric CO_(2)concentration.展开更多
Large grain is a favorable trait for appearance quality and a large sink potential in wheat breeding.The stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from ...Large grain is a favorable trait for appearance quality and a large sink potential in wheat breeding.The stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871(ZM871)and its sister line Zhongmai 895(ZM895).Here,a BC_(1)F_6 residual heterozygous line was selected from the cross of a ZM871/ZM895//ZM871 population,and six heterozygous recombinant plants were identified in the BC_(1)F_(7)population from self-pollination of the heterozygous line.QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2(25.3-27.5 Mb)by phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants.Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses.Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS.The gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed,and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population of 166 cultivars using this marker.These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat.展开更多
Small RNAs(sRNAs)are essential for regulating plant growth and development,and they possess the notable ability to travel long distances within organisms to regulate target gene expression.Our study examined the dcl2 ...Small RNAs(sRNAs)are essential for regulating plant growth and development,and they possess the notable ability to travel long distances within organisms to regulate target gene expression.Our study examined the dcl2 mutant,a key enzyme in s RNA biogenesis,to determine the role of the DCL2 protein in s RNA synthesis and to identify mobile s RNAs under DCL2 regulation.Through grafting experiments between dcl2 mutants and wild-type soybean plants,coupled with s RNA sequencing,we identified14,105 s RNAs significantly affected by DCL2 and discovered 375 mobile s RNAs under its regulation.Degradome analysis provided deeper insights into the regulatory effects of these mobile s RNAs on their target genes,enabling us to understand their potential influences on plant development and stress responses.Leveraging the systemic movement of s RNAs from roots to shoots,we propose a novel strategy for manipulating gene expression in aboveground tissues.Overall,our research findings not only deepen our understanding of the complex regulatory networks involving mobile s RNAs regulated by DCL2,but also provide a new strategy for gene regulation,which could have a positive impact on agricultural biotechnology.展开更多
A genome-wide association study(GWAS)was conducted on a collection of 166 Chinese rice mini-core germplasms to investigate cold tolerance traits across various rice growth stages.Population structure analysis revealed...A genome-wide association study(GWAS)was conducted on a collection of 166 Chinese rice mini-core germplasms to investigate cold tolerance traits across various rice growth stages.Population structure analysis revealed that these accessions could be categorized into six subgroups,consistent with their geographical origins.展开更多
Heterosis,also known as hybrid vigor,is commonly observed in rice crosses.The hybridization of rice species or subspecies exhibits robust hybrid vigor,however,the direct harnessing of this vigor is hindered by reprodu...Heterosis,also known as hybrid vigor,is commonly observed in rice crosses.The hybridization of rice species or subspecies exhibits robust hybrid vigor,however,the direct harnessing of this vigor is hindered by reproductive isolation.Here,we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids.This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species,emphasizing the essential role of mitochondria in this process.Additionally,we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes,elucidating their significant contribution to reproductive isolation.Furthermore,our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice.Building on these advances,we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.展开更多
Genotyping arrays based on single nucleotide polymorphisms(SNPs)provide a low-cost,highthroughput platform.The development of a SNP array that fully reflects the genetic diversity of maize(Zea mays L.)germplasm and is...Genotyping arrays based on single nucleotide polymorphisms(SNPs)provide a low-cost,highthroughput platform.The development of a SNP array that fully reflects the genetic diversity of maize(Zea mays L.)germplasm and is applicable to molecular breeding programs is desirable.In this study,we developed a MaizeGerm50K array comprising 50,852 SNPs selected from the resequencing data of 1604 maize inbred lines and other markers.A genome-wide association study using a landrace panel genotyped with the array permitted mapping of several known genes.We also verified a candidate gene,RNA-binding motif protein 24-like 1(ZmRBM24L1),delaying flowering through overexpression lines.Genomic selection for yield and agronomic traits showed high prediction accuracy.The MaizeGerm50K array is thus a valuable genomic tool for maize genetic studies and breeding.展开更多
Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a princi...Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.展开更多
The crown root system is the most important root component in maize at both the vegetative and reproductive stages. However, the genetic basis of maize crown root traits(CRT) is still unclear, and the relationship bet...The crown root system is the most important root component in maize at both the vegetative and reproductive stages. However, the genetic basis of maize crown root traits(CRT) is still unclear, and the relationship between CRT and aboveground agronomic traits in maize is poorly understood. In this study, an association panel including 531 elite maize inbred lines was planted to phenotype the CRT and aboveground agronomic traits in different field environments. We found that root traits were significantly and positively correlated with most aboveground agronomic traits, including flowering time, plant architecture and grain yield. Using a genome-wide association study(GWAS)coupled with resequencing, a total of 115 associated loci and 22 high-confidence candidate genes were identified for CRT. Approximately one-third of the genetic variation in crown root was co-located with 46 QTLs derived from flowering and plant architecture. Furthermore, 103 (89.6%) of 115 crown root loci were located within known domestication-and/or improvement-selective sweeps, suggesting that crown roots might experience indirect selection in maize during domestication and improvement. Furthermore, the expression of Zm00001d036901, a high-confidence candidate gene, may contribute to the phenotypic variation in maize crown roots, and Zm00001d036901 was selected during the domestication and improvement of maize. This study promotes our understanding of the genetic basis of root architecture and provides resources for genomics-enabled improvements in maize root architecture.展开更多
Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we...Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we identify a wheat TaPRR95 gene by genome-wide association studies to be associated with plant height.Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height,particularly the peduncle,with an earlier heading date.The longer peduncle is mainly caused by the increased cell elon-gation at its upper section,whilst the early heading date is accompanied by elevated expression of flow-ering genes,such as TaFT and TacO1.A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAAVAux genes for auxin signaling inpr95abad plants that may act as a regulatory mechanism to promote robust plant growth.A haplotype analysis identifies a TaPRR95-B haplotype(Hap2)to be closely associated with reduced plant height and increased thousand-grain weight.Moreover,the Hap2 frequency is higher in cultivars than that in landraces,suggesting the artifi-cial selection on the allele during wheat breeding.These findings suggest that TaPRR95 is a regulator for plant height and heading date,thereby providing an important target for wheat yield improvement.展开更多
Flag leaf angle is one of the key target traits in high yield wheat breeding.A smaller flag leaf angle reduces shading and enables plants to grow at a higher density,which increases yield.Here we identified a mutant,j...Flag leaf angle is one of the key target traits in high yield wheat breeding.A smaller flag leaf angle reduces shading and enables plants to grow at a higher density,which increases yield.Here we identified a mutant,je0407,with an 84.34%-89.35%smaller flag leaf angle compared with the wild type.The mutant also had an abnormal lamina joint and no ligule or auricle.Genetic analysis indicated that the ligule was controlled by two recessive genes,which were mapped to chromosomes 2AS and 2DL.The mutant allele on chromosome 2AS was named Tafla1b,and it was fine mapped to a 1 Mb physical interval.The mutant allele on chr.2DL was identified as Taspl8b,a novel allele of TaSPL8 with a missense mutation in the second exon,which was used to develop a cleaved amplified polymorphic sequence marker.F3 and F4 lines derived from crosses between Jing411 and je0407 were genotyped to investigate interactions between the Tafla1b and Taspl8b alleles.Plants with the Tafla1b/Taspl8a genotype had 58.41%-82.76%smaller flag leaf angles,6.4%-24.9%shorter spikes,and a greater spikelet density(0.382 more spikelets per cm)compared with the wild type.Plants with the Tafla1a/Taspl8b genotype had 52.62%-82.24%smaller flag leaf angles and no differences in plant height or spikelet density compared with the wild type.Tafla1b/Taspl8b plants produced erect leaves with an abnormal lamina joint.The two alleles had dosage effects on ligule formation and flag leaf angle,but no significant effect on thousand-grain weight.The mutant alleles provide novel resources for improvement of wheat plant architecture.展开更多
MicroRNAs(miRNAs)are versatile regulators of gene expression at both the transcription and posttranscription levels.The microRNA miR396 plays vital roles in growth,development,and resistance to abiotic stresses in man...MicroRNAs(miRNAs)are versatile regulators of gene expression at both the transcription and posttranscription levels.The microRNA miR396 plays vital roles in growth,development,and resistance to abiotic stresses in many plant species.However,the roles and functions of miR396 in soybeans are not well understood.Here,we report that Gm-miR396a influences soybean development and salinity tolerance.We found that soybean miR396a was responsive to salt stress.Gm-miR396a gene-edited lines(miR396a-GEs),created using CRISPR/Cas9,exhibited more branches,higher grain yields,and greater salinity tolerance than control plants.The transcripts in lines with altered abundance of miR396a-GE were significantly enriched for biological processes related to hormone regulation.Overexpression of the Gm-miR396a precursor(pre-miR396a-OE)resulted in developmental deficiencies including dwarfness,abnormal inflorescences and flowers,smaller and fewer seeds,and small leaves with larger and more numerous stomata.Transcriptome analysis indicated photosynthesis-related genes were downregulated in pre-miR396a-OE plants.These results contribute valuable insights into the function of GmmiR396a in soybeans and hold promise for enhancing soybean yield and salinity tolerance through germplasm innovation.展开更多
Wheat(Triticum aestivum L.)is an important staple food crop in the world and supplies about 20%of human caloric and protein consumption(Giraldo et al.,2019;Xiao et al.,2022).Wheat production accounts for~30%of global ...Wheat(Triticum aestivum L.)is an important staple food crop in the world and supplies about 20%of human caloric and protein consumption(Giraldo et al.,2019;Xiao et al.,2022).Wheat production accounts for~30%of global cereal crops(Li et al.,2019).With the global population increasing and the frequency of natural disasters rising,enhancing wheat yield is crucial to meet food demand.Spike traits such as increased grain number per spike are key determinants of wheat yield.Pre-harvest sprouting(PHS)is a significant natural disaster that severely impacts grain yield and end-use quality of wheat(Tai et al.,2021,2024).展开更多
Endodermal cells and starch-accumulating amyloplasts are well-known gravity sensors initiating shoot gravitropism in Arabidopsis thaliana.The transcription factors SHR and SGR1 regulate endodermal cell formation,while...Endodermal cells and starch-accumulating amyloplasts are well-known gravity sensors initiating shoot gravitropism in Arabidopsis thaliana.The transcription factors SHR and SGR1 regulate endodermal cell formation,while PGM has been demonstrated to regulate starch biosynthesis within chloroplasts,which eventually leads to starch accumulation in amyloplasts.However,the molecular mechanisms of gravity sensing in monocot shoots remain largely unexplored.In this study,we investigated the roles of these genes in rice(Oryza sativa),a model monocot,using CRISPR-Cas9 to generate single,double,and higher-order mutants.The rice genome harbors two orthologs each of SHR and SGR and a single ortholog of PGM.Our results revealed that single mutants of OsPGM,but not OsSHR or OsSGR,showed compromised shoot gravitropism.However,double mutants shr1shr2 and sgr1sgr2 displayed wider tiller angles and reduced gravity sensing,suggesting functional redundancy within each gene pair.Higher-order mutants exhibited progressively severe phenotypes,with quintuple mutants almost unresponsive to gravity stimulation.These findings suggest that these genes act additively through distinct but converging pathways in shoot gravitropism regulation.This study provides novel insights into the molecular mechanisms underlying gravity sensing in monocots and offers valuable knowledge for precision breeding to optimize rice architecture.展开更多
Foxtail millet(Setaria italica)is an important crop and an emerging model plant.Photoperiodic flowering is a key determinant of its production and geographic expansion.In this study,we found that SiPRR37 is responsibl...Foxtail millet(Setaria italica)is an important crop and an emerging model plant.Photoperiodic flowering is a key determinant of its production and geographic expansion.In this study,we found that SiPRR37 is responsible for the major quantitative trait locus(QTL)Heading date 2(Hd2)identified in 680 foxtail millets using a genome-wide association study.Overexpression of SiPRR37 in foxtail millet significantly delayed the heading date under both natural long-day and short-day conditions.CRISPR/Cas9-induced Siprr37 mutants exhibited earlier flowering in long-day conditions but later flowering in short-day conditions.The critical day length(CDL)for the reversal of Siprr37’s function was around 14.3 h.Haplotype analysis revealed that accessions with the Tc1-Mariner transposon insertion in SiPRR37(Hap 1)flowered significantly earlier at higher latitudes,and later at lower latitudes,indicating that natural variants of SiPRR37 exert dual functions in flowering regulation according to geographic latitude.The gradual,successive decrease in the frequency of Hap 2 from low to high latitudes,with the concurrent increase of Hap 1,demonstrates that these haplotypes have undergone artificial selection.Further FST analysis demonstrated that SiPRR37 has contributed to the ecological adaption of foxtail millet.Additionally,we reveal that OsPRR37 promotes flowering in rice,while GmPRR37 may only inhibit flowering in soybean.Further diurnal expression and transgenic analyses suggest that the dual function of SiPRR37 might depend on SiHd1.Our study uncovered the distinct functional reversal of SiPRR37 and functional diversification of PRR37 homologs in SD crops.These findings not only enrich knowledge about the regulation of photoperiodic flowering,but also contribute to genetic improvement of crops’regional adaptability.展开更多
The unreasonable application of nitrogen fertilizer poses a threat to agricultural productivity and the environment protection in Northeast China.Therefore,accurately assessing crop nitrogen requirements and optimizin...The unreasonable application of nitrogen fertilizer poses a threat to agricultural productivity and the environment protection in Northeast China.Therefore,accurately assessing crop nitrogen requirements and optimizing fertilization are crucial for sustainable agricultural production.A three-year field experiment was conducted to evaluate the effects of planting density on the critical nitrogen concentration dilution curve(CNDC)for spring maize under drip irrigation and fertilization integration,incorporating two planting densities:D1(60,000 plants ha^(-1))and D2(90,000 plants ha^(-1))and six nitrogen levels:no nitrogen(N0),90(N90),180(N180),270(N270),360(N360),and 450(N450)kg ha^(-1).A Bayesian hierarchical model was used to develop CNDC models based on dry matter(DM)and leaf area index(LAI).The results revealed that the critical nitrogen concentration exhibited a power function relationship with both DM and LAI,while planting density had no significant impact on the CNDC parameters.Based on these findings,we propose unified CNDC equations for maize under drip irrigation and fertilization integration:Nc=4.505DM-0.384(based on DM)and Nc=3.793LAI-0.327(based on LAI).Additionally,the nitrogen nutrition index(NNI),derived from the CNDC,increased with higher nitrogen application rates.The nitrogen nutrition index(NNI)approached 1 with a nitrogen application rate of 180 kg ha^(-1)under the D1 planting density,while it reached 1 at 270 kg ha^(-1)under the D2 planting density.The relationship between NNI and relative yield(RY)followed a“linear+plateau”model,with maximum RY observed when the NNI approached 1.Thus,under the condition of drip irrigation and fertilization integration in Northeast China’s spring maize production,the optimal nitrogen application rates for achieving the highest yields were 180 kg ha^(-1)at a planting density of 60,000 plants ha^(-1),and 270 kg ha^(-1)at a density of 90,000 plants ha^(-1).The CNDC and NNI models developed in this study are valuable tools for diagnosing nitrogen nutrition and guiding precise fertilization practices in maize production under integrated drip irrigation and fertilization systems in Northeast China.展开更多
Black point is a black discoloration of the grain embryo that reduces the grain quality and commodity grade.Identifying the underlying genetic loci can facilitate the improvement of black point resistance in wheat.Her...Black point is a black discoloration of the grain embryo that reduces the grain quality and commodity grade.Identifying the underlying genetic loci can facilitate the improvement of black point resistance in wheat.Here,262 recombinant inbred lines(RILs)from the cross of Zhongmai 578/Jimai 22 were evaluated for their black point reactions in fve environments.A high-density genetic linkage map of the RIL population was constructed with the wheat 50K single nucleotide polymorphism(SNP)array.Six stable QTLs for black point resistance were detected,QBp.caas-2A,QBp.caas-2B1,QBp.caas-2B2,QBp.caas-2D,QBp.caas-3A,and QBp.caas-5B,which explained 2.1-28.8%of the phenotypic variances.The resistance alleles of QBp.caas-2B1 and QBp.caas-2B2 were contributed by Zhongmai 578 while the others were from Jimai 22.QBp.caas-2B2,QBp.caas-2D and QBp.caas-3A overlapped with previously reported loci,whereas QBp.caas-2A,QBp.caas-2B1 and QBp.caas-5B are likely to be new.Five kompetitive allele-specifc PCR(KASP)markers,Kasp_2A_BP,Kasp_2B1_BP,Kasp_2B2_BP,Kasp_3A_BP,and Kasp_5B_BP,were validated in a natural population of 165 cultivars.The fndings of this study provide useful QTLs and molecular markers for the improvement of black point resistance in wheat through marker-assisted breeding.展开更多
Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.展开更多
High molecular weight glutenin subunits(HMW-GS),major components of seed storage proteins in wheat,have large effects on processing quality.GLU-1 genes encode HMW-GS and their expression is mainly controlled at the tr...High molecular weight glutenin subunits(HMW-GS),major components of seed storage proteins in wheat,have large effects on processing quality.GLU-1 genes encode HMW-GS and their expression is mainly controlled at the transcriptional level by interactions between cis-regulatory elements and transcription factors.We previously identified an Aux/IAA transcription factor TaIAA10-6D that bound to a conserved cis-regulatory module CCRM1-1,the most essential conserved cis-regulatory module in GLU-1.Here,we confirmed the binding of TaIAA10-6D to CCRM1-1 using yeast one hybrid and dualluciferase reporter assays.The enhanced expression of TaIAA10-6D suppressed glutenin accumulation and increased gliadin content.Dynamic transcriptome analyses revealed that TaIAA10-6D overexpression down-regulated glutenin and gliadin genes during an early stage of grain filling,but up-regulated gliadin genes during a late stage probably by endoplasmic reticulum stress,accounting for its effect on the tradeoff between glutenin and gliadin.Rheological property and processing quality assays showed that TaIAA10-6D overproduction reduced stabilization time and bread quality,but enhanced cookie quality.Overexpression of TaIAA10-6D also reduced plant height,leaf size,kernel number and grain yield.We identified two major haplotypes of TaIAA10-6D,Hap I and Hap II,and developed a breeding-friendly diagnostic marker.Hap I conferred higher expression of TaIAA10-6D and concomitantly reduced plant height and kernel number,but had little effect on grain yield,contributing to lodging resistance without yield penalty.Hap I was subjected to positive selection in breeding.The findings provide a useful gene for wheat improvement and broaden insights into the regulatory machinery underpinning auxin-mediated quality formation,plant morphogenesis and yield gain.展开更多
基金financially supported by the National Natural Science Foundation of China (32161143033, 32272178, and 32001574)National Key Research and Development Program of China (2021YFD1201605)the Agricultural Science and Technology Innovation Project of CAAS。
文摘The improvement of soybean seed carotenoid contents is very important due to the beneficial role of carotenoids in human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthesis remains largely unknown. In the present study, we employed next generation sequencing-based bulked-segregant analysis to identify new genomic regions governing seed carotenoids in 1,551 natural soybean accessions. The genomic DNA samples of individual plants with extreme phenotypes were pooled to form two bulks with high(50 accessions) and low(50 accessions) carotenoid contents for Illumina sequencing. A total of 125.09 Gb of clean bases and 89.82% of Q30 were obtained, and the average alignment efficiency was 99.45% with an average coverage depth of 62.20× and 99.75% genome coverage. Based on the G prime statistic algorithm(G') method analysis, 16 candidate genomic loci with a total length 20.41 Mb were found to be related to the trait. Of these loci, the most significant regions displaying the highest elevated G' values were found in chromosome 06 at a position of 18.53–22.67 Mb, and chromosome 19 at genomic region intervals of 8.36–10.94, 12.06–13.79 and 18.45–20.26 Mb. These regions were then used to identify the key candidate genes. In these regions, 250 predicted genes were found and analyzed to obtain 90 significantly enriched(P<0.05) Gene Ontology(GO) terms. Based on ANNOVAR analysis, 50 genes with non-synonymous and stopgained mutations were preferentially selected as potential candidate genes. Of those 50 genes, following their gene annotation functions and high significant haplotype variations in various environments,five genes were identified as the most promising candidate genes regulating soybean seed carotenoid accumulation, and they should be investigated in further functional validation studies. Collectively, understanding the genetic basis of carotenoid pigments and identifying genes underpinning carotenoid accumulation via a bulked-segregant analysis-based sequencing(BSA-seq) approach provide new insights for exploring future molecular breeding efforts to produce soybean cultivars with high carotenoid content.
基金supported by the Open Project of Key Laboratory,Xinjiang Uygur Autonomous Region(2023D04070)the Agricultural Science and Technology Innovation Program of CAAS(CAAS-CSCB-202403)。
文摘Pre-harvest sprouting(PHS)or vivipary is a major problem affecting cereal quality and grain quantity and is primarily linked to the dysregulation of abscisic acid(ABA)biosynthesis in plants.Therefore,elucidating the molecular mechanisms governing seed dormancy is crucial for developing strategies to improve crop productivity.In this study,we identified a novel viviparous maize mutant,viviparous-like 5(vp-like5),which exhibits precocious germination in developing seeds.Through map-based cloning,we discovered that ZmCNX6,which encodes a small subunit of molybdopterin synthase essential for molybdenum cofactor(MoCo)biosynthesis,is the causal gene responsible for the vp-like5 phenotype.Biochemical assays have demonstrated significantly reduced activities of MoCo-dependent enzymes,including aldehyde oxidase(AO),xanthine dehydrogenase(XDH),and nitrate reductase(NR),in vplike5.AO is essential for the ABA biosynthesis,and the observed ABA deficiency in vp-like5 likely drives the viviparous phenotype.Expression analysis showed that ZmCNX6 was stably expressed during seed development,indicating its significant role in seed development.Furthermore,overexpression of ZmCNX6 not only enhanced the activities of MoCo-dependent enzymes but also improved drought tolerance in maize.Collectively,our study revealed ZmCNX6 as a multifunctional hub coordinating MoCo metabolism,ABA-dependent dormancy regulation,and abiotic stress responses,offering a potential target for simultaneously mitigating vivipary and improving drought resistance in maize.
基金supported by the Nanfan special project,CAAS(YBXM2408)the Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-CSIAF-202303)to Huihui Li+1 种基金a grant from Sanya Municipal Program for Science and Technology Innovation(2022KJCX87)the Nanfan special project,CAAS(YBXM2319),to Jun Zhao。
文摘Despite its negative impacts on plant functioning,climate change benefits plants at the cellular level.For example,the stimulation of C3 photosynthesis by elevated CO_(2)can increase N2 fixation by 73%and grain yield by 10%–11%.The global elevated atmospheric CO_(2)concentration has already decreased the nitrogen content in C3 crop species and C3 woody vegetation by 14%and 21%,respectively,regardless of added nitrogen fertilizer.^(15)N-feeding experiments have shown that,after 19 h under elevated CO_(2),the^(15)N concentration in the stems,roots plus rhizomes,and whole plants of Scirpus olneyi(S.olneyi)decreased by 51%,63%,and 74%,respectively.Moreover,S.olneyi showed reduced NH_(4)^(+)assimilation under elevated CO_(2),which decreased the amino acid contents in the stems by 25.6%for glycine and 65.0%for serine,and that in the roots plus rhizomes by 2%for gamma-aminobutyric acid(GABA)and 80%for glutamate.Wheat grain protein has also been found to decrease by 7.4%under elevated CO_(2)due to reductions in threonine,valine,iso-leucine,leucine,and phenylalanine.The mineral nutrient contents in grains of rice and maize were similarly found to decrease under high CO_(2)by 1.0%and 7.1%for phosphorus,7.8%and 2.1%for sulfur,5.2%and 5.8%for iron,3.3%and 5.2%for zinc,10.6%and 9.9%for copper,and 7.5%and 4.2%for manganese,respectively.In general,mineral concentrations in C3 plants are predicted to decrease by 8%under elevated CO_(2),while total non-structural carbohydrates(mainly starch and sugars)are expected to increase.These decreases in grain protein,amino acids,and mineral nutrients could double the incidence of global protein-calorie malnutrition and micronutrient deficiency—especially in Africa,where agricultural soils are inherently low in nutrient elements.Additionally,the increase in total non-structural carbohydrates(mainly starch and sugars)in cereal crops could elevate diabetes incidence due to heavy reliance on starchy diets.The negative effects of elevated CO_(2)on rice,maize,and wheat—the world's three major staple crops—suggest an increase in global food insecurity with rising atmospheric CO_(2)concentration.
基金funded by the National Natural Science Foundation of China(31961143007)the Key Research and Development Program of Xinjiang Uygur Autonomous Region,China(2023B02006)+1 种基金the Core Research Budget of the Non-profit Governmental Research Institutions,Institute of Crop Sciences,Chinese Academy of Agricultural Sciences(S2021ZD04 and S2022ZD04)the Natural Science Foundation of Hebei Province,China(C2021205013)。
文摘Large grain is a favorable trait for appearance quality and a large sink potential in wheat breeding.The stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871(ZM871)and its sister line Zhongmai 895(ZM895).Here,a BC_(1)F_6 residual heterozygous line was selected from the cross of a ZM871/ZM895//ZM871 population,and six heterozygous recombinant plants were identified in the BC_(1)F_(7)population from self-pollination of the heterozygous line.QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2(25.3-27.5 Mb)by phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants.Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses.Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS.The gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed,and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population of 166 cultivars using this marker.These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24010205)the CAS Project for Young Scientists in Basic Research(YSBR-011)+1 种基金National Natural Science Foundation of China(32272101)the Agricultural Science and Technology Innovation Program of CAAS。
文摘Small RNAs(sRNAs)are essential for regulating plant growth and development,and they possess the notable ability to travel long distances within organisms to regulate target gene expression.Our study examined the dcl2 mutant,a key enzyme in s RNA biogenesis,to determine the role of the DCL2 protein in s RNA synthesis and to identify mobile s RNAs under DCL2 regulation.Through grafting experiments between dcl2 mutants and wild-type soybean plants,coupled with s RNA sequencing,we identified14,105 s RNAs significantly affected by DCL2 and discovered 375 mobile s RNAs under its regulation.Degradome analysis provided deeper insights into the regulatory effects of these mobile s RNAs on their target genes,enabling us to understand their potential influences on plant development and stress responses.Leveraging the systemic movement of s RNAs from roots to shoots,we propose a novel strategy for manipulating gene expression in aboveground tissues.Overall,our research findings not only deepen our understanding of the complex regulatory networks involving mobile s RNAs regulated by DCL2,but also provide a new strategy for gene regulation,which could have a positive impact on agricultural biotechnology.
基金supported by the Key Research and Development Program of Ningxia Hui Autonomous Region,China(Grant No.2023BCF01010)the National Natural Science Foundation of China(Grant No.32201765)+2 种基金the Key Research and Development Program of Shandong Province,China(Grant No.2019-GNC106107)the Science and Technology Innovation Program of Chinese Academy of Agricultural Sciencesthe National Crop Germplasm Resources Center,China(Grant No.NCGRC-2023-02).
文摘A genome-wide association study(GWAS)was conducted on a collection of 166 Chinese rice mini-core germplasms to investigate cold tolerance traits across various rice growth stages.Population structure analysis revealed that these accessions could be categorized into six subgroups,consistent with their geographical origins.
基金supported by National Key R&D Program of China(2022YFD1200801)National Natural Science Foundation of China(31991224 and U2002202)+3 种基金Jiangsu Research and Development Program(BE2021360)the Natural Science Foundation of Jiangsu Province,China(BK20200023)the Fundamental Research Funds for the Central Universities(ZJ22195020)the Jiangsu Collaborative Innovation Center for Modern Crop Production.
文摘Heterosis,also known as hybrid vigor,is commonly observed in rice crosses.The hybridization of rice species or subspecies exhibits robust hybrid vigor,however,the direct harnessing of this vigor is hindered by reproductive isolation.Here,we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids.This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species,emphasizing the essential role of mitochondria in this process.Additionally,we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes,elucidating their significant contribution to reproductive isolation.Furthermore,our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice.Building on these advances,we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.
基金supported by grants from Scientific Innovation 2030 Project (C.W,2022ZD0401703)National Key Research and Development Program of China (2021YFD1200700)+2 种基金National Natural Science Foundation of China (32372082)China Agriculture Research System (CARS-02-03)Innovation Program of Chinese Academy of Agricultural Sciences.
文摘Genotyping arrays based on single nucleotide polymorphisms(SNPs)provide a low-cost,highthroughput platform.The development of a SNP array that fully reflects the genetic diversity of maize(Zea mays L.)germplasm and is applicable to molecular breeding programs is desirable.In this study,we developed a MaizeGerm50K array comprising 50,852 SNPs selected from the resequencing data of 1604 maize inbred lines and other markers.A genome-wide association study using a landrace panel genotyped with the array permitted mapping of several known genes.We also verified a candidate gene,RNA-binding motif protein 24-like 1(ZmRBM24L1),delaying flowering through overexpression lines.Genomic selection for yield and agronomic traits showed high prediction accuracy.The MaizeGerm50K array is thus a valuable genomic tool for maize genetic studies and breeding.
基金supported by grants from the National Natural Science Foundation of China(32272079 and 32060474)the Yunnan Provincial Science and Technology Department,China(202101AS070001 and 202201BF070001-011)。
文摘Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.
基金supported by grants from the National Natural Science Foundation of China (31971891)the Guangxi Key Research and Development Projects, China (GuikeAB21238004)+1 种基金the Scientific Innovation 2030 Project, China (2022ZD0401703)the Modern AgroIndustry Technology Research System of Maize, China (CARS-02-03)。
文摘The crown root system is the most important root component in maize at both the vegetative and reproductive stages. However, the genetic basis of maize crown root traits(CRT) is still unclear, and the relationship between CRT and aboveground agronomic traits in maize is poorly understood. In this study, an association panel including 531 elite maize inbred lines was planted to phenotype the CRT and aboveground agronomic traits in different field environments. We found that root traits were significantly and positively correlated with most aboveground agronomic traits, including flowering time, plant architecture and grain yield. Using a genome-wide association study(GWAS)coupled with resequencing, a total of 115 associated loci and 22 high-confidence candidate genes were identified for CRT. Approximately one-third of the genetic variation in crown root was co-located with 46 QTLs derived from flowering and plant architecture. Furthermore, 103 (89.6%) of 115 crown root loci were located within known domestication-and/or improvement-selective sweeps, suggesting that crown roots might experience indirect selection in maize during domestication and improvement. Furthermore, the expression of Zm00001d036901, a high-confidence candidate gene, may contribute to the phenotypic variation in maize crown roots, and Zm00001d036901 was selected during the domestication and improvement of maize. This study promotes our understanding of the genetic basis of root architecture and provides resources for genomics-enabled improvements in maize root architecture.
基金We are grateful for the funding from STI 2030-Major Projects(2023ZD0406802)the National Natural Science Foundation of China(32072066,32172050,3220151460)+2 种基金Hainan Yazhou Bay Seed Lab(B21HJ0215)CAAS Agricultural Science and Technology Innovation Program(CAAS-ZDRW202002,CAAS-ZDRW202201)Hebei Natural Science Foundation(C2021205013).
文摘Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we identify a wheat TaPRR95 gene by genome-wide association studies to be associated with plant height.Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height,particularly the peduncle,with an earlier heading date.The longer peduncle is mainly caused by the increased cell elon-gation at its upper section,whilst the early heading date is accompanied by elevated expression of flow-ering genes,such as TaFT and TacO1.A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAAVAux genes for auxin signaling inpr95abad plants that may act as a regulatory mechanism to promote robust plant growth.A haplotype analysis identifies a TaPRR95-B haplotype(Hap2)to be closely associated with reduced plant height and increased thousand-grain weight.Moreover,the Hap2 frequency is higher in cultivars than that in landraces,suggesting the artifi-cial selection on the allele during wheat breeding.These findings suggest that TaPRR95 is a regulator for plant height and heading date,thereby providing an important target for wheat yield improvement.
基金supported by the National Key Research and Development Project of China(2022YFD1200700)the Crop Varietal Improvement and Insect Pests Control by Nuclear Radiation,Innovation Program of Chinese Academy of Agricultural Sciences,and the China Agriculture Research System(CARS-03).
文摘Flag leaf angle is one of the key target traits in high yield wheat breeding.A smaller flag leaf angle reduces shading and enables plants to grow at a higher density,which increases yield.Here we identified a mutant,je0407,with an 84.34%-89.35%smaller flag leaf angle compared with the wild type.The mutant also had an abnormal lamina joint and no ligule or auricle.Genetic analysis indicated that the ligule was controlled by two recessive genes,which were mapped to chromosomes 2AS and 2DL.The mutant allele on chromosome 2AS was named Tafla1b,and it was fine mapped to a 1 Mb physical interval.The mutant allele on chr.2DL was identified as Taspl8b,a novel allele of TaSPL8 with a missense mutation in the second exon,which was used to develop a cleaved amplified polymorphic sequence marker.F3 and F4 lines derived from crosses between Jing411 and je0407 were genotyped to investigate interactions between the Tafla1b and Taspl8b alleles.Plants with the Tafla1b/Taspl8a genotype had 58.41%-82.76%smaller flag leaf angles,6.4%-24.9%shorter spikes,and a greater spikelet density(0.382 more spikelets per cm)compared with the wild type.Plants with the Tafla1a/Taspl8b genotype had 52.62%-82.24%smaller flag leaf angles and no differences in plant height or spikelet density compared with the wild type.Tafla1b/Taspl8b plants produced erect leaves with an abnormal lamina joint.The two alleles had dosage effects on ligule formation and flag leaf angle,but no significant effect on thousand-grain weight.The mutant alleles provide novel resources for improvement of wheat plant architecture.
基金supported by the National Key Research and Development Program of China (2021YFD1201603,2023YFD1202900)the Key Research and Development Program of Shandong Province (Agricultural Seed Improvement Project) (ZDYF2023LZGC001)+1 种基金the Key Research and Development Program of Hainan Province (ZDYF2022XDNY135)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (ASTIP No.CAAS-ZDRW202407,01-ICS-02).
文摘MicroRNAs(miRNAs)are versatile regulators of gene expression at both the transcription and posttranscription levels.The microRNA miR396 plays vital roles in growth,development,and resistance to abiotic stresses in many plant species.However,the roles and functions of miR396 in soybeans are not well understood.Here,we report that Gm-miR396a influences soybean development and salinity tolerance.We found that soybean miR396a was responsive to salt stress.Gm-miR396a gene-edited lines(miR396a-GEs),created using CRISPR/Cas9,exhibited more branches,higher grain yields,and greater salinity tolerance than control plants.The transcripts in lines with altered abundance of miR396a-GE were significantly enriched for biological processes related to hormone regulation.Overexpression of the Gm-miR396a precursor(pre-miR396a-OE)resulted in developmental deficiencies including dwarfness,abnormal inflorescences and flowers,smaller and fewer seeds,and small leaves with larger and more numerous stomata.Transcriptome analysis indicated photosynthesis-related genes were downregulated in pre-miR396a-OE plants.These results contribute valuable insights into the function of GmmiR396a in soybeans and hold promise for enhancing soybean yield and salinity tolerance through germplasm innovation.
基金supported by the National Key Research and Development Program of China(2023YFD1200403 and 2023YFF1000600)the Innovation Program of Chinese Academy of Agricultural Sciences。
文摘Wheat(Triticum aestivum L.)is an important staple food crop in the world and supplies about 20%of human caloric and protein consumption(Giraldo et al.,2019;Xiao et al.,2022).Wheat production accounts for~30%of global cereal crops(Li et al.,2019).With the global population increasing and the frequency of natural disasters rising,enhancing wheat yield is crucial to meet food demand.Spike traits such as increased grain number per spike are key determinants of wheat yield.Pre-harvest sprouting(PHS)is a significant natural disaster that severely impacts grain yield and end-use quality of wheat(Tai et al.,2021,2024).
基金supported by grants from the Biological Breeding-National Science and Technology Major Project(2024ZD04077)the National Natural Science Foundation of China(31801323)+1 种基金the Innovation Program of the Chinese Academy of Agricultural Sciencesthe Science and Technology Innovation Project of the Shandong Academy of Agricultural Sciences(CXGC2023F14)。
文摘Endodermal cells and starch-accumulating amyloplasts are well-known gravity sensors initiating shoot gravitropism in Arabidopsis thaliana.The transcription factors SHR and SGR1 regulate endodermal cell formation,while PGM has been demonstrated to regulate starch biosynthesis within chloroplasts,which eventually leads to starch accumulation in amyloplasts.However,the molecular mechanisms of gravity sensing in monocot shoots remain largely unexplored.In this study,we investigated the roles of these genes in rice(Oryza sativa),a model monocot,using CRISPR-Cas9 to generate single,double,and higher-order mutants.The rice genome harbors two orthologs each of SHR and SGR and a single ortholog of PGM.Our results revealed that single mutants of OsPGM,but not OsSHR or OsSGR,showed compromised shoot gravitropism.However,double mutants shr1shr2 and sgr1sgr2 displayed wider tiller angles and reduced gravity sensing,suggesting functional redundancy within each gene pair.Higher-order mutants exhibited progressively severe phenotypes,with quintuple mutants almost unresponsive to gravity stimulation.These findings suggest that these genes act additively through distinct but converging pathways in shoot gravitropism regulation.This study provides novel insights into the molecular mechanisms underlying gravity sensing in monocots and offers valuable knowledge for precision breeding to optimize rice architecture.
基金supported by the National Natural Science Foundation of China(32101759,32241042)the National Key Research and Development Program of China(2023YFD1200700 and 2023YFD1200704).
文摘Foxtail millet(Setaria italica)is an important crop and an emerging model plant.Photoperiodic flowering is a key determinant of its production and geographic expansion.In this study,we found that SiPRR37 is responsible for the major quantitative trait locus(QTL)Heading date 2(Hd2)identified in 680 foxtail millets using a genome-wide association study.Overexpression of SiPRR37 in foxtail millet significantly delayed the heading date under both natural long-day and short-day conditions.CRISPR/Cas9-induced Siprr37 mutants exhibited earlier flowering in long-day conditions but later flowering in short-day conditions.The critical day length(CDL)for the reversal of Siprr37’s function was around 14.3 h.Haplotype analysis revealed that accessions with the Tc1-Mariner transposon insertion in SiPRR37(Hap 1)flowered significantly earlier at higher latitudes,and later at lower latitudes,indicating that natural variants of SiPRR37 exert dual functions in flowering regulation according to geographic latitude.The gradual,successive decrease in the frequency of Hap 2 from low to high latitudes,with the concurrent increase of Hap 1,demonstrates that these haplotypes have undergone artificial selection.Further FST analysis demonstrated that SiPRR37 has contributed to the ecological adaption of foxtail millet.Additionally,we reveal that OsPRR37 promotes flowering in rice,while GmPRR37 may only inhibit flowering in soybean.Further diurnal expression and transgenic analyses suggest that the dual function of SiPRR37 might depend on SiHd1.Our study uncovered the distinct functional reversal of SiPRR37 and functional diversification of PRR37 homologs in SD crops.These findings not only enrich knowledge about the regulation of photoperiodic flowering,but also contribute to genetic improvement of crops’regional adaptability.
基金supported by the grants from National Key Research and Development Program of China(2023YFD2303300)China Agriculture Research System(CARS-02-15)the Agricultural Science and Technology Innovation Program(CAAS-ZDRW202004).
文摘The unreasonable application of nitrogen fertilizer poses a threat to agricultural productivity and the environment protection in Northeast China.Therefore,accurately assessing crop nitrogen requirements and optimizing fertilization are crucial for sustainable agricultural production.A three-year field experiment was conducted to evaluate the effects of planting density on the critical nitrogen concentration dilution curve(CNDC)for spring maize under drip irrigation and fertilization integration,incorporating two planting densities:D1(60,000 plants ha^(-1))and D2(90,000 plants ha^(-1))and six nitrogen levels:no nitrogen(N0),90(N90),180(N180),270(N270),360(N360),and 450(N450)kg ha^(-1).A Bayesian hierarchical model was used to develop CNDC models based on dry matter(DM)and leaf area index(LAI).The results revealed that the critical nitrogen concentration exhibited a power function relationship with both DM and LAI,while planting density had no significant impact on the CNDC parameters.Based on these findings,we propose unified CNDC equations for maize under drip irrigation and fertilization integration:Nc=4.505DM-0.384(based on DM)and Nc=3.793LAI-0.327(based on LAI).Additionally,the nitrogen nutrition index(NNI),derived from the CNDC,increased with higher nitrogen application rates.The nitrogen nutrition index(NNI)approached 1 with a nitrogen application rate of 180 kg ha^(-1)under the D1 planting density,while it reached 1 at 270 kg ha^(-1)under the D2 planting density.The relationship between NNI and relative yield(RY)followed a“linear+plateau”model,with maximum RY observed when the NNI approached 1.Thus,under the condition of drip irrigation and fertilization integration in Northeast China’s spring maize production,the optimal nitrogen application rates for achieving the highest yields were 180 kg ha^(-1)at a planting density of 60,000 plants ha^(-1),and 270 kg ha^(-1)at a density of 90,000 plants ha^(-1).The CNDC and NNI models developed in this study are valuable tools for diagnosing nitrogen nutrition and guiding precise fertilization practices in maize production under integrated drip irrigation and fertilization systems in Northeast China.
基金funded by the National Natural Science Foundation of China(32272186)the Beijing Natural Science Foundation,China(6242031)+5 种基金the Basal Research Fund of the Chinese Academy of Agricultural Sciences(CAAS)(S2022QH04)the National Key R&D Program of China(2022YFD1201500)the Young Elite Scientists Sponsorship Program by China Association for Science and Technology(YESS,2020QNRC001)the Modern Cold and Drought Characteristic Agricultural Seed Industry Research Project-2025,Gansu Province,China(ZYGG-2025-8)the Nanfan Special Project,CAAS(YBXM2303)the Science and Technology Innovation Program of CAAS。
文摘Black point is a black discoloration of the grain embryo that reduces the grain quality and commodity grade.Identifying the underlying genetic loci can facilitate the improvement of black point resistance in wheat.Here,262 recombinant inbred lines(RILs)from the cross of Zhongmai 578/Jimai 22 were evaluated for their black point reactions in fve environments.A high-density genetic linkage map of the RIL population was constructed with the wheat 50K single nucleotide polymorphism(SNP)array.Six stable QTLs for black point resistance were detected,QBp.caas-2A,QBp.caas-2B1,QBp.caas-2B2,QBp.caas-2D,QBp.caas-3A,and QBp.caas-5B,which explained 2.1-28.8%of the phenotypic variances.The resistance alleles of QBp.caas-2B1 and QBp.caas-2B2 were contributed by Zhongmai 578 while the others were from Jimai 22.QBp.caas-2B2,QBp.caas-2D and QBp.caas-3A overlapped with previously reported loci,whereas QBp.caas-2A,QBp.caas-2B1 and QBp.caas-5B are likely to be new.Five kompetitive allele-specifc PCR(KASP)markers,Kasp_2A_BP,Kasp_2B1_BP,Kasp_2B2_BP,Kasp_3A_BP,and Kasp_5B_BP,were validated in a natural population of 165 cultivars.The fndings of this study provide useful QTLs and molecular markers for the improvement of black point resistance in wheat through marker-assisted breeding.
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金supported by the STI 2030-Major Projects(2023ZD0406903)the National Natural and Science Foundation of China(32272182)+1 种基金the Postdoctoral Fellowship Program of CPSF(GZC20241955)the Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(CAAS).
文摘High molecular weight glutenin subunits(HMW-GS),major components of seed storage proteins in wheat,have large effects on processing quality.GLU-1 genes encode HMW-GS and their expression is mainly controlled at the transcriptional level by interactions between cis-regulatory elements and transcription factors.We previously identified an Aux/IAA transcription factor TaIAA10-6D that bound to a conserved cis-regulatory module CCRM1-1,the most essential conserved cis-regulatory module in GLU-1.Here,we confirmed the binding of TaIAA10-6D to CCRM1-1 using yeast one hybrid and dualluciferase reporter assays.The enhanced expression of TaIAA10-6D suppressed glutenin accumulation and increased gliadin content.Dynamic transcriptome analyses revealed that TaIAA10-6D overexpression down-regulated glutenin and gliadin genes during an early stage of grain filling,but up-regulated gliadin genes during a late stage probably by endoplasmic reticulum stress,accounting for its effect on the tradeoff between glutenin and gliadin.Rheological property and processing quality assays showed that TaIAA10-6D overproduction reduced stabilization time and bread quality,but enhanced cookie quality.Overexpression of TaIAA10-6D also reduced plant height,leaf size,kernel number and grain yield.We identified two major haplotypes of TaIAA10-6D,Hap I and Hap II,and developed a breeding-friendly diagnostic marker.Hap I conferred higher expression of TaIAA10-6D and concomitantly reduced plant height and kernel number,but had little effect on grain yield,contributing to lodging resistance without yield penalty.Hap I was subjected to positive selection in breeding.The findings provide a useful gene for wheat improvement and broaden insights into the regulatory machinery underpinning auxin-mediated quality formation,plant morphogenesis and yield gain.
