小麦胚芽鞘长度QTL定位和GWAS分析

在干旱条件下,小麦(Triticum aestivum L.)适当深播可提高出苗率,胚芽鞘长度决定了小麦播种的最大深度,因此培育长胚芽鞘小麦品种至关重要。为了挖掘控制小麦胚芽鞘长度相关的数量性状位点(quantitative trait loci,QTL),本研究以275份豆麦/石4185重组自交系(recombinant inbred lines,RIL)群体和186份自然群体为材料,根据90K SNP芯片的分型结果,利用3个环境下小麦胚芽鞘长度表型数据进行QTL鉴定。采用完备区间作图法(inclusive composite interval mapping,ICIM)在RIL群体中鉴定到2个稳定的QTL位点,分别位于4BS(30.17~40.59 Mb)和6BL(700.08~703.53 Mb)染色体上,解释表型变异率(PVE)分别为26.29%~28.46%和4.16%~4.36%;全基因组关联分析(GWAS)采用混合线性模型(Mixed linear model,MLM)方法,共鉴定到36个稳定的QTL位点,分别位于1A(3)、1B(3)、1D(2)、2A(1)、3A(2)、3B(2)、4B(11)、5A(1)、5B(3)、6B(4)、7A(2)、7B(2)染色体上,在3个环境中重复检测到的显著关联位点有7个,其中3个位点与已报道的位点重叠或邻近,其他4个位点推测为新位点,分别位于1A(499.03 Mb)、3A(73.06 Mb)、4B(648.74~648.87 Mb)、7A(36.31 Mb)染色体上,预测了5个候选基因(TraesCS1A03G0748300、Rht1、TraesCS4B03G0110000、TraesCS4B03G0112200和TraesCS7A03G0146600)。在两个群体中均鉴定到位于4BS(30.17~40.59 Mb)染色体上的主效QTL位点,该位点的候选基因Rht1已被证实能降低小麦胚芽鞘长度。该研究结果为挖掘控制小麦胚芽鞘长度的基因以及胚芽鞘长度相关性状分子标记辅助选择育种奠定了基础。

基于GWAS模型的邯郸市水资源优化配置研究

近年来邯郸市上游河流入境水量减少,地下水开采总量愈加限制,难以满足不同行业大幅度上升的用水需求,加之南水北调、引黄和引卫工程建设后对一部分行业供水水源的置换,邯郸市水资源短缺问题和供需矛盾越发尖锐复杂。通过分析邯郸市的水资源特点及水利工程分布特征,并对各区县进行水量供需预测,基于GWAS构建了邯郸市多水源、多用户和多目标的水资源优化配置模型。结果显示:邯郸市2025年P=50%保证率的总需水量为3013.01×10^(6)m^(3),总分配水量为2473.97×10^(6)m^(3),缺水率为17.89%;P=75%保证率的总需水量为3434.90×10^(6)m^(3),总分配水量为2498.22×10^(6)m^(3),缺水率为27.27%。缺水主要集中在第一产业。配置结果符合邯郸市的实际用水情况,研究成果可为邯郸市水资源管理提供技术参考。

Combined ATAC-seq,RNA-seq,and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster(Crassostrea ariakensis)

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.

基于GWAS模型的山东省枣庄市水资源优化配置

水资源优化配置是解决水资源与用水户供需矛盾的有效途径。近年来,山东省枣庄市经济社会快速发展,各行业用水需求明显增加。由于上游河流来水量减少和地下水抽取总量的限制,南水北调、引黄、引渭等大量水源被用于替代生活用水和工业用水。为支持山东省枣庄市水资源的动态供需,将输水概括为虚拟水库,并将其引入全基因组关联分析(GWAS)模型。分配结果显示。且由于E、F县供水主要集中由水库供水,因此利用GWAS模型增加水库供水量,优化配置后的水库供水量为573.45 Mm^(3),占总配水量的23.73%。研究成果可为山东省枣庄市水资源配置提供技术参考。

基于GWAS模型的武安市水资源优化配置

为缓解河北武安市水资源供需不平衡的突出矛盾,立足水资源精细化管理的需求,构建了武安市GWAS(general water allocation and simulation)模型,并开展规划年(2025年与2030年)不同情景下武安市各乡镇水资源优化配置研究。结果表明:2025年和2030年,平水情景(P=50%)下模型优化配置水量基本可以满足各乡镇水量需求,枯水情景(P=75%)下各乡镇存在不同程度的缺水情况;全市普遍农业缺水,2025年平枯情景农业缺水率分别为6.45%和44.11%,2030年平枯情景农业缺水率分别为5.05%和42.47%;优化后的供水结构改善效果显著,地下水供水量占比在各规划年平枯情景下均有所下降。

大豆低聚糖优异种质鉴定及GWAS分析

大豆中含有丰富的营养物质和活性物质,其中低聚糖有许多对人体健康有益的功能,大范围的鉴定评价并筛选大豆低聚糖特异种质具有重要的育种意义。本研究利用高效液相色谱法(HPLC,high performance liquid chromatography),测量了包含264份大豆材料的自然群体的蔗糖含量、棉子糖含量、水苏糖含量以及总低聚糖含量。结果表明3种低聚糖中蔗糖占总低聚糖的比例最高,棉子糖占比最低,海南三亚和江苏南京两个环境下大豆的总低聚糖含量范围分别为6.18%~11.46%和4.19%~13.80%,共筛选出不同环境下表现稳定的10份大豆低聚糖特异种质。结合大豆自然群体的低聚糖含量表型数据和基因型数据进行了全基因组关联分析,在不同环境下分别鉴定到与低聚糖显著关联的SNPs,并挖掘目的性状候选基因。本研究为特用大豆品种选育提供了材料支撑,为发掘大豆低聚糖候选基因和开发分子标记提供了较好的基础。

鸡重要性状GWAS分析的研究进展

全基因组关联分析(Genome-wide association study,GWAS)是在关联分析的基础上对全基因组范围内的遗传标记进行检测,用以挖掘复杂疾病与动植物经济性状的相关基因。国内外研究人员对鸡重要经济性状进行GWAS分析,并取得了有效进展。文章在介绍GWAS原理及研究方法的基础上,对GWAS在鸡的体重、产蛋性状、免疫功能、饲料利用率、羽毛颜色、骨骼等重要经济性状的研究进展进行综述,以期为进一步利用GWAS进行鸡的各种性状的遗传基础研究提供参考。

基于GWAS和WGCNA分析挖掘玉米花期相关候选基因

花期是玉米重要性状之一,解析玉米花期的遗传基础,挖掘玉米花期关键基因,对于选育广适玉米品种具有重要意义。在580份玉米自交系构成的自然群体中,3年种植测定散粉期、吐丝期和散粉吐丝间隔期等3个花期性状,利用分布全基因组的31,826个SNPs(single nucleotide polymorphisms)标记进行全基因组关联分析(genome wide association study,GWAS),结合自交系B73的14个不同发育阶段的转录组数据进行权重基因共表达网络分析(weighted gene co-expression network analysis,WGCNA),挑选与玉米开花相关的组织特异性模块和关键基因。GWAS在多环境(2个环境以上)下共定位标记14个,挖掘到潜在候选基因10个,WGCNA挖掘到花期潜在候选基因17个,2种方法共同挖掘到候选基因3个。Zm00001d052180编码一个MADS-box转录因子19,Zm00001d016814编码NAC转录因子133,Zm00001d048082编码MADS-box转录因子8,这些基因主要参与调节花序生长发育。研究结果为解析玉米花期遗传基础及分子机制提供参考。

GWAS在葫芦科作物遗传改良中的研究进展

为推进全基因组关联分析(GWAS,genome-wide association study)在葫芦科瓜类作物重要农艺性状关键遗传变异位点精准挖掘中的应用,文章介绍了GWAS的原理和统计模型,归纳了GWAS在鉴定群体中的遗传变异位点、解析植物代谢机制,并对其在实施精准遗传改良策略中体现出的优势进行了概述,系统梳理了GWAS在西瓜、甜瓜、黄瓜、南瓜等主要葫芦科瓜类作物遗传改良研究中的最新进展,同时对葫芦科作物育种研究中的多组学联合分析和数据库构建进行了展望,以期为葫芦科作物的遗传改良过程中提供更多的依据和参考。

Multiple-model GWAS identifies optimal allelic combinations of quantitative trait loci for malic acid in tomato

Malic acid(MA)is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways.It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to understand MA-mediated biological processes.However,themetabolic accumulation of MA is controlled by complex heredity and environmental factors,making it difficult to predict and regulate the metabolism of MA.In this study,we carried out a genome-wide association study(GWAS)on MA using eight milestone models with two-environment repeats.A series of associated SNP variations were identified from the GWAS,and 15 high-confidence annotated geneswere further predicted based on linkage disequilibrium and lead SNPs.The transcriptome data of candidate geneswere explored within different tomato organs as well as various fruit tissues,and suggested specific expression patterns in fruit pericarp.Based on the genetic parameters of population differentiation and SNP distribution,tomato MA content has been more influenced by domestication sweeps and less affected by improvement sweeps in the long-term history of tomato breeding.In addition,genotype×environment interaction might contribute to the difference in domestication phenotypic data under different environments.This study provides new genetic insights into how tomato changed its MA content during breeding and makes available function-based markers for breeding by marker-assisted selection.

日本沼虾体重和出肉率联合GWAS分析

[目的]定位筛选影响日本沼虾体重及出肉率性状的候选基因。[方法]收集成熟期且表现健康的日本沼虾,记录体重、出肉率,提取DNA进行测序并进行基因分型,获得单核苷酸多态性(Single-nucleotide polymorphisms,SNP)标记数据,利用多性状联合的全基因关联分析(Genome-wide association study,GWAS)方法检验与体重、出肉率性状存在显著相关的SNP位点,根据SNP的物理信息实现候选功能基因的筛选和定位。[结果]联合分析共定位到6个SNP位点,检测效率远高于单一分析的1个SNP,根据6个显著位点共定位到5个候选功能基因,除1个功能未知的新基因外,剩余4个基因都与机体代谢、发育相关。[结论]完成了日本沼虾体重、出肉率性状相关基因的定位,可为日本沼虾生长代谢的基因组水平揭示提供理论基础,也可为日本沼虾的其他数量性状研究提供思路。

Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time

Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic populations.Genome-wide association studies(GWASs)are a powerful tool to detect these alleles of interest(and so QTLs).In this study,we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions.Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups,all formed by accessions with a common origin.One of these groups was formed exclusively by Spanish accessions,while the rest were mainly formed by accessions from China,Italy,France,and the USA.These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases:Asiatic,Mediterranean,Californian,and southern hemisphere.In total,we found 13 independent QTLs for nut weight,crack-out percentage,double kernels percentage,and blooming time.Of the 13 QTLs found,only one had an additive effect.Through candidate gene analysis,we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage,Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage,and Prudul26A000954 as a candidate gene for the QTL found in blooming time.Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Adventitious rooting(AR)is critical to the propagation,breeding,and genetic engineering of trees.The capacity for plants to undergo this process is highly heritable and of a polygenic nature;however,the basis of its genetic variation is largely uncharacterized.To identify genetic regulators of AR,we performed a genome-wide association study(GWAS)using 1148 genotypes of Populus trichocarpa.GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale;to help overcome this limitation,we developed a computer vision system to measure an array of traits related to adventitious root development in poplar,including temporal measures of lateral and basal root length and area.GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power.These analyses yielded a total of 277 unique associations,suggesting that genes that control rooting include regulators of hormone signaling,cell division and structure,reactive oxygen species signaling,and other processes with known roles in root development.Numerous genes with uncharacterized functions and/or cryptic roles were also identified.These candidates provide targets for functional analysis,including physiological and epistatic analyses,to better characterize the complex polygenic regulation of AR.

Breeding design in wheat by combining the QTL information in a GWAS panel with a general genetic map and computer simulation

A large amount of genome-wide association study(GWAS)panels together with quantitative-trait locus(QTL)information associated with breeding-targeted traits have been described in wheat(Triticum aestivum L.).However,the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge.In this study,we first report a general genetic map which was constructed from 44 published linkage maps.It permits the estimation of genetic distances between any two genetic loci with physical map positions,thereby unifying the linkage relationships between QTL,genes,and genomic markers from multiple genetic populations.Second,we describe QTL mapping in a wheat GWAS panel of 688 accessions,identifying 77 QTL associated with 12 yield and grain-quality traits.Because these QTL have known physical map positions,they could be mapped onto the general map.Finally,we present a design approach to wheat breeding by using known QTL information and computer simulation.Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype,trait correlations in simulated progeny populations,and genetic gain of selected progenies.It is possible to simultaneously improve yield and grain quality by suitable parental selection,progeny population size,and progeny selection scheme.Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment,increasing predictability and efficiency in wheat breeding.

甘薯苗期氮高效利用性状的GWAS分析及候选基因的筛选与验证

【目的】解析甘薯氮高效利用的遗传机制,挖掘氮利用性状的关联位点及氮高效候选基因,为甘薯氮高效型分子育种、品种遗传改良提供支持。【方法】以来自世界各地的129个甘薯栽培种为材料,设置缺氮(0 mmol·L^(-1)纯氮)和正常氮(14 mmol·L^(-1)纯氮)处理,采用水培试验对甘薯苗期地上部生物增加量、地下部生物增加量、地上部氮累积量、地下部氮累积量、地上部氮生理利用效率和地下部氮生理利用效率共6个表型性状进行基于混合线性模型(mixed linear model,MLM)的全基因组关联分析(genome-wide association study,GWAS)。根据分析结果确定氮高效候选基因,并对候选基因进行RT-qPCR验证。【结果】6个甘薯苗期氮高效利用性状在正常氮和缺氮处理条件下存在着广泛变异。其中,缺氮处理条件下,地上部生物增加量变异系数最大,为69.5%;地下部氮生理利用效率变异系数最小,为12.1%。除地下部氮生理利用效率外,其他5个性状彼此均显著相关。GWAS定位到与地上部生物增加量、地下部生物增加量、地下部氮累积量和地上部氮生理利用效率4个性状显著关联的134个区段内888个SNP位点。筛选、过滤得到与地上部氮生理利用效率显著关联且可靠性较高的10个区段内的93个SNP标记,基因注释得到6个甘薯氮高效候选基因。RT-qPCR验证认为3个候选基因(itf01g08120.t1、itf01g22030.t1和itf01g22100.t2)分别编码谷氨酸脱氢酶、NPH3蛋白和TIP41-like蛋白,具有进一步研究价值。【结论】在129份甘薯种质资源中共检测到888个与甘薯苗期氮高效利用性状关联的SNP位点,其中,与地上部氮生理利用效率显著相关的SNP位点93个,筛选、鉴定到6个甘薯氮高效利用的候选基因。itf01g08120.t1、itf01g22030.t1和itf01g22100.t2存在进一步研究价值。

大豆籽粒Ve含量的全基因组关联分析

维生素E(Ve)是大豆油中一种天然抗氧化剂,是评价大豆油营养价值的重要指标。本研究利用含有264份的大豆自然群体在2021年和2022年测定了籽粒中α-、γ-和δ-生育酚含量,并进行全基因组关联分析(Genome-wide association study,GWAS)。本研究共检测到199个与大豆Ve含量显著关联的SNP位点,其中9个可在2个环境或者2个性状被重复检测到,分别位于3号、7号、11号、12号、13号、15号、17号和18号染色体上。其中位于7号染色体上的显著关联信号是控制α-生育酚含量的主效位点,可在2年环境中被检测到,表型变异解释率为9.83%。对该位点候选基因进行筛选,获得一个编码myb转录因子的基因Glyma.07G054000,可能是这个位点的效应基因。另外,在12号染色体上得到2个编码γ-生育酚甲基转移酶的基因Glyma.12G014200和Glyma.12G014300,有可能是影响Ve含量的重要基因。本研究结果有助于解析大豆籽粒Ve含量的遗传基础及其调控机制,为大豆品质遗传改良奠定了基础。

大豆叶型性状全基因组关联分析与候选基因鉴定

大豆叶片的形状和垂直分布影响群体冠层结构和光合效率并最终影响大豆的产量。植物叶片大小、形态因着生位置不同而产生差异的现象称为异形叶,虽然异形叶现象在被子植物中广泛存在,但目前关于大豆叶片发育过程中异形叶的调控的研究还很有限。本研究通过对283份大豆种质资源的叶长、叶宽、叶形指数和异形叶指数等叶型相关的性状在江苏南京进行连续2年的考察,利用全基因组关联分析检测到181个叶型性状相关位点,其中能够在2个环境或多个性状中重复检测到的位点18个。利用检测到的与叶型相关的SNP位点,结合基因的表达谱数据、拟南芥中同源基因的功能,鉴定与大豆叶片发育和异形叶形成相关的候选基因。其中在20号染色体的相关位点Chr20:36152820上游发现已知的大豆叶形调控基因Ln(Glyma.20G116200)。此外,在19号染色体的相关位点Chr19:45155943附近鉴定到2个候选基因Glyma.19G192700、Glyma.19G194100,分别被注释为Growth-regulating factor 4(GRF4)和LITTLE ZIPPER 3(ZPR3)基因的同源基因,为阐明大豆异形叶等叶型性状遗传的分子机制奠定了基础。

基于GWAS模型研究的沙颍河生态流量调度浅析

生态流量是保障河流生态环境稳定的关键要素,也是保障国家水安全和建设水生态文明的重要基础。运用“水资源通用配置与模拟软件(GWAS)”对沙颍河流域水资源进行分区配置,以沙颍河燕山水库、白龟山水库等6座大型水库,及槐店闸、李坟闸、颍上闸等7个重要闸口为单元节点,对主要河段生态调度流量调度过程进行模拟。研究结果可为流域管理部门制定生态流量预警调度方案提供可参考的科学手段。

Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens

Most variants associated with complex traits and diseases identified by genome-wide association studies(GWAS)map to noncoding regions of the genome with unknown effects.Using ancestrally diverse,biobank-scale GWAS data,massively parallel CRISPR screens,and single-cell transcriptomic and proteomic sequencing,we discovered 124 cis-target genes of 91 noncoding blood trait GWAS loci.Using precise variant insertion through base editing,we connected specific variants with gene expression changes.We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs.Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits.This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both cis and trans.

娄门鸭胸肌性状相关指标的全基因组关联分析

为寻找与鸭胸肌性状相关的候选基因,鉴定鸭胸肌性状相关分子标记,试验以199只娄门鸭为试验材料,采集血液提取DNA,用基因组重测序方法进行基因分型,利用PLINK 1.90对分型结果进行质控后,采用rMVP软件中的FarmCPU模型对SNPs(Single nucleo⁃tide polymorphisims)与胸宽、胸深、胸肌重和胸肌率4个性状指标做GWAS分析,定位出显著位点。结果显示:与胸宽相关的SNPs位点有4个,位于1、11、18号染色体上;与胸肌重相关的SNPs位点有2个,位于2、3号染色体上;与胸肌率相关的SNPs位点有2个,位于2号染色体上。通过基因功能注释,这些位点对应的胸肌性状候选基因有8个,分别是LOC119715526、RLBP1、ABHD2、KYAT1、SPOUT1、LOC101800569、EVA1A和NOL4。研究表明,在不同染色体上共鉴定到8个与胸肌性状显著相关的SNPs位点,这些位点共涉及8个候选基因。