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。

Identification of an Aux/IAA regulator for flesh firmness using combined GWAS and bulked segregant RNA-Seq analysis in watermelon

Watermelon is a highly cultivated fruit crop renowned for its quality properties of fruit flesh.Among various quality factors,fruit flesh firmness is a crucial quality parameter influencing the fruit texture,shelf life and its commercial value.The auxin/indole-3-acetic acid(Aux/IAA)plays a significant role in fruit development and ripening of non-climacteric fruits.However,the regulatory mechanism of Aux/IAA in controlling fruit flesh firmness and ripening in watermelon remains unknown.In this study,we employed an integrative approach combining genome-wide association study(GWAS)and bulked segregant RNA-Seq analysis(BSR-Seq)to identify an overlapping candidate region between 12776310 and 12968331 bp on chromosome 6,underlying an auxin-responsive gene(Aux/IAA)associated with flesh firmness in watermelon.Transcriptome analysis,followed by real-time quantitative reverse transcription PCR(qRT-PCR),confirmed that the expression of Aux/IAA was consistently higher in fruits with high flesh firmness.The sequence alignment revealed a single base mutation in the coding region of Aux/IAA.Furthermore,the concomitant Kompetitive/Competitive allele-specific PCR(KASP)genotyping data sets for F2 population and germplasm accessions identified Aux/IAA as a strong candidate gene associated with flesh firmness.Aux/IAA was enriched in the plant hormone signal transduction pathway,involving cell enlargement and leading to low flesh firmness.We determined the higher accumulation of abscisic acid(ABA)in fruits with low flesh firmness than hard flesh.Moreover,overexpression of Aux/IAA induced higher flesh firmness with an increased number of fruit flesh cells while reducing ABA content and flesh cell sizes.Additionally,the allelic variation in Aux/IAA for soft flesh firmness was found to exist in Citrullus mucosospermus and gradually fixed into Citrullus lanatus during domestication,indicating that soft flesh firmness was a domesticated trait.These findings significantly enhanced our understanding of watermelon fruit flesh firmness and consequently the watermelon fruit quality.

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。

基于GWAS挖掘东北和华东地区薄皮甜瓜白粉病抗性基因相关位点

以东北和华东地区118份薄皮甜瓜种质资源为试材,采用重测序方法,研究了全基因组关联分析(genome-wide association study, GWAS)策略在薄皮甜瓜白粉病抗性基础理论研究上的可行性,以期为丰富薄皮甜瓜白粉病抗性育种材料提供参考依据。结果表明:共获得高质量SNP位点4 460 133个,2种模型筛选与白粉病相关优异等位基因61个。结合功能注释,预测为DPH3抗体蛋白、PPR蛋白、黄酮醇合酶、类甲基酯酶和类DMR6加氧酶蛋白等。主要参与生物合成、氨基酸代谢、信号通路传导、RNA降解和DNA修复等代谢过程。其中,7号染色体上的CsTLP基因在黄瓜霜霉病抗性中起到至关重要的作用;1号染色体上的EFM1可作为逆境响应机制研究及抗逆育种的优良候选基因。

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。

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。

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.

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.

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.

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.

华西牛胴体性状GWAS分析

胴体性状是肉牛生产实践中最重要的经济性状之一。本研究以840头华西牛成年公牛为研究对象,屠宰后分别测量胴体重(CW)、胴体长(CL)、胴体胸深(CD)3个性状的表型值,基于Illumina BovineHD芯片基因分型结果,利用单变量混合线性模型(LMM)和多变量混合线性模型(mvLMM)2种方法进行全基因组关联分析(GWAS),采取Bonferroni方法确定显著性阈值,挖掘影响华西牛胴体性状的显著位点和重要候选基因。结果显示,单性状GWAS分析中仅在CD性状中检测到6个SNPs位点达到染色体显著水平(P<1.65×10^(-6)),注释到5个基因(PDE1C、PPARGC1B、MTX3、RCAN2、DOK6),而在CW与CL 2个性状中没有检测到显著的SNPs位点;多性状GWAS分析结果显示,在CW-CL、CW-CD、CL-CD、CWCL-CD4个组合中分别检测到1、5、2、3个显著关联的SNPs位点,共注释到了4个基因(STXBP5L、PDE1C、PPARGC1B、RCAN2)。通过对华西牛胴体性状进行GWAS分析,综合利用LMM和mvLMM2种分析方法以提高位点检测效力和准确性,最终共找到9个显著关联的SNPs位点及STXBP5L、PDE1C、PPARGC1B、MTX3、RCAN2、DOK66个基因,其中PPARGC1B、RCAN22个基因被不同方法检测到的多个SNPs位点同时注释到,参与体重调节、脂肪细胞增殖和分化等生物过程,以上结果为华西牛胴体性状的改良提供了有效的分子标记。

基于GWAS模型的灌区水资源优化配置研究:以淠史杭灌区为例

针对淠史杭灌区"蓄、引、提、调"相结合的"长藤结瓜"式灌溉系统,为实现灌区间、上下游的优化联合配置,采用GWAS模型,通过划分水资源配置子单元和设置调蓄节点,采用公平性最优和供水缺水率最小作为目标函数,总量控制、供水能力、分质供水等作为约束条件,将水资源优化配置问题模拟为生物进化问题,采用基于精英策略的非支配遗传改进算法求解,建立了适用于淠史杭灌区的水资源优化配置模型。配置结果表明:灌区引水量最大,其次为当地地表水和边界提水站提水,中水和浅层地下水作为补充。通过序列年水资源配置,发现相同频率年在处于不同丰枯年份时,可供水量存在明显差异,因此在进行区域水资源配置时,仅分析50%、80%或90%几个频率年往往不能真实反映可供水情况,需进行长序列调配分析。基准年、2025年和2035年在50%和80%保证率下基本不缺水,灌区水资源可实现基本供需平衡。如遇连续干旱年,90%保证率下缺水较严重,可通过合理开发当地水、新增外调水来降低缺水程度。

馒头色泽与质构性状的GWAS分析

为从分子水平研究控制馒头色泽与质构性状的基因位点,以205份不同小麦品种为实验材料,利用分布于小麦全基因组的24 355个单核苷酸多态性(SNP)标记对馒头色泽与质构性状进行关联分析。结果检测到276个馒头色泽性状显著关联位点,其中23个极显著(P <0. 000 1)关联位点,30个高遗传贡献率位点(R^2>10%),9个位点在2个以上环境中检测到,分布于小麦21条染色体中的13条。检测到23个与馒头质构性状存在显著关联的多效性位点,分布于小麦的15条染色体,本研究所得到的这些标记为结合分子育种技术改良馒头用小麦品种提供了有价值的参考。

斑玉蕈栽培菌株遗传变异与生长速率GWAS分析

以38份斑玉蕈(Hypsizygus marmoreus)种质资源为研究对象,采用全基因组重测序获得供试菌株的SNP(single nucleotide polymorphism)数据,结合在不同温度(10、15、20、25、30℃)下的菌丝生长速率测定结果,开展全基因组关联分析(genome wide association study,GWAS)。结果表明:供试群体分为4大类群;在实验范围内,20、25℃为斑玉蕈适宜生长温度;GWAS分析显示20、25℃分别存在10、14个与生长速率显著关联的SNP位点,其中1个属于潜在功能性SNP位点。

利用GWAS研究母猪繁殖性状的进展

母猪繁殖性状一直是猪的重要性状之一,母猪繁殖性能的高低关乎着养猪场的规模和养猪业的发展。目前利用GWAS(全基因组关联分析)发现影响母猪产仔数、初生重、断奶重和乳头数等繁殖性状的SNP(单核苷酸多态性)位点,进而发现关联的基因已经成为研究热点之一,并且利用GWAS研究母猪的繁殖性状取得了一定的进展。因此,文章主要对利用GWAS研究母猪繁殖性状的进展进行概述。