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Genome wide association studies (GWAS) were carried out to map Quantitative Trait Loci (QTL) associated with element contents in the grain using 336 spring barley. Of the elements analyzed, Fe content ranged from 21.9 to 91.0 mg kg−1, Zn from 10.4 to 54.5 mg kg−1, Ba from 0.2 to 8.9, Ca from 186.4 to 977.5, Cu from 1.5 to 9.8, K from 353.2 to 7721.5, Mg from 1049.8 to 2024.2, Mn from 8.1 to 22.9, Na from 55.9 to 627.9, P from 2272.9 to 5428.8, S from 880.7 to 1898.0, Si from 19.1 to 663.2, and Sr from 0.35 to 2.62 mg kg−1. GWAS were carried out using 6519 SNP markers and multiple elements in MLM:PCA + K model in TASSEL software. Population analyses showed two sub-populations, primarily based on row types. GWAS for row types showed association with INTERMEDIUM-C, a modifier gene for lateral spikelet fertility in the 4H chromosome, validating current GWAS approach. GWAS also showed that 2 QTL for Ba, 2 for Ca, 4 for Cu, 11 for Fe, 2 for K, 3 for Mg, 6 for Mn, 4 for Na, 3 for S, 5 for Si, and 3 for Zn were mapped in barley chromosomes. The QTL identified in the current study are valuable for breeding nutrient dense barley cultivars in the future, especially Zn and Fe. 相似文献
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Phenolic acids are major components of cell walls in wheat and have important implications on human health as antioxidants with anti-tumor activity. Our objectives were to identify phenolic acid genes in wheat by single nucleotide polymorphisms (SNPs) detected within the coding sequences of candidate genes, and to identify chromosomal regions associated with single phenolic acids and total soluble phenolic compounds. A set of candidate genes involved in the biosynthesis of hydroxycinnamic acid derivatives were identified by comparative genomics. SNPs found in the coding sequences of six genes (PAL1, PAL2, C4H, C3H, COMT1 and COMT2) were used to determine their chromosomal location and accurate map position on two reference consensus linkage maps. The genome-wide association study (GWAS), based on genotyping a tetraploid wheat collection with 81,587 gene-associated SNPs, detected 22 quantitative trait loci (QTL) distributed on almost all durum wheat chromosomes. Two QTL for p-coumaric acid were coincident with the phenylalanine ammonia-lyase (PAL2) and p-coumarate 3-hydroxylase (C3H) genes on chromosome arms 2AL and 1AL, respectively. The availability of candidate gene-based markers can allow elucidating the mechanism of phenolic acids accumulation in wheat kernels and exploiting the genetic variability of phenolic acids content for the nutritional improvement of wheat end-products. 相似文献
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Yun Wang Yunlong Pang Kai Chen Laiyuan Zhai Congcong Shen Shu Wang Jianlong Xu 《作物学报(英文版)》2020,(1):119-131
The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection. 相似文献
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小麦茎秆断裂强度相关性状QTL的连锁和关联分析 总被引：3，自引：0，他引：3
小麦茎秆断裂强度与倒伏特性关系密切,并对产量有很大影响。本研究旨在解析茎秆断裂强度的遗传机制,开发与该性状紧密连锁/关联的分子标记。利用山农01-35′藁城9411重组自交系(RIL)群体(含173个F8:9株系)和由205个品种(系)构成的自然群体,借助90 k小麦SNP基因芯片、DArT芯片及传统分子标记技术,在2个环境中对两群体的茎秆断裂强度相关性状进行连锁分析和全基因组关联分析。利用已构建的高密度连锁图谱,在4B染色体的TDURUM_CONTIG63670_287–IACX557和EX_C101685–RAC875_C27536等区段上,检测到9个控制小麦茎秆断裂强度、株高、茎秆第2节间充实度、茎秆第2节壁厚相关性状的加性QTL,可解释表型变异9.40%~36.30%。同时,利用包含24 355个SNP位点的复合遗传图谱,在自然群体中检测到37个与茎秆断裂强度相关性状(P0.0001)的标记,分别位于1A、1B、2B、2D、3A、3B、4A、4B、5A、5B、5D、6B、7A、7B和7D染色体,可解释表型变异7.76%~36.36%。在4B染色体上,以连锁分析检测到控制茎秆断裂强度的RAC875_C27536与关联分析检测到的Tdurum_contig4974_355标记,在复合遗传图谱上的距离为6.7 cM,说明该区段存在控制小麦茎秆断裂强度的重要基因。 相似文献
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旨在鉴别影响苏山猪初生体尺和乳头数性状的遗传位点,开发可用于辅助育种的分子标记,为苏山猪生长和繁殖性能的持续选育提供理论基础。本试验对269头苏山猪初生仔猪(出生后24 h内)的体尺和乳头数表型进行测定,并采集耳组织样品。基于全基因组重测序及基因型填充策略,利用全基因组关联分析(genome-wide association study, GWAS)和群体分化指数(fixation index,Fst)的方法挖掘与目的性状强关联位点,并对位置功能候选基因开展GO和KEGG分析,确定最有可能的主效基因。本研究共鉴别到4个候选位点,分布在13、14和X染色体上,其中与初生体尺性状显著关联的位点有2个,与乳头数性状显著关联的位点有2个。本研究筛选出1个与体长性状相关的候选基因ACTA2;1个与胸围性状相关的候选基因COL4A6;3个与乳头数性状相关的候选基因ACTA2、CRTAP和SEPTIN6,为苏山猪初生体尺性状和乳头数性状的遗传改良提供了重要的分子标记。 相似文献
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MO Jiayuan GAO Jiuyu FENG Lingli LI Yueyue TIAN Weilong LIU Xiaoxiao CHENG Feng LIANG Liang LEI Shuqiao WEN Wei LIANG Jing LAN Ganqiu 《中国畜牧兽医》2007,47(12):3965-3975
In order to identify the molecular markers related to alive litter size of Bama Xiang pigs,the genome-wide association study (GWAS) was used to map and screen the candidate genes affecting the alive litter size trait.Ear tissue samples of 297 Bama Xiang pigs with multiple parity records were collected,and DNA was extracted and genotyped by porcine 50K SNP beadchip.After quality control and genotype imputation,the alive litter size of Bama Xiang pigs were GWAS by Tassel.The results showed that the average number born alive per litter of Bama Xiang pigs increased gradually with the increasing of parity in the range of 1-9 parities.A total of 32 816 SNPs were obtained after quality control and filtration.8 SNPs related to alive litter size of Bama Xiang pigs were screened by genome-wide association analysis,which were significant at genome or chromosome level.Based on the enrichment analysis of the coding genes in the region between 500 kb upstream and downstream of the associated significant SNP loci,and the QTL regions and gene functions related to porcine reproductive traits,4 genes (CAPZB,MSH3,CITED2 and HSD17B7) were finally identified to be candidate genes related to alive litter size of Bama Xiang pigs. 相似文献
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Onur Yilmaz Mehmet Kizilaslan Yunus Arzik Sedat Behrem Nezih Ata Orhan Karaca Cengiz Elmaci Ibrahim Cemal 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2022,139(1):26-39
Sheep are considered as a major contributor of global food security. Moreover, sheep preweaning growth traits as well as in vivo carcass composition traits such as ultrasonic measurements of Longissimus dorsi muscle depth (UMD) and back-fat thickness (UFD) are crucially important indicators of meat yield and hot carcass composition. Despite their relative importance for productivity and profitability of a sheep production system, detected QTL for these traits are quite scarce. Therefore, we implemented GWAS for these traits using animal mixed model-based association approach provided by GenABEL in Esme sheep. Three genome-wide and 14 individual chromosome-wide associated SNPs were discovered. As a result, ESRP1, LOC105613082, ZNF641, DUSP5, TEAD1, SMOX, PTPRT, RALYL, POM121C, PHIP, LOC101106051, ZIM3, PEG3, TRPC7, FBXL4, LOC105610397, LOC105616489 and DNAAF2 were suggested as candidates. Some of the discovered genes and involved pathways were already annotated to contribute growth and development in various species including human, mice and cattle. All in all, the results of this study are expected to strongly contribute to shed a light on the underlying molecular mechanisms behind growth and carcass composition traits, with potential implications on studies aiming faster genetic improvement, targeted low-resolution SNP panel designs and genome-editing studies. 相似文献
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【目的】籽粒性状是影响小麦产量的重要因素,通过对小麦籽粒性状进行全基因组关联分析,发掘控制小麦籽粒性状显著位点,为小麦籽粒性状的遗传改良研究提供理论参考。【方法】以在新疆种植的121份小麦为材料,利用小麦50K SNP芯片,对粒长、粒宽、籽粒长宽比、籽粒面积、籽粒周长和千粒重6个性状进行基于混合线性模型MLM（Q+K）的全基因组关联分析。【结果】在不同环境间6个籽粒性状均表现出广泛的表型变异,其中千粒重变异系数最大为13.91%—17.79%,各籽粒性状遗传力为0.85—0.90。多态性信息含量PIC值为0.09—0.38,最小等位基因频率MAF值为0.05—0.50。群体结构分析表明,试验所用自然群体可分为4个亚群。GWAS结果表明,共检测到592个与6个性状显著关联位点（P<0.001）,其中,涉及6个性状的29个SNP在2个及以上的环境中被重复检测到,分布于1A（5）、1B（2）、1D、2A（5）、3B、5A、5D、6B（4）、6D、7B和7D（7）染色体上,解释9.3%—22.7%的表型变异。检测到6个与粒长稳定的关联位点,分布在1A、2A和7D染色体上,解释9.9%—22.7%的表型变异;检测到2个与粒宽稳定的关联位点,分布在3B和5D染色体上,解释9.6%—12.2%的表型变异;检测到6个与籽粒长宽比稳定的关联位点,分布在2A（2）、5A、7B和7D（2）染色体上,解释10.1%—19.4%的表型变异;检测到3个与籽粒面积稳定的关联位点,分布在1A、1B和1D染色体上,解释9.9%—18.2%的表型变异;检测到6个与籽粒周长稳定的关联位点,分布在1A（2）、2A、6D和7D（2）染色体上,解释9.3%—22.6%的表型变异;检测到6个与千粒重稳定的关联位点,分布在1B、2A和6B染色体上,解释9.7%—12.9%的表型变异。挖掘到5个控制小麦籽粒性状一因多效显著关联位点,分布在1A、2A（2）和7D（2）染色体上,解释9.9%—22.7%的表型变异。【结论】本研究材料遗传多样性丰富,在自然群体中共发现29个与6个籽粒性状在2个及以上环境中稳定显著的关联位点。 相似文献
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Progress of genome wide association study in domestic animals 总被引：1，自引：0，他引：1
ABSTRACT: Domestic animals are invaluable resources for study of the molecular architecture of complex traits. Although the mapping of quantitative trait loci (QTL) responsible for economically important traits in domestic animals has achieved remarkable results in recent decades, not all of the genetic variation in the complex traits has been captured because of the low density of markers used in QTL mapping studies. The genome wide association study (GWAS), which utilizes high-density single-nucleotide polymorphism (SNP), provides a new way to tackle this issue. Encouraging achievements in dissection of the genetic mechanisms of complex diseases in humans have resulted from the use of GWAS. At present, GWAS has been applied to the field of domestic animal breeding and genetics, and some advances have been made. Many genes or markers that affect economic traits of interest in domestic animals have been identified. In this review, advances in the use of GWAS in domestic animals are described. 相似文献