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31.
基于SNP标记的大麦遗传多样性与群体遗传结构分析 总被引：2，自引：0，他引：2
为了评价大麦种质组合的配制,本研究对384份不同来源大麦种质资源的农艺性状和遗传背景进行分析,并选取了分布于大麦7条染色体上具有多态性的6 454个SNP标记进行群体遗传结构分析,结果表明:(1) 384份参试大麦种质资源的6个农艺性状中,除分蘖数外,其他性状表现基本接近正态分布。6个参试农艺性状统计量指标在环境、基因型、基因型与环境互作效应方面均达到极显著水平(p<0.01)。(2) SNP标记基因分型共分为8种类型。其中A/G类型的最多为2 386个;T/A类型的最少,为104个。平均各条染色体上分布922个,其中4H染色体上最多,为1 288个;1H染色体最少,为642个。(3)遗传结构分析结果显示,384份参试材料分为3个亚群,第1亚群有48份材料,第2亚群有149份材料,第3亚群有187份材料。本研究结果为分子标记辅助育种提供科学依据。 相似文献
32.
甘蓝型油菜每角粒数的全基因组关联分析 总被引：1，自引：0，他引：1
每角粒数是油菜重要的产量构成因子,增加每角粒数有助于提高油菜的籽粒产量。利用Illumina 60K SNP芯片对496份具有代表性的油菜资源进行基因型分析,考察该群体在2个环境中的每角粒数,利用MLM和GLM模型进行全基因组关联分析。结果表明,本群体在2个环境中每角粒数的广义遗传力为57.7%。利用MLM和GLM模型分别检测到9个和20个位点,所有MLM位点均得到GLM结果的验证。6个位点与前人定位的QTL重叠,其中2个位点得到2次验证,其余14个是新位点。在7个位点附近找到了候选基因,其中在C09染色体的位点Bn-scaff155761-p74980附近找到已克隆的油菜每角粒数基因BnaC9.SMG7b,在其余6个位点附近找到GRDP1、SPATULA、HVA22D、DA2等已知的拟南芥每角粒数基因的同源基因。本研究结果有助于解析油菜每角粒数的遗传基础及其调控机制,为每角粒数的遗传改良奠定了基础。 相似文献
33.
干旱是影响大麦产量的主要非生物胁迫之一。挖掘大麦干旱响应基因,有利于大麦耐旱品种的改良。本研究以167份中亚大麦品种为材料,测定正常灌水(出苗期、拔节期、孕穗期、抽穗期、灌浆期各灌水1次)、灌水2次(出苗期、孕穗期各灌水1次)以及灌水1次(出苗期灌水1次)处理下大麦的株高、穗长、单株穗数和主穗小穗数,结合群体分子信息,对这4个性状进行全基因组关联分析(genome-wide association study,GWAS)。结果表明,167份中亚大麦没有明显的地理亚群。全基因组关联分析共鉴定到8个与性状关联的位点,筛选到17个与大麦抗旱性相关的潜在候选基因,其中,调控大麦株高、穗长、主穗小穗数和单株穗数的候选基因分别有7、4、4和2个。同时,对耐旱系数(drought tolerance index,DI)进行GWAS关联分析,鉴定到7个与大麦耐旱相关的QTL,分布在1H、4H、5H和7H染色体上,存在96个潜在候选基因。该研究为后期大麦分子育种和抗旱功能基因克隆提供了基础数据。 相似文献
34.
油菜是修复土壤重金属污染的理想作物,为筛选甘蓝型油菜耐砷性的显著关联单核苷酸多态性位点及相关候选基因,本研究以140份不同来源的甘蓝型油菜自交系为材料,测定和利用油菜60KSNP芯片对正常和砷胁迫条件下的相对根长(RRL)、相对下胚轴长(RHL)和相对鲜重(RFW)进行了全基因组关联分析。结果表明,与RRL、RHL和RFW显著关联的SNP位点分别为15、20和35个,单个SNP位点表型贡献率分别介于13.31%～24.39%、18.04%～33.82%和20.19%～25.06%之间;其中在A02、A07和C02染色体上同时存在与RRL、RHL和RFW显著关联的LD区间。基于油菜基因组信息在LD区间内共筛选到61个可能与砷胁迫相关的候选基因,其中PHT3;3、PHT1;9、GST、OTC5、NRAMP1和ZIP12等与重金属吸收和转运相关。实时荧光定量PCR分析结果表明, PHT3;3和PHT1;9是与甘蓝型油菜砷离子吸收转运相关的重要候选基因。本研究结果对于甘蓝型油菜耐砷胁迫机理的研究、性状的改良具有重要参考价值。 相似文献
35.
Masayuki Takeda Yoshinobu Uemoto Keiichi Inoue Atushi Ogino Takayoshi Nozaki Kazuhito Kurogi Takanori Yasumori Masahiro Satoh 《Animal Science Journal》2020,91(1)
The objectives of this study were to better understand the genetic architecture and the possibility of genomic evaluation for feed efficiency traits by (i) performing genome‐wide association studies (GWAS), and (ii) assessing the accuracy of genomic evaluation for feed efficiency traits, using single‐step genomic best linear unbiased prediction (ssGBLUP)‐based methods. The analyses were performed in residual feed intake (RFI), residual body weight gain (RG), and residual intake and body weight gain (RIG) during three different fattening periods. The phenotypes from 4,578 Japanese Black steers, which were progenies of 362 progeny‐tested bulls and the genotypes from the bulls were used in this study. The results of GWAS showed that a total of 16, 8, and 12 gene ontology terms were related to RFI, RG, and RIG, respectively, and the candidate genes identified in RFI and RG were involved in olfactory transduction and the phosphatidylinositol signaling system, respectively. The realized reliabilities of genomic estimated breeding values were low to moderate in the feed efficiency traits. In conclusion, ssGBLUP‐based method can lead to understand some biological functions related to feed efficiency traits, even with small population with genotypes, however, an alternative strategy will be needed to enhance the reliability of genomic evaluation. 相似文献
36.
Kiri Hayakawa Takayuki Sakamoto Atsushi Ishii Keita Yamaji Yoshinobu Uemoto Nanae Sasago Eiji Kobayashi Naohiko Kobayashi Tamako Matsuhashi Shin Maruyama Hirokazu Matsumoto Kenji Oyama Hideyuki Mannen Shinji Sasazaki 《Animal Science Journal》2015,86(8):737-746
The objective of the current study is to evaluate the association between fatty acid composition and fatty acid synthase gene polymorphisms as responsible mutations. For this purpose, we selected seven previously reported single nucleotide polymorphisms (SNPs) in FASN gene, including one within promoter region (g.841G>C) and six non‐synonymous SNPs (g.8805C>T, g.13126C>T, g.15532A>C, g.16024A>G, g.16039C>T, g.17924A>G), and genotyped them in Japanese Black cattle. Genotyping results revealed that g.8805 C>T and g.17924 A>G were monomorphic loci. Genome‐wide association analysis including the other five SNPs revealed that only g.841G>C showed significant associations with the percentages of C14:0, C14:1, C16:1 and C18:1 at 5% genome‐wide significance level. In order to further evaluate the effect, we genotyped g.841G>C using additional three populations, including two Japanese Black populations and a Holstein cattle population. g.16024A>G was also genotyped and included in the analysis because it has been reported to be associated with fatty acid composition in Japanese Black cattle. In the result of analysis of variance, g.841G>C showed stronger effects on fatty acid percentage than those of g.16024A>G in all populations. These results suggested that g.841G>C would be a responsible mutation for fatty acid composition and contribute to production of high‐grade beef as a selection marker in beef cattle. 相似文献
37.
为了寻找影响鸡(Gallus gallus)繁殖性状的候选基因,本研究利用单核苷酸多态(single nucleotide polymorphism,SNP)芯片分型技术,利用已报道的影响鸡繁殖性状的29个位点对396只京海黄鸡母鸡的29个位点直接进行SNP分型,并对11个繁殖性状进行关联分析。结果发现,29个SNP中,有12个SNP与至少1个繁殖性状关联显著(P0.05),其中有7个SNP同时与2个繁殖性状关联显著(P0.05)。所有繁殖性状中,与京海黄鸡开产体重关联显著的SNP有1个,与京海黄鸡462 d产蛋数关联显著的SNP有2个,与蛋重关联显著的SNP有6个,与开产体重关联显著的SNP有6个,与综合选择指数关联显著的SNP有2个,与后代健雏率关联显著的SNP有1个,没有发现与300 d产蛋数、300~462 d产蛋数和后代孵化率关联显著的SNP。同时,根据这些位点的群体遗传参数发现,12个SNP的平均多态信息含量偏低,说明京海黄鸡有持续选育提高的可能性和必要性。大部分有利基因型为纯合基因型,但有部分基因型为杂合基因型。对与12个SNP最近的功能基因犰狳(Priodontes maximus)重复基因(armadillo repeat gene deleted in velocardiofacial syndrome,ARVCF)、集落刺激因子3受体基因(colony stimulating factor 3receptor,CSF3R)和ODZ同源物2基因(odz,odd Oz/ten-m homolog 2,ODZ2)的功能探讨发现,这些基因可以通过不同的途径影响鸡的繁殖性状。本研究为鸡繁殖性状候选基因的进一步研究提供了基础资料。 相似文献
38.
千粒重是油菜产量构成的重要因素之一。本研究利用高通量SNP芯片对496份具有代表性的油菜种质资源进行基因型分析,考察群体在3个环境(14NJ、15TZ、16TZ)中的千粒重表型,利用混合线性模型(mixed linear model,MLM)和一般线性模型(general linear model,GLM)进行全基因组关联分析。结果表明,本群体在3个环境中千粒重的广义遗传力为63.12%。MLM模型检测到6个显著位点,解释28.92%的表型变异;GLM模型检测到61个显著位点,解释47.08%的表型变异。合并共同位点后得到62个显著位点,联合解释47.31%的表型变异。这些位点分布在基因组所有染色体上,在A07、A03和C06染色体上分别检测到数目最多的9、8和7个位点。其中效应最大的位点Bn-scaff_17526_1-p1066214位于C09染色体,在MLM和GLM模型中表型贡献值分别为5.55%和15.26%。21个位点与前人报道的QTL重叠,其中8个位点得到至少2个群体的验证。其余41个位点为新鉴定的位点,其中多个位点效应高且在多环境中被检测到,如位点Bn-A03-p560769、Bn-scaff_15743_1-p599416和Bn-scaff_15743_1-p590955等。在11个位点附近找到DGAT、EOD3、AGL61、WRI1、DA2、RAV1等拟南芥已报道千粒重基因的同源基因。本研究结果有助于解析甘蓝型油菜千粒重的遗传基础,为研究千粒重的调控机制、指导千粒重的遗传改良奠定基础。 相似文献
39.
Fuminori Kobayashi Tsuyoshi Tanaka Hiroyuki Kanamori Jianzhong Wu Yuichi Katayose Hirokazu Handa 《Breeding Science》2016,66(2):213-225
A core collection of Japanese wheat varieties (JWC) consisting of 96 accessions was established based on their passport data and breeding pedigrees. To clarify the molecular basis of the JWC collection, genome-wide single-nucleotide polymorphism (SNP) genotyping was performed using the genotyping-by-sequencing (GBS) approach. Phylogenetic tree and population structure analyses using these SNP data revealed the genetic diversity and relationships among the JWC accessions, classifying them into four groups; “varieties in the Hokkaido area”, “modern varieties in the northeast part of Japan”, “modern varieties in the southwest part of Japan” and “classical varieties including landraces”. This clustering closely reflected the history of wheat breeding in Japan. Furthermore, to demonstrate the utility of the JWC collection, we performed a genome-wide association study (GWAS) for three traits, namely, “days to heading in autumn sowing”, “days to heading in spring sowing” and “culm length”. We found significantly associated SNP markers with each trait, and some of these were closely linked to known major genes for heading date or culm length on the genetic map. Our study indicates that this JWC collection is a useful set of germplasm for basic and applied research aimed at understanding and utilizing the genetic diversity among Japanese wheat varieties. 相似文献
40.
整合GWAS和WGCNA分析挖掘甘蓝型油菜黄籽微效作用位点 总被引：1，自引：0，他引：1
甘蓝型油菜是世界上最重要的油料作物之一, 黄籽是提高品质的重要育种目标。本研究以520份具有代表性的甘蓝型油菜品种(系)为材料, 结合种子发育过程中8个时期的转录组数据, 采取整合全基因组关联分析(GWAS)和权重基因共表达网络分析(WGCNA)的策略, 挖掘油菜黄籽性状微效作用位点, 2年共检测到199个SNP位点, 在SNP位点附近共挖掘出1826个名义候选基因。利用R语言中的WGCNA软件包构建了8个共表达模块, 基因功能富集分析显示, turquoise模块和blue模块与黄籽表型相关。苯丙烷代谢途径、类黄酮途径的关键基因BnATCAD4、BnF3H以及BnANS为turquoise模块的枢纽基因(hub gene)。通过已知的黄籽相关基因, 挖掘出了一部分黄籽微效作用基因, 这些基因多参与苯丙烷、类黄酮以及原花青素代谢途径。本研究挖掘的这些位点和候选基因可作为影响油菜黄籽形成的重要候选区域和基因, 有助于探究甘蓝型油菜黄籽基因资源信息、揭示油菜黄籽性状的遗传基础和分子机制、丰富分子育种理论以及提高油菜品质。 相似文献