籽粒百粒重是大豆产量构成三要素之一,百粒重大小决定大豆产量并影响其商品性,百粒重也是大豆遗传改良关键性状。为进一步挖掘籽粒大小相关基因,解析籽粒大小的调控机制。利用碳离子束(Carbon Ion Beam,CIB)辐射野生大豆(ZYD7068),构建...籽粒百粒重是大豆产量构成三要素之一,百粒重大小决定大豆产量并影响其商品性,百粒重也是大豆遗传改良关键性状。为进一步挖掘籽粒大小相关基因,解析籽粒大小的调控机制。利用碳离子束(Carbon Ion Beam,CIB)辐射野生大豆(ZYD7068),构建了200份百粒重变异丰富的野生大豆突变群体。结果表明,群体籽粒百粒重在4.37~16.74 g之间,平均值为7.13 g,突变群体百粒重较野生大豆百粒重提高了4.98倍。对200个突变体采用全基因组测序,共获得184.1亿bp的测序数据,基因组覆盖率68.10%~70.96%。突变主要是单碱基突变(SNP),其中C到T突变占突变总数的40%。对候选SNP基因进行富集分析,突变基因主要富集在Go:0009626(植物超敏反应)、Go:0034050(共生体诱导宿主程序性细胞死亡)、Go:0012501(程序性细胞死亡)、Go:0043680(丝状器)以及Go:0045087(先天免疫反应)等途径。利用全基因组测序获得的SNPs标记,采用MLM模型,对突变群体籽粒百粒重进行全基因组关联分析(Genome-Wide Association GWAS),共检测到71个关联SNPs(-lgP>11),分别位于大豆2、3、5、6、9、10、14、16、18号染色体上,其中5、10号染色体和14号染色体以及18号染色体分别检测到9、21、9、23个SNPs,71个关联SNPs位点涉及33个基因。展开更多
辣椒红色素是目前全球销量最大的纯天然可食用色素,培育高辣椒红色素品种为辣椒产业重要任务。通过对255份一年生栽培种辣椒核心种质的辣椒红素含量进行全基因组关联分析(genome-wide association study,GWAS),在第1、2、3、5、6、8、9...辣椒红色素是目前全球销量最大的纯天然可食用色素,培育高辣椒红色素品种为辣椒产业重要任务。通过对255份一年生栽培种辣椒核心种质的辣椒红素含量进行全基因组关联分析(genome-wide association study,GWAS),在第1、2、3、5、6、8、9、10、11和12号染色体均关联到与辣椒红素含量显著相关的区间,关联区间内共包括93个基因,根据功能注释和转录表达数据预测了3个影响辣椒果实中辣椒红素含量的候选基因。通过对高辣椒红色素材料Pep-340、低辣椒红色素材料Pep-276构建的F2群体进行混合分组分析法-测序(bulked segregant analysis-sequencing,BSA-seq)分析,在第1、3、5和10号染色体定位到与辣椒红色素含量相关区间,其中第3和5号染色体上的定位区间与GWAS分析中的显著相关区间相近或重合;利用这两个区间的In Del分子标记,进行遗传连锁分析,将调控辣椒红色素含量基因定位在3号染色体的q CC3.1,物理位置为22.8~25.9 Mb,其中含有99个基因,根据功能注释和转录组分析,预测了4个影响辣椒果实中辣椒红色素含量的候选基因Capana03g001314、Capana03g001325、Capana03g001334和Capana03g001387。研究结果为调控辣椒中辣椒红色素含量基因精细定位及分子标记辅助选择育种奠定基础。展开更多
为深入挖掘玉米籽粒容重的相关优势基因,以348份包含普通玉米、甜玉米、糯玉米、爆裂玉米等遗传多样性丰富的玉米自交系为关联群体进行全基因组关联分析(Genome-Wide Association Study,GWAS),分别对2022年浙江东阳、2022和2023年海南...为深入挖掘玉米籽粒容重的相关优势基因,以348份包含普通玉米、甜玉米、糯玉米、爆裂玉米等遗传多样性丰富的玉米自交系为关联群体进行全基因组关联分析(Genome-Wide Association Study,GWAS),分别对2022年浙江东阳、2022和2023年海南乐东收获的自交系种子进行容重测定和全基因组关联分析,分析不同品种玉米籽粒容重性状差异,挖掘容重相关位点和控制容重的候选基因。结果表明:浙江东阳和海南乐东的玉米籽粒容重性状指标的频率分布呈单峰型曲线,符合正态分布。利用SNP标记全基因组关联分析,以阈值P>8.7筛选出与玉米籽粒容重性状显著相关的SNP位点,2022年浙江东阳地区筛选出SNP位点146个,2022年海南乐东地区筛选出261个,2023年海南乐东地区筛选出705个,重叠SNP位点共67个,最终在相关SNP位点附近筛选出候选基因14个。其中,同时在浙江东阳(2022年)、海南乐东(2022和2023年)不同环境下均检测到的SNP S3_219692500位于Zm00001d044129(Shrunken2)基因区域,该基因为玉米甜度控制基因,即该基因突变后产生超甜玉米,籽粒皱缩,玉米容重下降。展开更多
为研究哺乳仔猪抗腹泻的遗传因素和通路,通过对640头腹泻仔猪进行采样和统计分析,选取其中600个样本,包括大白猪453头、长白猪105头和杜洛克猪42头进行低深度重测序(1×),对测序结果质控后开展全基因组关联分析(genome-wide associa...为研究哺乳仔猪抗腹泻的遗传因素和通路,通过对640头腹泻仔猪进行采样和统计分析,选取其中600个样本,包括大白猪453头、长白猪105头和杜洛克猪42头进行低深度重测序(1×),对测序结果质控后开展全基因组关联分析(genome-wide association study,GWAS),在大白猪和长白猪中分别筛选出42个和107个显著SNPs,这些位点上下游20 kb区域分别涉及32个和82个基因,对这些基因进行GO和KEGG富集分析,最终分别确定了6个(PLA2G4A、C1RL、PTPN6、C1R、PPP1R12A和GRID2)和8个(DAPK1、TMC8、ITM2C、CHMP4B、CAST、PDE4D、HSPA4和GRID2)可能与哺乳仔猪腹泻性状相关的重要候选基因,其中GRID2在大白猪和长白猪中同时被筛选到。结果表明,仔猪腹泻性状候选基因与细胞凋亡、免疫、细胞屏障和物质的跨膜运输相关功能有关。展开更多
大豆种子的耐储藏性是决定储藏种子发芽势和发芽率的重要因素,对农业生产和食品加工具有重要意义。通过测定879份大豆种质自然条件下储藏3.5年种子的发芽势和发芽率,利用全基因组关联研究(genome-wide association study,GWAS),检测到5...大豆种子的耐储藏性是决定储藏种子发芽势和发芽率的重要因素,对农业生产和食品加工具有重要意义。通过测定879份大豆种质自然条件下储藏3.5年种子的发芽势和发芽率,利用全基因组关联研究(genome-wide association study,GWAS),检测到58个显著性SNP位点,其中1个SNP位点与发芽势显著相关,57个SNP位点与发芽率显著相关。这些显著相关的SNP位点或孤立或成簇分布在10条不同的染色体上,将位于第2、9和10号染色体成簇分布的SNP位点确认为发芽率相关的3个QTL。其定位区间与5个已知的QTL位点区间重叠并包含2个候选基因Glyma.02g170500和Glyma.09g182900。根据重测序SNP数据对这2个基因进行单倍型分析,结果表明Glyma.02g17050基因的11个标签SNP主要位于非翻译区,可以划分为4个block,其中3个block的不同单倍型间发芽势和发芽率差异显著;Glyma.09g182900具有38个标签SNP,形成一个大的block,共有840个单倍型,因每种单倍型所含的种质数量太少而未能进行单倍型分析。在候选基因Glyma.02g17050的不同block中同时具有高发芽势和高发芽率的优良单倍型拥有黄淮地区来源的种质多于其他地区的种质,地方种质多于栽培种质。本研究结果将为后续培育耐储藏性大豆品种和解析大豆耐储藏遗传机理提供理论基础和技术支持。展开更多
水资源优化配置是均衡水资源与发展的关键措施,能够缓和水资源供需矛盾,促进经济和生态协调发展。通过借助水资源评价方法对海原县水资源开发利用状况进行分析,构建GWAS(General Water Allocation and Simulation Model)配置模型,并进...水资源优化配置是均衡水资源与发展的关键措施,能够缓和水资源供需矛盾,促进经济和生态协调发展。通过借助水资源评价方法对海原县水资源开发利用状况进行分析,构建GWAS(General Water Allocation and Simulation Model)配置模型,并进行规划年(2025年、2035年)海原县水资源优化配置研究,为海原县实现水资源、流域和区域经济社会与生态环境保护协调发展提供理论依据。配置结果显示,在75%的来水条件下规划年(2025年、2035年)可供水量分别达12 706万m^(3)和12 892万m^(3),不能满足用水量的全部配置,建议加强非常规水源的利用,合理配置引黄水和地下水资源,实现县域水资源的优化配置。展开更多
Background Birth weight is a critical economic trait in livestock production.However,its genetic architecture remains poorly understood due to historical limitations in sample size and reliance on low-density SNP arra...Background Birth weight is a critical economic trait in livestock production.However,its genetic architecture remains poorly understood due to historical limitations in sample size and reliance on low-density SNP arrays.In this study,we utilized low-coverage whole-genome sequencing(lcWGS)to genotype 3,007 Hu sheep,bypassing the cost and resolution constraints of conventional genotyping arrays while achieving scalable genome-wide variant detection.Results LcWGS with high imputation accuracy(97.8%allelic concordance)enabled genome-wide association studies(GWAS)identifying two novel quantitative trait loci(QTLs)on chromosomes 6 and 9.The chromosome 9 QTL encompassed a regulatory region functionally linked to PLAG1 expression through expression quantitative trait locus(eQTL)mapping.Compared with wild-type homozygotes,heterozygous carriers of the lead SNP(chr9:g.35920172A>G)presented a 9.85%increase in birth weight(3.35 kg vs.3.68 kg;Δ=0.33 kg).Notably,the derived allele of this SNP exhibited low frequencies of<0.1 across most global sheep breeds except Dorper,highlighting its potential for selective breeding applications.Leveraging lcWGS data,haplotype-based fine-mapping prioritized three candidate causal variants.A secondary QTL on chromosome 6 colocalized with the FecB mutation,a well-established locus associated with increased litter size.Intriguingly,individuals carrying one FecB allele showed a 6.18%reduction(0.22 kg)in birth weight,which tentatively indicates potential pleiotropic influences on both growth and reproductive traits.Conclusion This study demonstrates the utility of lcWGS as a cost-effective,high-resolution tool for dissecting complex traits in livestock.Our findings not only advance the understanding of birth weight genetics in sheep but also offer a blueprint for accelerating genetic improvement programs in global livestock production through costeffective,genome-wide approaches.展开更多
Drought is a major environmental constraint that significantly affects seedling emergence,yield,and quality of Tartary buckwheat,thereby hindering the development of its industry.However,the molecular mechanisms under...Drought is a major environmental constraint that significantly affects seedling emergence,yield,and quality of Tartary buckwheat,thereby hindering the development of its industry.However,the molecular mechanisms underlying drought tolerance genes in Tartary buckwheat remain largely unexplored.Alcohol dehydrogenase(ADH),an essential plant protein,plays a crucial role in growth,development,and stress responses;however,its specific role in drought resistance remains unclear.This study identifies an ADH gene,FtADH1,using a membership function value of drought tolerance(MFVD)combined with a genome-wide association study(GWAS)and transcriptomic profiles that confer drought tolerance in Tartary buckwheat.Our findings demonstrated that the overexpression of FtADH1 in Arabidopsis and Tartary buckwheat hairy roots enhances drought tolerance by promoting root elongation and mitigating elevated levels of reactive oxygen species(ROS).Our findings demonstrate that FtADH1 can enhance drought tolerance in Tartary buckwheat and Arabidopsis.This study identifies FtADH1 as a new regulator of Tartary buckwheat’s ROS levels and stress responses,functioning by regulating protective enzyme activities at a high level to scavenge ROS and modulating root growth under drought stress.Further,it identifies proteins interacting with FtADH1 through a prokaryotic expression pull-down assay combined with mass spectrometry,revealing that FtADH1 interacts explicitly with the S-adenosyl-L-methionine(SAM)synthetase protein,FtSAMS1.Overexpression of FtSAMS1 enhances ADH enzymatic activity,leading to increased SAM content in overexpressing Tartary buckwheat hairy roots under water-deficit conditions.Additionally,overexpression of FtSAMS1 induces a drought-resistant phenotype in Arabidopsis and Tartary buckwheat hairy roots under drought stress,revealing the biological function of FtADH1.Evolutionary analysis indicates that ADH1 in Fagopyrum species has undergone significant evolutionary events,including duplication and purifying selection,which may contribute to functional diversification and adaptive advantages such as drought resistance in cultivated buckwheat.In summary,this study suggests that FtADH1 is a key contributor to drought tolerance,and its interaction with FtSAMS1 offers promising potential for developing drought-resistant varieties in Tartary buckwheat and its relative species.展开更多
Background Semen quality is one of the most important indicators of boar reproductive performance.In the past,boar breeding has mostly emphasized characteristics such as lean meat percentage,feed conversion efficiency...Background Semen quality is one of the most important indicators of boar reproductive performance.In the past,boar breeding has mostly emphasized characteristics such as lean meat percentage,feed conversion efficiency,and growth rate,while overlooking the genetic improvement of reproductive traits.This study employs advanced multi-omics approaches,such as transcriptome-wide association studies(TWAS)and colocalization between genome-wide association studies(GWAS)and expression quantitative trait loci(eQTLs),to provide a comprehensive understanding of the genetic mechanisms governing semen quality traits in boars.Results Here,we collected 190,000 ejaculate records across 11 semen quality traits from 3,604 Duroc boars.The heritability of semen quality traits ranged from 0.095 to 0.343.Genetic correlations between semen quality traits varied from−0.802 to 0.661,and phenotypic correlations ranged from−0.833 to 0.776.Single-trait GWAS identified 19 independent variants,corresponding to 13 quantitative trait loci(QTLs).By integrating PigGTEx and FAANG resources,we combined TWAS and colocalization analyses to reveal genetic regulation of semen quality traits.Notably,both GWAS and colocalization analyses pinpointed the DCAF12 as a crucial gene associated with multiple semen quality traits.Additionally,the ZSCAN9 gene and the variant rs322211455 were found to significantly affect sperm motility(SPMOT),possibly through hypothalamic-pituitary-gonadal axis.PheWAS further highlighted an association between rs322211455 and sperm abnormality rate,demonstrating the crucial role of ZSCAN9 in male fertility.Conclusion This study reveals the genetic basis and regulatory mechanisms underlying semen quality traits in Duroc boars,identifying key candidate genes such as DCAF12 and ZSCAN9.These findings provide important insight into the genetic regulation of semen quality in boars.展开更多
Stem strength is an important indicator of lodging that significantly influences yield and quality in soybean.Therefore,understanding the regulatory mechanisms underlying stem strength is critical for ensuring soybean...Stem strength is an important indicator of lodging that significantly influences yield and quality in soybean.Therefore,understanding the regulatory mechanisms underlying stem strength is critical for ensuring soybean production.However,the genetic basis underlying this trait remains largely elusive.Here,we explored the key loci and regulators of stem strength by integrating quantitative trait locus(QTL)mapping with genome-wide association study(GWAS)using the recombinant inbred line(RIL)population and natural accessions.Finally,a major QTL covering an interval containing 15 genes was identified.One of these genes encodes a transcription factor related to WUSCHEL-related homeobox 4(GmWOX4-like),a high-confidence candidate for regulating stem strength based on bulk transcriptome deep sequencing and single-cell sequencing.Anatomical analysis of residual heterozygous lines(RHLs)suggested that GmWOX4-like may influence stem strength by modulating cambium differentiation through various pathways.Natural variations in the GmWOX4-like promoter region showed significant correlation with stem strength and lodging ratio across the natural population.These findings provide valuable insights into the molecular mechanisms of stem strength and will contribute to marker-assisted selection for stem strength in soybean breeding.展开更多
Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and...Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield components.In this study,a natural population of 201 maize inbred lines was used for genome-wide association analysis,which identified nine SNPs on chromosomes 2,5,8,9,and 10 that were significantly associated with ear leaf type structure.Further verification through qRT-PCR confirmed the association of five candidate genes with these SNPs,with the Zm00001d008651 gene showing significant differential expression in the compact and flat maize inbred lines.Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)databasessuggested that this gene is involved in the glycolysis process.An analysis of the basic properties of this gene revealed that it encodes a stable,basic protein consisting of 593 amino acids with some hydrophobic properties.The promoter region contains stress and hormone(abscisic acid(ABA))related elements.The mutant of this gene increased the first ear leaf angle(eLA)and leaf angle of the first leaf below the first ear(bLA)by 4.96 and 0.97°,respectively,compared with normal inbred lines.Overall,this research sheds light on the regulatory mechanism of ear and leaf structures that influence density tolerance and provides solid foundational work for the development of new varieties.展开更多
Chrysanthemum is rich in active compounds such as flavonoids and phenolic acids,and its dried head flowers are commonly used for tea and medicinal purposes.However,the genetic determinism underlying chrysanthemum acti...Chrysanthemum is rich in active compounds such as flavonoids and phenolic acids,and its dried head flowers are commonly used for tea and medicinal purposes.However,the genetic determinism underlying chrysanthemum active compounds remains elusive.In this study,we evaluated a panel of 137 chrysanthemum accessions for total flavonoids,chlorogenic acid,luteolin,and isochlorogenic acid A across two consecutive years.The four active compounds exhibited considerable variation,with a coefficient of variation ranging from 44.96%to 76.30%.Significant differences were observed in genotype and environments,and the broad-sense heritability was estimated at 0.5-0.63 for all examined traits.Significant pair-wise correlation was found between the four active compounds.Several accessions showing the highest active compounds were figured out for breeding use by integrating the membership function and hierarchical cluster analysis methods.Based on the327042 high-quality SNPs,a genome-wide association study(GWAS)captured 59 significant SNPs for the four active compounds,of which 24elite alleles exhibited pyramiding effects.A total of 18 potential candidate genes were mined,among which evm.model.scaffold_1149.273(QUA1)has one linkage disequilibrium(LD)block corresponding to Hap4 with the highest luteolin content.The findings are beneficial to understanding the genetic basis of the active compounds and provide parental materials and valuable markers for the genetic improvement of active compounds in chrysanthemums.展开更多
文摘籽粒百粒重是大豆产量构成三要素之一,百粒重大小决定大豆产量并影响其商品性,百粒重也是大豆遗传改良关键性状。为进一步挖掘籽粒大小相关基因,解析籽粒大小的调控机制。利用碳离子束(Carbon Ion Beam,CIB)辐射野生大豆(ZYD7068),构建了200份百粒重变异丰富的野生大豆突变群体。结果表明,群体籽粒百粒重在4.37~16.74 g之间,平均值为7.13 g,突变群体百粒重较野生大豆百粒重提高了4.98倍。对200个突变体采用全基因组测序,共获得184.1亿bp的测序数据,基因组覆盖率68.10%~70.96%。突变主要是单碱基突变(SNP),其中C到T突变占突变总数的40%。对候选SNP基因进行富集分析,突变基因主要富集在Go:0009626(植物超敏反应)、Go:0034050(共生体诱导宿主程序性细胞死亡)、Go:0012501(程序性细胞死亡)、Go:0043680(丝状器)以及Go:0045087(先天免疫反应)等途径。利用全基因组测序获得的SNPs标记,采用MLM模型,对突变群体籽粒百粒重进行全基因组关联分析(Genome-Wide Association GWAS),共检测到71个关联SNPs(-lgP>11),分别位于大豆2、3、5、6、9、10、14、16、18号染色体上,其中5、10号染色体和14号染色体以及18号染色体分别检测到9、21、9、23个SNPs,71个关联SNPs位点涉及33个基因。
文摘为深入挖掘玉米籽粒容重的相关优势基因,以348份包含普通玉米、甜玉米、糯玉米、爆裂玉米等遗传多样性丰富的玉米自交系为关联群体进行全基因组关联分析(Genome-Wide Association Study,GWAS),分别对2022年浙江东阳、2022和2023年海南乐东收获的自交系种子进行容重测定和全基因组关联分析,分析不同品种玉米籽粒容重性状差异,挖掘容重相关位点和控制容重的候选基因。结果表明:浙江东阳和海南乐东的玉米籽粒容重性状指标的频率分布呈单峰型曲线,符合正态分布。利用SNP标记全基因组关联分析,以阈值P>8.7筛选出与玉米籽粒容重性状显著相关的SNP位点,2022年浙江东阳地区筛选出SNP位点146个,2022年海南乐东地区筛选出261个,2023年海南乐东地区筛选出705个,重叠SNP位点共67个,最终在相关SNP位点附近筛选出候选基因14个。其中,同时在浙江东阳(2022年)、海南乐东(2022和2023年)不同环境下均检测到的SNP S3_219692500位于Zm00001d044129(Shrunken2)基因区域,该基因为玉米甜度控制基因,即该基因突变后产生超甜玉米,籽粒皱缩,玉米容重下降。
文摘为研究哺乳仔猪抗腹泻的遗传因素和通路,通过对640头腹泻仔猪进行采样和统计分析,选取其中600个样本,包括大白猪453头、长白猪105头和杜洛克猪42头进行低深度重测序(1×),对测序结果质控后开展全基因组关联分析(genome-wide association study,GWAS),在大白猪和长白猪中分别筛选出42个和107个显著SNPs,这些位点上下游20 kb区域分别涉及32个和82个基因,对这些基因进行GO和KEGG富集分析,最终分别确定了6个(PLA2G4A、C1RL、PTPN6、C1R、PPP1R12A和GRID2)和8个(DAPK1、TMC8、ITM2C、CHMP4B、CAST、PDE4D、HSPA4和GRID2)可能与哺乳仔猪腹泻性状相关的重要候选基因,其中GRID2在大白猪和长白猪中同时被筛选到。结果表明,仔猪腹泻性状候选基因与细胞凋亡、免疫、细胞屏障和物质的跨膜运输相关功能有关。
文摘大豆种子的耐储藏性是决定储藏种子发芽势和发芽率的重要因素,对农业生产和食品加工具有重要意义。通过测定879份大豆种质自然条件下储藏3.5年种子的发芽势和发芽率,利用全基因组关联研究(genome-wide association study,GWAS),检测到58个显著性SNP位点,其中1个SNP位点与发芽势显著相关,57个SNP位点与发芽率显著相关。这些显著相关的SNP位点或孤立或成簇分布在10条不同的染色体上,将位于第2、9和10号染色体成簇分布的SNP位点确认为发芽率相关的3个QTL。其定位区间与5个已知的QTL位点区间重叠并包含2个候选基因Glyma.02g170500和Glyma.09g182900。根据重测序SNP数据对这2个基因进行单倍型分析,结果表明Glyma.02g17050基因的11个标签SNP主要位于非翻译区,可以划分为4个block,其中3个block的不同单倍型间发芽势和发芽率差异显著;Glyma.09g182900具有38个标签SNP,形成一个大的block,共有840个单倍型,因每种单倍型所含的种质数量太少而未能进行单倍型分析。在候选基因Glyma.02g17050的不同block中同时具有高发芽势和高发芽率的优良单倍型拥有黄淮地区来源的种质多于其他地区的种质,地方种质多于栽培种质。本研究结果将为后续培育耐储藏性大豆品种和解析大豆耐储藏遗传机理提供理论基础和技术支持。
文摘水资源优化配置是均衡水资源与发展的关键措施,能够缓和水资源供需矛盾,促进经济和生态协调发展。通过借助水资源评价方法对海原县水资源开发利用状况进行分析,构建GWAS(General Water Allocation and Simulation Model)配置模型,并进行规划年(2025年、2035年)海原县水资源优化配置研究,为海原县实现水资源、流域和区域经济社会与生态环境保护协调发展提供理论依据。配置结果显示,在75%的来水条件下规划年(2025年、2035年)可供水量分别达12 706万m^(3)和12 892万m^(3),不能满足用水量的全部配置,建议加强非常规水源的利用,合理配置引黄水和地下水资源,实现县域水资源的优化配置。
基金supported by the Biological Breeding-National Science and Technology Major Project(2022ZD0401403)Shaanxi Provincial Key Research and Development Program(2024NC2-GJHX-15)Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project(2022GD-TSLD-46-0401).
文摘Background Birth weight is a critical economic trait in livestock production.However,its genetic architecture remains poorly understood due to historical limitations in sample size and reliance on low-density SNP arrays.In this study,we utilized low-coverage whole-genome sequencing(lcWGS)to genotype 3,007 Hu sheep,bypassing the cost and resolution constraints of conventional genotyping arrays while achieving scalable genome-wide variant detection.Results LcWGS with high imputation accuracy(97.8%allelic concordance)enabled genome-wide association studies(GWAS)identifying two novel quantitative trait loci(QTLs)on chromosomes 6 and 9.The chromosome 9 QTL encompassed a regulatory region functionally linked to PLAG1 expression through expression quantitative trait locus(eQTL)mapping.Compared with wild-type homozygotes,heterozygous carriers of the lead SNP(chr9:g.35920172A>G)presented a 9.85%increase in birth weight(3.35 kg vs.3.68 kg;Δ=0.33 kg).Notably,the derived allele of this SNP exhibited low frequencies of<0.1 across most global sheep breeds except Dorper,highlighting its potential for selective breeding applications.Leveraging lcWGS data,haplotype-based fine-mapping prioritized three candidate causal variants.A secondary QTL on chromosome 6 colocalized with the FecB mutation,a well-established locus associated with increased litter size.Intriguingly,individuals carrying one FecB allele showed a 6.18%reduction(0.22 kg)in birth weight,which tentatively indicates potential pleiotropic influences on both growth and reproductive traits.Conclusion This study demonstrates the utility of lcWGS as a cost-effective,high-resolution tool for dissecting complex traits in livestock.Our findings not only advance the understanding of birth weight genetics in sheep but also offer a blueprint for accelerating genetic improvement programs in global livestock production through costeffective,genome-wide approaches.
基金supported by the National Natural Science Foundation of China(32372045)the Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province,China(Qiankehezhongyindi(2023)008)the Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions,China(Qianjiaoji(2023)007).
文摘Drought is a major environmental constraint that significantly affects seedling emergence,yield,and quality of Tartary buckwheat,thereby hindering the development of its industry.However,the molecular mechanisms underlying drought tolerance genes in Tartary buckwheat remain largely unexplored.Alcohol dehydrogenase(ADH),an essential plant protein,plays a crucial role in growth,development,and stress responses;however,its specific role in drought resistance remains unclear.This study identifies an ADH gene,FtADH1,using a membership function value of drought tolerance(MFVD)combined with a genome-wide association study(GWAS)and transcriptomic profiles that confer drought tolerance in Tartary buckwheat.Our findings demonstrated that the overexpression of FtADH1 in Arabidopsis and Tartary buckwheat hairy roots enhances drought tolerance by promoting root elongation and mitigating elevated levels of reactive oxygen species(ROS).Our findings demonstrate that FtADH1 can enhance drought tolerance in Tartary buckwheat and Arabidopsis.This study identifies FtADH1 as a new regulator of Tartary buckwheat’s ROS levels and stress responses,functioning by regulating protective enzyme activities at a high level to scavenge ROS and modulating root growth under drought stress.Further,it identifies proteins interacting with FtADH1 through a prokaryotic expression pull-down assay combined with mass spectrometry,revealing that FtADH1 interacts explicitly with the S-adenosyl-L-methionine(SAM)synthetase protein,FtSAMS1.Overexpression of FtSAMS1 enhances ADH enzymatic activity,leading to increased SAM content in overexpressing Tartary buckwheat hairy roots under water-deficit conditions.Additionally,overexpression of FtSAMS1 induces a drought-resistant phenotype in Arabidopsis and Tartary buckwheat hairy roots under drought stress,revealing the biological function of FtADH1.Evolutionary analysis indicates that ADH1 in Fagopyrum species has undergone significant evolutionary events,including duplication and purifying selection,which may contribute to functional diversification and adaptive advantages such as drought resistance in cultivated buckwheat.In summary,this study suggests that FtADH1 is a key contributor to drought tolerance,and its interaction with FtSAMS1 offers promising potential for developing drought-resistant varieties in Tartary buckwheat and its relative species.
基金supported by grants from The Sci-Tech Innovation 2030 Agenda(2023ZD04045)Guangxi Key Research and Development Program(AB241484033).
文摘Background Semen quality is one of the most important indicators of boar reproductive performance.In the past,boar breeding has mostly emphasized characteristics such as lean meat percentage,feed conversion efficiency,and growth rate,while overlooking the genetic improvement of reproductive traits.This study employs advanced multi-omics approaches,such as transcriptome-wide association studies(TWAS)and colocalization between genome-wide association studies(GWAS)and expression quantitative trait loci(eQTLs),to provide a comprehensive understanding of the genetic mechanisms governing semen quality traits in boars.Results Here,we collected 190,000 ejaculate records across 11 semen quality traits from 3,604 Duroc boars.The heritability of semen quality traits ranged from 0.095 to 0.343.Genetic correlations between semen quality traits varied from−0.802 to 0.661,and phenotypic correlations ranged from−0.833 to 0.776.Single-trait GWAS identified 19 independent variants,corresponding to 13 quantitative trait loci(QTLs).By integrating PigGTEx and FAANG resources,we combined TWAS and colocalization analyses to reveal genetic regulation of semen quality traits.Notably,both GWAS and colocalization analyses pinpointed the DCAF12 as a crucial gene associated with multiple semen quality traits.Additionally,the ZSCAN9 gene and the variant rs322211455 were found to significantly affect sperm motility(SPMOT),possibly through hypothalamic-pituitary-gonadal axis.PheWAS further highlighted an association between rs322211455 and sperm abnormality rate,demonstrating the crucial role of ZSCAN9 in male fertility.Conclusion This study reveals the genetic basis and regulatory mechanisms underlying semen quality traits in Duroc boars,identifying key candidate genes such as DCAF12 and ZSCAN9.These findings provide important insight into the genetic regulation of semen quality in boars.
基金supported by the National Natural Science Foundation of China(32322062 and 32441057)the Natural Science Foundation of Shandong Province(ZR2023JQ009)+2 种基金the Agricultural Variety Improvement Project of Shandong Province(2024LZGC010,2024LZGC030)the National Key Research and Development Program of China(2021YFF1001100)the Modern Agro-industry Technology Research System of Shandong Province(SDAIT-28-01,SDAIT-28-06).
文摘Stem strength is an important indicator of lodging that significantly influences yield and quality in soybean.Therefore,understanding the regulatory mechanisms underlying stem strength is critical for ensuring soybean production.However,the genetic basis underlying this trait remains largely elusive.Here,we explored the key loci and regulators of stem strength by integrating quantitative trait locus(QTL)mapping with genome-wide association study(GWAS)using the recombinant inbred line(RIL)population and natural accessions.Finally,a major QTL covering an interval containing 15 genes was identified.One of these genes encodes a transcription factor related to WUSCHEL-related homeobox 4(GmWOX4-like),a high-confidence candidate for regulating stem strength based on bulk transcriptome deep sequencing and single-cell sequencing.Anatomical analysis of residual heterozygous lines(RHLs)suggested that GmWOX4-like may influence stem strength by modulating cambium differentiation through various pathways.Natural variations in the GmWOX4-like promoter region showed significant correlation with stem strength and lodging ratio across the natural population.These findings provide valuable insights into the molecular mechanisms of stem strength and will contribute to marker-assisted selection for stem strength in soybean breeding.
基金supported by the Key Research and Development Project of Heilongjiang Province,China(2022ZX02B01)。
文摘Planting density is a major limiting factor for maize yield,and breeding for density tolerance has become an urgent issue.The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield components.In this study,a natural population of 201 maize inbred lines was used for genome-wide association analysis,which identified nine SNPs on chromosomes 2,5,8,9,and 10 that were significantly associated with ear leaf type structure.Further verification through qRT-PCR confirmed the association of five candidate genes with these SNPs,with the Zm00001d008651 gene showing significant differential expression in the compact and flat maize inbred lines.Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)databasessuggested that this gene is involved in the glycolysis process.An analysis of the basic properties of this gene revealed that it encodes a stable,basic protein consisting of 593 amino acids with some hydrophobic properties.The promoter region contains stress and hormone(abscisic acid(ABA))related elements.The mutant of this gene increased the first ear leaf angle(eLA)and leaf angle of the first leaf below the first ear(bLA)by 4.96 and 0.97°,respectively,compared with normal inbred lines.Overall,this research sheds light on the regulatory mechanism of ear and leaf structures that influence density tolerance and provides solid foundational work for the development of new varieties.
基金supported by the National Key Research and Development Program of China(2022YFD1200504)the National Natural Science Foundation of China(32171857)+2 种基金China Agriculture Research System(CARS-23-A18)The“JBGS”Project of Seed Industry Revitalization in Jiangsu Province(JBGS[2021]094)the Priority Academic Program Development of Jiangsu Higher Education Institutions.
文摘Chrysanthemum is rich in active compounds such as flavonoids and phenolic acids,and its dried head flowers are commonly used for tea and medicinal purposes.However,the genetic determinism underlying chrysanthemum active compounds remains elusive.In this study,we evaluated a panel of 137 chrysanthemum accessions for total flavonoids,chlorogenic acid,luteolin,and isochlorogenic acid A across two consecutive years.The four active compounds exhibited considerable variation,with a coefficient of variation ranging from 44.96%to 76.30%.Significant differences were observed in genotype and environments,and the broad-sense heritability was estimated at 0.5-0.63 for all examined traits.Significant pair-wise correlation was found between the four active compounds.Several accessions showing the highest active compounds were figured out for breeding use by integrating the membership function and hierarchical cluster analysis methods.Based on the327042 high-quality SNPs,a genome-wide association study(GWAS)captured 59 significant SNPs for the four active compounds,of which 24elite alleles exhibited pyramiding effects.A total of 18 potential candidate genes were mined,among which evm.model.scaffold_1149.273(QUA1)has one linkage disequilibrium(LD)block corresponding to Hap4 with the highest luteolin content.The findings are beneficial to understanding the genetic basis of the active compounds and provide parental materials and valuable markers for the genetic improvement of active compounds in chrysanthemums.
