大豆育成品种农艺性状QTL与SSR标记的关联分析

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。     

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

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。     

新疆陆地棉经济性状优异等位基因位点的遗传解析

【目的】基于SSR(Simple sequence repeat,简单序列)标记展开对陆地棉经济性状的关联分析,挖掘优异等位变异位点,解析新疆陆地棉经济性状的遗传基础,为新疆陆地棉的遗传机理研究和高效的陆地棉分子设计育种提供理论依据。【方法】利用筛选出覆盖棉花全基因组的73对SSR标记对新疆156份陆地棉品种进行多态性扫描;采用R语言绘制boxplot图,利用TASSEL软件进行关联分析,挖掘与产量、纤维品质性状相关联的优异等位变异位点。【结果】通过对6个环境下新疆陆地棉品种的产量、品质相关性状进行关联分析,获得与产量性状相关的等位变异位点10个,表型变异解释率为6.69%～9.88%,平均值为8.43%;与纤维品质性状相关的等位变异位点23个,表型变异解释率为3.73%～13.22%,平均值为7.52%。其中22个QTL(Quantitative trait locus)已被报道,有10个QTL的关联性状与前人研究一致。【结论】新疆陆地棉品种的群体遗传结构简单,连锁不平衡水平低,6个环境条件下表型性状变化趋势较稳定。基于SSR的关联分析,发掘了与产量和纤维品质相关的优异等位变异基因及聚合优异等位基因位点的典型材料。     

大豆根部水压胁迫耐逆指数遗传体系解析

大豆是重要的植物蛋白质和植物油脂来源,干旱是影响大豆产量的重要环境因子之一。为解析大豆耐旱性的遗传基础,本研究在PEG水压胁迫条件下,对由409个家系组成的巢式关联作图群体(具有1个共同亲本的2个重组自交系群体组成)进行叶片脯氨酸含量测定,通过限制性二阶段多位点全基因组关联分析(restrictivetwo-stagemultilocus genome-wide association study,RTM-GWAS),解析了大豆根部水压胁迫耐逆指数(root hydraulic stress tolerance index,RHSTI)的遗传体系。结果表明,在春季和夏季环境下,3个亲本蒙8260(共同亲本)、通山薄皮黄豆甲和正阳白毛平顶在RHSTI上均存在显著差异,其衍生群体RHSTI表型变异丰富,变幅分别为0.11~2.94和0.03~1.93,遗传力分别为97.7%和97.9%;2个环境联合分析发现,家系遗传力和家系与环境互作遗传力分别为37.9%和60.1%,说明群体RHSTI的变异受遗传和环境共同控制。通过RTM-GWAS方法,共检测到45个与RHSTI相关的QTL,分布在大豆18条染色体上,可以解释37.58%的表型变异,其中7个QTL的表型贡献率超过1%,为大贡献位点;这些QTL中,有34个位点与环境存在显著互作,可以解释12.50%的表型变异。结合PEG胁迫下大豆转录组数据,在定位区间500kb范围内共筛选到38个差异表达基因,可归为ABA响应因子、逆境响应因子、转录因子、发育因子、蛋白代谢因子、未知功能和其他等7类,其中逆境响应因子、转录因子和发育因子是最大的3类;其中位于主效位点的6个基因,与ABA响应因子、逆境响应因子、转录因子相关,应为主要候选基因。上述结果表明,大豆耐旱性是一个由多位点、多基因控制的复杂数量性状,且与环境存在互作,遗传基础复杂。研究结果为大豆耐旱性分子育种提供了依据。     

全基因组关联分析在油菜遗传育种中的应用和研究进展

全基因组关联分析(genome-wide association studies,GWAS)是近几年发展起来的解析作物表型多样性遗传基础的有效分析手段。GWAS以连锁不平衡为基础鉴定某一作物群体内农艺性状即表型数据与全基因组基因型数据或候选基因间的具体关系,具有高通量(即在全基因组范围有效检测性状与基因位点的关联性)、精度高和花费时间少等显著优点,其在作物遗传育种中的作用日益凸显。本综述在系统介绍GWAS这种方法的基础上,详尽总结了其在油菜遗传育种中的应用和研究进展、存在的潜在问题及解决途径,以期为进一步利用GWAS进行油菜各种性状遗传基础的研究提供依据和参考。     

基于QTL定位和全基因组关联分析筛选甘蓝型油菜株高和一次有效分枝高度的候选基因

株高和一次有效分枝高度是与甘蓝型油菜结荚层厚度、收获指数紧密关联的重要农艺性状,有关株高的数量性状位点(quantitativetraitlocus,QTL)和全基因组关联分析(genome-wideassociationstudy,GWAS)已有很多报道,但对一次有效分枝高度的QTL和GWAS定位以及候选基因筛选的研究报道较少。本研究利用已构建的高密度遗传连锁图对2016和2017年2个环境的186个株系组成的重组自交系群体株高和一次有效分枝高度及其最佳线性无偏预测(bestlinearunbiasedprediction,BLUP)值进行QTL定位共检测到8个株高的QTL,分别位于A03、A04和A09染色体,单个QTL解释4.60%～13.29%的表型变异,其中位于A04染色体上的QTL(q-2017PH-A04-2和q-BLUP-PH-A04-2)在2017年和BLUP中均被检测到;检测到9个一次有效分枝高度QTL,分别位于A01、A02、A05、A09、C01和C05染色体上,单个QTL解释5.12%～19.10%的表型变异,其中q-2017BH-A09-1、q-BLUP-B...     

中国栽培和野生大豆农艺及品质性状与SSR标记的关联分析 II. 优异等位变异的发掘

在前文研究已检出与农艺品质性状显著关联的SSR位点的基础上, 本文进一步对与性状关联位点的等位变异作解析, 通过将携带某等位变异的所有材料表型均值与携带无效等位基因(null allele)材料表型均值做比较, 估计等位变异的潜在表型效应增量(减量), 进一步利用该信息估计位点增效(减效)等位变异的平均效应, 鉴别出一批农艺品质性状优异位点、等位变异及携带优异等位变异的载体材料。发现在栽培及野生种质中检出的优异等位变异有同、有异、有互补性。发现关联位点正、负效应等位变异均值间有差异, 可根据育种目标性状选择要求, 选取适合的位点及相应等位变异。同一标记位点可与多性状关联, 其等位变异在不同性状间各有其表型效应的方向和大小; 等位变异在相关性状效应上方向、大小的异同解释了性状间正、负相关的遗传原因。关联作图得到的信息可以弥补家系连锁法QTL定位信息的不足, 并直接利用等位变异信息进行亲本选拔、组合选配及后代等位条带辅助选择以提高育种成效。     

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

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。     

中国栽培和野生大豆农艺及品质性状与SSR标记的关联分析Ⅱ.优异等位变异的发掘

在前文研究已检出与农艺品质性状显著关联的SSR位点的基础上,本文进一步对与性状关联位点的等位变异作解析,通过将携带某等位变异的所有材料表型均值与携带无效等位基因（null allele）材料表型均值做比较,估计等位变异的潜在表型效应增量（减量）,进一步利用该信息估计位点增效（减效）等位变异的平均效应,鉴别出一批农艺品质性状优异位点、等位变异及携带优异等位变异的载体材料。发现在栽培及野生种质中检出的优异等位变异有同、有异、有互补性。发现关联位点正、负效应等位变异均值间有差异,可根据育种目标性状选择要求,选取适合的位点及相应等位变异。同一标记位点可与多性状关联,其等位变异在不同性状间各有其表型效应的方向和大小;等位变异在相关性状效应上方向、大小的异同解释了性状间正、负相关的遗传原因。关联作图得到的信息可以弥补家系连锁法QTL定位信息的不足,并直接利用等位变异信息进行亲本选拔、组合选配及后代等位条带辅助选择以提高育种成效。     

太湖流域粳稻两类群体种子活力性状有利等位变异的发掘

发掘粳稻种子活力性状的优异等位变异和携带优异等位变异的载体材料可为培育适于直播的高活力粳稻品种提供遗传信息和育种材料。以太湖流域粳稻94个品种构成的自然群体和粳稻品种秀水79与粳稻恢复系C堡衍生的247个重组自交家系(RIL)群体为试验材料,利用斜板发芽法发芽,调查生长7d的幼苗根长、苗高和干重3个种子活力性状,采用Tassel软件中的GLM方法和Win QTL Cartographer2.5软件中的CIM方法进行种子活力性状的QTL分析,发掘有利等位变异和相应载体品种。结果表明:(1)在太湖流域粳稻自然群体中共检测到11个与种子活力性状相关联的SSR标记位点,共发掘出42个控制种子活力性状的优异等位变异,其中控制根长的17个,控制苗高的13个,控制幼苗干重的12个。携带种子活力性状优异等位变异且效应值较大的载体材料有滇屯502选早、扬稻6号、开青、籼恢429和C堡等。(2)在RIL群体中共检测到9个与种子活力性状相关的QTL,其中2个控制根长,4个控制苗高,3个控制幼苗干重。除控制幼苗干重的qDW-2a的有利等位变异RM525-143bp来自秀水79以外,其余8个位点的有利等位变异均来自C堡。(3)两类群体均在第1染色体上检测到与根长关联的SSR标记位点,均在第2、第8和第11染色体上检测到与苗高关联的位点,均在第2染色体上检测到与幼苗干重关联的位点,且在自然群体中检测到优于和多于家系群体的等位变异。     

Identifying QTL–allele system of seed protein content in Chinese soybean landraces for population differentiation studies and optimal cross predictions

Soybean originated in ancient China has been quickly extended globally as a major protein and oil crop. The QTL–allele constitution of seed protein content (SPC) in the Chinese soybean landrace population (CSLRP) was studied using a representative sample composed of 365 accessions tested under multiple environments and analysed under the novel restricted two-stage multi-locus genome-wide association study (RTM-GWAS) procedure based on 29,121 SNPLDB (single nucleotide polymorphism linkage disequilibrium blocks) markers. The SPC varied from 37.51 to 50.46% among accessions, for which 89 QTLs, each with 2–9 alleles in a total of 255 alleles were identified, accounting for 83.16% of the phenotypic variation covering most of the genetic variation (h²?=?84.31%). The QTL–alleles of the 365 landraces were organized into a 255?×?365 QTL–allele matrix as the compact form of SPC genetic constitution in CSLRP. Of the 89 QTLs, 53 showed significantly differentiated allele frequency distribution patterns among geographic eco-regions (sub-populations). There were 32.09% alleles not common among sub-populations but found only in some sub-populations; new allele(s) emerged on some loci in some respective sub-populations, with Eco-region III showing less but Eco-region VI more emergence. The QTL–allele matrix was also used for prediction of optimal crosses for breeding purpose to reach a 99th percentile potential of up to 54.81%, more than the highest accession (50.46%). From the 89 QTLs, 59 SPC candidate genes involving biological processes, cellular components and molecular functions were annotated. Among them, Glyma18g13574 and Glyma20g21370 were inferred as two of the major SPC genes in the whole genome.     

植物关联分析方法的研究进展

关联分析在人类和动植物遗传研究中的应用日益广泛,新方法及其软件包不断涌现。为对其更好选择和应用,本文综述了关联分析的主要方法及其软件包。首先,介绍了群体结构对关联分析的影响;其次,重点介绍了单位点关联分析、多位点关联分析、上位性和多性状关联分析方法及其软件包;最后,展望了关联分析的发展动向。应当指出,基于群体结构和多基因整体背景控制的全基因组单标记快速扫描算法在目前的实际资料分析中应用较广泛,与其结果互补的是假阳性率较高的非参数方法。但是,今后的方法应当是以多位点模型、环境互作、上位性检验和多个相关性状联合分析为主。这为今后的理论与应用研究提供了有益信息。     

Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping

Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.     

Genetic analysis of plant height using two immortalized populations of “CRI12 × J8891” in Gossypium hirsutum L.

Plant height is an important plant architecture trait that determines the canopy structure, photosynthetic capacity and lodging resistance of upland cotton populations. To understand the genetic basis of plant height for marker-assisted breeding, quantitative trait loci (QTL) analysis was conducted based on the genetic map of recombinant inbred lines (RILs) derived from the cross “CRI12 × J8891” (Gossypium hirsutum L.). Three methods, including composite interval mapping, multiple interval mapping and multi-marker joint analysis, were used to detect QTL across multiple environments in the RILs and in the immortalized F₂ population developed through intermating between RILs. A total of 19 QTL with genetic main effects and/or genetic × environment interaction effects were identified on 15 chromosomes or linkage groups, each explaining 5.8–14.3 % of the phenotypic variation. Five digenic epistatic QTL pairs, mainly involving additive × additive and/or dominance × dominance, were detected in different environments. Seven out of eight interacting loci were main-effect QTL, suggesting that these loci act as major genes as well as modifying genes in the expression of plant height. The results demonstrate that additive effects, dominance and epistasis are all important for the genetic constitution of plant height, with additive effects playing a more important role in reducing plant height. QTL showing stability across environments that were repeatedly detected by different methods can be used in marker-assisted breeding.     

利用籼粳交探讨水稻株高和抽穗期的遗传基础

广亲和基因的发现,克服了籼粳交杂种不育的矛盾,但杂种后代株高过高、抽穗期延迟等问题仍然限制着籼粳亚种间杂种优势的利用。本试验利用一个籼粳交(珍汕97/武育粳2号)双单倍体群体(doublehaploidpopulation,DH系)及其分别与两亲本回交构建的两个回交群体,考查了株高和抽穗期的遗传,将三个群体的表型值和两个回交群体的中亲优势值进行了数量性状位点(quantitativetraitlocus,QTL)检测及效应分析,并对结果进行了比较。2个性状在3个相关群体中一共检测到了21个主效QTL和10个上位性QTL,主效QTL的数目和贡献率都比上位性QTL大,而且,在10个上位性QTL中,发生在2个主效QTL间的互作有3个,主效QTL与背景位点间的互作有6个,2个互补位点间的互作仅有1个,进一步说明了主效QTL在株高和抽穗期遗传中的重要作用。比较加性和非加性QTL的作用,发现加性效应、显性效应和上位性效应是籼粳亚种间杂种株高和生育期变化的共同遗传基础。     

Genome-wide genetic dissection of germplasm resources and implications for breeding by design in soybean

“Breeding by Design” as a concept described by Peleman and van der Voort aims to bring together superior alleles for all genes of agronomic importance from potential genetic resources. This might be achievable through high-resolution allele detection based on precise QTL (quantitative trait locus/loci) mapping of potential parental resources. The present paper reviews the works at the Chinese National Center for Soybean Improvement (NCSI) on exploration of QTL and their superior alleles of agronomic traits for genetic dissection of germplasm resources in soybeans towards practicing “Breeding by Design”. Among the major germplasm resources, i.e. released commercial cultivar (RC), farmers’ landrace (LR) and annual wild soybean accession (WS), the RC was recognized as the primary potential adapted parental sources, with a great number of new alleles (45.9%) having emerged and accumulated during the 90 years’ scientific breeding processes. A mapping strategy, i.e. a full model procedure (including additive (A), epistasis (AA), A × environment (E) and AA × E effects), scanning with QTLNetwork2.0 and followed by verification with other procedures, was suggested and used for the experimental data when the underlying genetic model was usually unknown. In total, 110 data sets of 81 agronomically important traits were analyzed for their QTL, with 14.5% of the data sets showing major QTL (contribution rate more than 10.0% for each QTL), 55.5% showing a few major QTL but more small QTL, and 30.0% having only small QTL. In addition to the detected QTL, the collective unmapped minor QTL sometimes accounted for more than 50% of the genetic variation in a number of traits. Integrated with linkage mapping, association mappings were conducted on germplasm populations and validated to be able to provide complete information on multiple QTL and their multiple alleles. Accordingly, the QTL and their alleles of agronomic traits for large samples of RC, LR and WS were identified and then the QTL-allele matrices were established. Based on which the parental materials can be chosen for complementary recombination among loci and alleles to make the crossing plans genetically optimized. This approach has provided a way towards breeding by design, but the accuracy will depend on the precision of the loci and allele matrices.     

Genomics-assisted breeding in fruit trees

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.     

Selection of soybean elite cultivars based on phenotypic and genomic characters related to lodging tolerance

Soybean lodging can result in serious yield reduction. Detecting the quantitative trait loci (QTL) associated with lodging tolerance for their further application in marker‐assisted selection (MAS) has the potential to enhance soybean breeding efficiency. In this study, a genome‐wide association analysis (GWAS) was performed to identify soybean accessions that could potentially be used to produce lodging‐tolerant varieties, based on the comprehensive evaluation of lodging scores (LS) obtained for the parental cultivar “Tokachi nagaha” and its 137 derived cultivars. Results showed that genotype, environment and genotype × environment interaction significantly influenced LS. Of the 31 significant SNPs identified, 22 were consistently detected in two or more environments and 27 SNPs were located in or close to agronomically important QTL mapped by linkage analysis. Best linear unbiased predictors (BLUPs) of LS tend to decrease with the elite alleles contained by accessions increasing. Some excellent accessions, with lower BLUPs and D_i (stability coefficients) values and more elite alleles, were selected. This study contributed to understand the genetic mechanism of lodging, providing genetic and phenotypic information for MAS.