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中国栽培和野生大豆农艺品质性状与SSR标记的关联分析 I. 群体结构及关联标记 总被引：17，自引：10，他引：17
关联作图是一种利用连锁不平衡(linkage disequilibrium, LD)检测自然群体中基因位点及其等位变异的方法。利用60个SSR标记, 对全国大豆地方品种群体(393份代表性材料)和野生大豆群体(196份代表性材料)的基因组变异进行扫描, 分析两类群体的连锁不平衡位点、群体结构, 并采用TASSEL软件的GLM (general linear model)方法对16个农艺、品质性状观测值进行标记与性状的关联分析。结果表明: (1)在公共图谱上不论共线性的或是非共线性的SSR位点组合都有一定程度的LD, 说明历史上发生过连锁群间的重组; 栽培群体的连锁不平衡成对位点数较野生群体多, 但野生群体位点间连锁不平衡程度高, 随距离的衰减慢。(2) 群体SSR数据遗传结构分析发现, 栽培群体和野生群体分别由9和4个亚群体组成, 亚群的划分与群体地理生态类型相关联, 证实地理生态类型划分有其遗传基础。(3) 栽培群体中累计有27个位点与性状相关; 野生大豆种质中累计有34个位点与性状相关。部分标记在两类群体中都表现与同一性状关联, 检出的位点有一致性, 也有互补性; 一些标记同时与2个或多个性状相关联, 可能是性状相关乃至一因多效的遗传基础; 关联位点中累计有24位点(次)与遗传群体连锁分析定位的QTL一致。 相似文献
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中国野生大豆群体农艺加工性状与SSR关联分析和特异材料的遗传构成 总被引：4，自引：0，他引：4
选用204对SSR标记对全国野生大豆群体(174份代表性样本)的基因组扫描,采用TASSEL软件的GLM (general linear model)方法对百粒重、开花期、成熟期、干豆腐得率、干豆乳得率和耐淹性性状值关联分析,解析与性状关联位点的优异等位变异,鉴别出一批与农艺、加工性状关联的优异等位变异及携带优异等位变异的载体材料;进一步分析极值表型材料的遗传构成。结果表明: (1)累计51个位点(次)与性状关联,有些标记同时与2个或多个性状相关联,可能是性状相关的遗传基础;关联位点中累计16位点(次)与连锁分析定位的QTL一致;(2)与地方品种群体和育成品种群体的关联位点比较,发现野生群体关联位点只有少数与之相同,群体间育种性状的遗传结构有明显差异。(3)与多性状关联的位点其等位变异对不同性状的效应方向可相同可不同,如GMES5532a-A332对百粒重和耐淹性的相对死苗率都是增效效应,而GMES5532a-A344对百粒重是减效效应,对相对死苗率是增效效应;(4)极值表型材料间的遗传构成有很大差异。表型值大的材料携带较多增效效应大的位点等位变异,例如N23349的百粒重是9.08 g,含有4个增效效应较大的位点等位变异;表型值小的材料携带较多减效效应大的位点等位变异,如N23387的百粒重是0.75 g,含有4个减效效应较大的位点等位变异。关联作图得到的信息可以弥补连锁定位信息的不足,尤其是全基因组位点上复等位变异的信息为育种提供了亲本选配和后代等位条带辅助选择的依据。 相似文献
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大豆育成品种农艺性状QTL与SSR标记的关联分析 总被引：15，自引：3，他引：12
利用85个SSR标记,对大豆育成品种群体(190份代表性材料)的基因组进行扫描,在检测群体结构基础上搜索连锁不平衡位点,并采用TASSEL软件的GLM方法对11个大豆农艺性状QTL进行关联分析。结果表明：(1) 在公共图谱上共线性或非共线性的SSR位点组合均广泛存在连锁不平衡(LD),但不平衡程度D′>0.5的组合数只占总位点组合的1.71%,共线位点D′值随遗传距离衰减较快;(2) SSR数据遗传结构分析表明,育成品种群体由7个亚群体组成,矫正后全群体共有45个位点累计136个位点(次)与11个大豆农艺性状QTL关联,其中22个位点(次)与家系连锁定位的QTL区间相重,有43个位点(次) 2年重复出现;(3) 一些标记同时与2个或多个性状关联,可能是性状相关或一因多效的遗传基础;(4) 育成品种群体关联位点与地方品种群体和野生群体只有少数相同,群体间育种性状的遗传结构有相当大差异;(5) 发掘出农艺性状优异等位变异及其载体品种,包括增效最大的产量等位变异Satt347-300 (+932 kg hm-2,中豆26),生物量等位变异Satt365-294(+3 123 kg hm-2,黄毛豆),蛋白质含量等位变异Be475343-198 (+0.41%,淮豆4号),脂肪含量等位变异Satt150-273 (+2.32%,科丰15)等。在此基础上作了设计育种的探讨。 相似文献
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半野生棉棉仁含油量与SSR标记的关联分析 总被引：2，自引：0，他引：2
为探究半野生棉群体材料的遗传变异和群体结构,挖掘与含油量相关的标记位点,利用215对SSR引物,对89份半野生棉自然群体进行遗传多样性、群体结构和亲缘关系分析,并进行棉仁含油量性状与标记的关联分析。结果表明,位点多态信息含量(PIC)为0.0222~0.7390,平均为0.3452;基因型多样性(H′)介于0.0616~1.4412,平均为0.5614。群体结构分析将89份材料分为2个亚群,群体结构简单,遗传变异比较丰富,可以用于半野生棉目标性状的关联分析。应用关联分析,在3个年份环境下重复检测出12个与棉仁含油量显著相关的位点(P0.05),这12个位点可能与含油量性状存在稳定的关联,可为棉仁含油量性状的分子标记辅助选择提供依据,为开展半野生棉其它性状的关联分析提供参考。阔叶棉141平均棉仁含油量为41.90%,为高油份含量品种的遗传改良提供理想材料。 相似文献
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利用陆地棉MAGIC群体定位产量、生育期和株高性状的QTL 总被引：1，自引：0，他引：1
棉花的产量、生育期和株高是重要的农艺性状, 决定着棉花的经济效益和生产方式。为了研究这些性状的遗传基础, 利用8个亲本构建的包含960个株系的陆地棉MAGIC (multi-parent advanced generation inter-cross)群体和SSR标记对这些性状进行关联分析。对产量、生育期和株高共8个相关性状进行了3年3个地点共5个环境的田间试验。经过最佳线性无偏预测(BLUP)综合多环境的表型数据, 发现MAGIC群体比亲本有更丰富的表型变异。8个性状的广义遗传力(H 2)变化范围为0.17~0.71。结合284个SSR标记基因型数据, 利用混合线性模型对产量、生育期和株高相关性状进行关联分析, 分别检测到51、27和9个显著关联的位点, 这些位点都表现出微效性, 表明该陆地棉MAGIC群体在性状位点的挖掘方面具有高效性。检测到20个标记位点或区间控制多个性状, 还发现单株有效铃数、单铃皮棉重、第一果枝节位和株高存在染色体热点区域, 对多性状综合研究或单性状深入挖掘具有重要价值。本研究为后续深入利用MAGIC群体进行遗传研究提供参考, 一些表型优良的材料和关联到的位点为育种改良奠定了基础。 相似文献
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陆地棉中G6主要性状主效和上位性QTL分析 总被引：2，自引：0，他引：2
利用基于混合线性模犁的复合区间作图法对重组近交系(recombinant inbreed line,RIL)"中G6"进行QTL定位,生育期性状共定位了主效QTL位点5个,上位性QTL位点4对,纤维品质性状定位了主效QTL位点1个,上位性QTL位点6对,产量性状定位了主效QTL位点3个,上位性QTL位点5对.其中定位的果枝始节、吐絮期、上半部平均长度、衣分的主效QTL位点均距离最近标记1 cM以下,这有利于在育种实践中主效QTL跟踪检测.定位的霜前花率主效QTL位点具有较高的加性效应和遗传贡献率,应进行QTL精细定位、图位克隆,将会对早熟性育种工作有一定的推动意义.定位的马克隆值、衣分和予指总的遗传贡献率均在30%以上,对性状特征均影响显著.对主效及上位性QTL位点进行遗传效应分析,验证了前人有关数量性状遗传符合主基因与多基因混合遗传的论断,认为此模型是研究数量性状遗传的有效途经;对主效及上位性QTL位点进行A、D亚基因组定位,并对主效及上位性QTL位点在A、D亚基因组上的分布及互作方式进行了详细的分析.全文认为上位性QTL位点和主效QTL位点一样在物种遗传变异和聚合育种中起着重要作用. 相似文献
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宋健 熊亚俊 陈伊洁 徐瑞新 刘康林 郭庆元 洪慧龙 高华伟 谷勇哲 张丽娟 郭勇 阎哲 刘章雄 关荣霞 李英慧 王晓波 郭兵福 孙如建 闫龙 王好让 姬月梅 常汝镇 王俊 邱丽娟 《作物学报》2024,(3):556-575
巢式关联作图(Nested Association Mapping, NAM)群体在作物学遗传与育种研究中具有广泛的应用。本研究在前期大豆种质资源评价基础上,利用35份不同地区来源的代表性种质与中豆41 (公共母本)杂交,构建了一套大豆NAM群体。PCA和聚类分析发现,不同亲本组合的RIL群体基本聚在一起,显示出清晰的遗传结构。利用该NAM群体亲本间花色和种皮色具有显著差异的RIL群体进行全基因组关联分析,定位到1个主要位点qFC13-1与花色显著关联,该位点与W1位点重合;定位到12个位点与种皮色显著相关,其中9个位点为3种以上方法共定位,3个位点为2种方法共定位,包括4个已知位点和8个新位点。研究结果表明,构建的NAM群体适于进行大豆相关性状遗传分析,为大豆复杂性状的遗传解析和育种实践提供了良好的基础材料。 相似文献
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甘蓝型油菜产量及其构成因素的QTL定位与分析 总被引：7，自引：2，他引：7
产量性状是复杂的数量性状, 对种子的单株产量及其构成因素(全株总有效角果数、每角粒数、千粒重)进行QTL定位和上位性分析,确定其在染色体上的位置及其遗传效应,可以探讨油菜杂种优势产生原因,提高育种中对产量性状优良基因型选择的效率,达到提高油菜产量的目的。在双低油菜细胞质雄性不育保持系1141B和双高恢复系垦C1构建的F2作图群体中,运用SRAP、AFLP和SSR三种标记技术构建了一个甘蓝型油菜(Brassica napus L.)的分子标记遗传连锁图谱。共包含244个标记,分布于20个主要连锁群、1个三联体上,图谱总长度为2 769.5 cM。采用Windows QTL Cartographer Version 2.0统计软件及复合区间作图法,对油菜单株产量及其3大构成因素进行QTL定位,共检测到QTLs 16个分布在9个连锁群上,其中第6和13连锁群最多,均有3个。单个QTL解释性状表型变异的0.38%～73.34%。对于同一性状,等位基因的增效作用既来自母本,亦源自父本;采用双向方差分析法对位点间互作及其上位性进行分析,检测到26对影响产量构成性状的上位性互作效应QTL,说明油菜基因组中存在大量控制产量的互作位点,油菜产量性状的上位性存在着多效性,上位性互作包括QTL与非QTL位点,其中以非QTL位点较多。一般互作位点的独立效应值较小,而互作的效应值显著增大,且一般超过两位点独立效应值之和。反映了控制产量性状基因的复杂性。上位性是甘蓝型油菜产量性状杂种优势的重要遗传基础。 相似文献
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为了研究玉米叶型性状的QTL以及它们的上位性效应,本研究以豫82为母本、豫87-1为父本发展而成的一套重组自交系群体为材料,通过一年3点的表型鉴定,利用遍布玉米全基因组的SNP标记,对玉米叶向值、叶夹角、叶长、叶高点长和叶宽5个性状进行QTL定位及上位性效应分析。定位结果表明,5个性状共定位到24个QTL,贡献率6.89%~13.43%,所有主效QTL均与环境没有显著的互作效应。其中,q LA1-1、q LA8-1、q Lf2-1、q Lf5-1、q LOV3-1、q LL2-1、q LL4-1、q LW1-1和q LW3-1的贡献率均在10%以上,说明这些位点对叶型的影响较为重要。上位性效应分析结果表明,共检测有15对上位性互作位点表现出显著性,并且所有的互作位点对都发生在不同染色体之间;多数互作位点对,均发生在未显著性效应的位点之间;所有的上位性互作位点对间的互作效应与环境也无显著的互作效应,这表明叶型相关性状的加性效应和上位性效应,均不受地点间环境条件的影响。本研究为进一步图位克隆相关关键基因及分子标记辅助育种改良玉米株型提供了重要的参考价值。 相似文献
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限制性两阶段多位点全基因组关联分析方法的特点与计算程序 总被引：4，自引：0，他引：4
全基因组关联分析(genome-wide association study, GWAS)的理论及应用是近十几年来国内外数量性状研究的热点, 但是以往GWAS方法注重于个别主要QTL/基因的检测与发掘。为了相对全面地解析全基因组QTL及其等位基因构成, 本研究提出了限制性两阶段多位点GWAS方法(RTM-GWAS, https://github.com/njau-sri/rtm-gwas)。RTM-GWAS首先将多个相邻且紧密连锁的SNP分组, 成为具有多个单倍型(复等位变异)的连锁不平衡区段(SNPLDB)标记, 然后采用两阶段分析策略, 基于多位点复等位变异遗传模型, 在节省计算空间的条件下保障全基因组QTL及其复等位变异检出的精确度。和以往GWAS方法相比, RTM-GWAS以性状遗传率为上限, 能够较充分地检测出QTL及其相应的复等位变异并能有效地控制假阳性的膨胀。由其结果建立的QTL-allele矩阵代表了群体中所研究性状的全部遗传组成。依据这种QTL-allele矩阵的信息, 可以设计最优基因型的遗传组成, 预测群体中最优化的杂交组合, 并用以进行群体遗传和特有与新生等位变异的研究。本研究首先对RTM-GWAS方法的特点和计算程序功能进行说明, 然后通过大豆试验数据说明RTM-GWAS计算程序的使用方法。 相似文献
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Hiroyoshi Iwata Mai F. Minamikawa Hiromi Kajiya-Kanegae Motoyuki Ishimori Takeshi Hayashi 《Breeding Science》2016,66(1):100-115
Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding. 相似文献
13.
Genome‐wide association studies in elite varieties of German winter barley using single‐marker and haplotype‐based methods 
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下载免费PDF全文 Inka Gawenda Patrick Thorwarth Torsten Günther Frank Ordon Karl J. Schmid 《Plant Breeding》2015,134(1):28-39
Genome‐wide association studies (GWAS) became a widely used method to map qualitative and quantitative traits in plants. We compared existing single‐marker and haplotype‐based methods for GWAS with a focus on barley. Based on German winter barley cultivars, four different single‐marker and haplotype‐based methods were tested for their power to detect significant associations in a large genome with a limited number of markers. We identified significant associations for yield and quality‐related traits using the iSelect array with 3886 mapped single nucleotide polymorphism (SNP) markers in a structured population consisting of 109 genotypes. Genome simulations with different numbers of genotypes, marker densities and marker effects were used to compare different GWAS methods. Results of simulations revealed a higher power in detecting significant associations for haplotype‐ than for single‐marker approaches, but showed a higher false discovery rate for SNP detection, due to lack of correction for population structure. Our simulations revealed that a population size of about 500 individuals is required to detect QTLs explaining a small trait variance (<10%). 相似文献
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基于MapGIS和AutoCAD土地开发整理规划的研究 总被引：2，自引：1，他引：1
MapGIS和AutoCAD各具特点,各有优势,已被广泛应用于土地开发整理领域。在土地开发整理规划设计中,灵活运用这2个软件可以准确提取数据信息、充分利用各种数据资源、提高规划设计效率并最终实现数据共享,这对不断提高土地整理技术以及保持耕地总量平衡有着重要意义。笔者从MapGIS与土地利用规划、AutoCAD与规划设计之间的联系入手,分析了实现两者数据共享所需解决的坐标转换和数据共享的问题,并以某土地整理项目为例,介绍分析了MapGIS和AutoCAD在土地整理中的应用,并完成了该项目的土地利用图和土地利用结构表。 相似文献
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遗传标记在核桃属植物遗传多样性研究中的应用 总被引：1，自引：1，他引：0
为了更好地评价利用好中国核桃种植资源,加强核桃育种的基础性研究工作,本文总结归纳了形态学标记、细胞学标记、生化标记和近年来广泛应用的分子标记在核桃种质资源评价中的应用情况,并在此基础上评述了这些标记的应用前景,指出在以后的研究中应开展多种水平遗传标记的关联分析研究,发掘中国栽培、野生群体中与主要育种相关联的遗传标记位点及其等位变异,获取载体材料,以便实现快速育种的目的。 相似文献
16.
In this introductory paper to the special issue on crop model prediction uncertainty, we present and compare the methodological choices in the studies included in this issue, and highlight some remaining challenges. As a common framework for all studies, we define prediction uncertainty as the distribution of prediction error, which can be written as the sum of a bias plus a predictor uncertainty term that represents the random variation due to uncertainty in model structure, model parameters or model inputs. Several themes recur in many of the studies: Use of multi-model ensembles (MMEs) to quantify model structural uncertainty; Emphasis on uncertainty in those inputs related to prediction of regional results or climate change impact assessment; Simultaneous consideration of multiple sources of uncertainty; Emphasis on exploring the variability of uncertainty over space or time; Use of sensitivity analysis techniques to disaggregate the separate contributions to prediction uncertainty. Relatively new approaches include the estimation of both the bias and predictor uncertainty terms of prediction error, the construction of MMEs specifically designed to explore the uncertainty in model structure, the use of emulators for sensitivity analysis and the exploration of ways to reduce prediction uncertainty other than through model improvement. Major remaining challenges are standardization of approaches to quantifying uncertainty in model structure, parameters and inputs, going beyond studies of specific sources of uncertainty to estimation of overall prediction uncertainty, comparing and combining validation and uncertainty studies, and evaluation of uncertainty estimates. Looking forward, we suggest that assessment of prediction uncertainty should be a standard part of any modelling project. The studies here will contribute toward that goal. 相似文献
17.
The phenotypic analysis of field experiments includes information about the experimental design, the randomization structure
and a number of putative dependencies of environment and design factors on the trait investigated. In QTL studies, the genetic
correlation across environments, which arises when the same set of lines is tested in multiple environments, plays an important
role. This paper investigates the effect of model choice on the set and magnitude of detected root QTL in rice. Published
studies on QTLs for root traits indicate that different results are obtained if varying genetic populations are used and also
if different environmental conditions are included. An experiment was conducted with 168 RILs of the Bala × Azucena mapping
population plus parents as checks under four environmental conditions (low light, low nitrogen, drought and a control environment).
We propose a model that incorporates all relevant experimental information into a composite interval mapping approach based
on a mixed model, which especially considers the correlation of genotypes in different environments. An extensive sequential
model selection procedure was applied based on the phenotypic model, using the AIC to determine an appropriate random structure
and Type 3 Wald F-tests for selection of fixed effects. In a first step we checked whether any of the fixed effects and random
(nested) design effects could be dropped. Secondly, an appropriate covariance structure was chosen for genotype × environment
interaction. In a third step Box-Cox transformations were applied based on residual analysis. We compared profiles of composite
interval mapping scans with and without the inclusion of genotype × environment interaction and the experimental design information.
Some distinct differences in profiles indicate that insufficient modeling of the non-QTL part can lead to an overly optimistic
interpretation of QTL main effects in interval mapping. It is concluded that mixed model QTL mapping offers a reasonable way
to separate environmental and genetic influences in the evaluation of quantitative genes and especially enables a more realistic
assessment of QTL and QTL × environment effects than standard approaches by including all relevant effects. 相似文献
18.
While hybrid breeding is widely applied in outbreeding species, for many self‐pollinating crop plants, it has only recently been established. This may have had its reason in the limitations of methods available for hybrid performance prediction, in particular when established heterotic pools were absent. Genomic selection has been suggested as a promising approach to resolve these limitations. In our review, we briefly introduce the principles of genomic selection as an extension of marker‐assisted selection using genome‐wide high‐density molecular marker data and discuss the advantages and limitations of currently used algorithms. Including the outcome from a recent extended approach to hybrid wheat as a timely example, we summarize current progress in empirical studies on the application of genomic selection for prediction of hybrid performance. Here, we put emphasis on the factors affecting the accuracy of prediction, pointing in particular to the relevance of relatedness, genotype x environment interaction and experimental design. Finally, we discuss future research needs and potential applications. 相似文献
19.
Renganathan Vellaichamy Gandhimeyyan Vanniarajan Chockalingam Raveendran Muthurajan Renuka Raman 《Plant Breeding》2023,142(4):389-406
Millets are known for their resilience and nutritional benefits and hence believed to have a promising role in ensuring food and nutritional security under changing climatic conditions. Research on millets has intensified in recent years, especially in dissecting the genetic components of yield, stress tolerance and nutritional quality traits. Recent advances in next-generation sequencing, bioinformatics and associated statistical procedures for genome-wide association studies (GWAS) have provided wide opportunities to resolve the genetic complexity of polygenic traits by measuring historical and evolutionary recombination events in the natural population(s). During the past decade, GWAS has been successfully employed to identify key genes controlling growth, development, stress tolerance, nutrient use efficiency and nutritional quality traits in sorghum, pearl millet, foxtail millet and finger millet. However, progress in other minor millets is still in its infancy. Genetic dissection of these complex traits in millets may pave the way for genetic alteration of climate resilience, photosynthesis and nutrient accumulation in rice and wheat. In this review, progress in GWAS analysis in detecting QTLs underlying complex traits in sorghum and other millets is highlighted. 相似文献
20.
阿维菌素类药物是一种常用的杀虫剂,现有报道的食品和环境基质样品中阿维菌素残留分析最为常用的检测仪器为液相色谱-串联质谱。基于此,已建立了一系列的不同样基质中多种阿维菌素类药物残留量的检测方法,本研究除了关注常见的多种阿维菌素残留量的测定方法,也关注了食品和环境样品中单种阿维菌素化合物的专一性检测方法。本研究从阿维菌素在食品和环境领域的应用以及赋存状态、前处理方式（提取和净化方法）、检测方法（液相色谱法、酶联免疫法和液相色谱-串联质谱法）及定量方式和基质干扰等方面,综述了2010—2020年不同检测技术在食品和环境样品基质中阿维菌素类化合物残留分析中的研究与应用进展。最后,综述了多残留量检测方法的局限性,未来的关注点以及对阿维菌素残留分析方法的发展趋势。本研究可为开展烟草中阿维菌素类化合物残留分析技术研究提供参考。 相似文献