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。     

ICRISAT花生微核心种质农艺性状和黄曲霉抗性关联分析

以国际半干旱热带地区作物研究所(ICRISAT)花生微核心种质146份资源为品种,鉴定农艺性状和黄曲霉抗性,用26对SSR引物检测多态性位点,在分析连锁不平衡、群体结构和Kinship的基础上进行关联分析。连锁不平衡的分布显示R²平均值为0.185,表明26对SSR引物扩增的120个位点之间具有较低的连锁不平衡程度。群体结构分析结果将146份花生品种分为2个亚群,分别对应疏枝亚种和密枝亚种,与植物学分类和遗传分化分析的结果基本一致。关联分析表明,共有39个位点与10个农艺性状(株高、总分枝数、第一分枝数、小叶宽、结果分枝数、百果重、出仁率、单株生产力、种子长、种子宽)相关联,表型变异解释率为1.50%~20.34%,16个SSR位点与黄曲霉侵染病情指数、黄曲霉产毒量相关联,表型变异解释率为5.23%~17.19%,与农艺性状、黄曲霉抗性同时相关联的SSR位点有13个。关联位点的等位变异效应分析表明,10个农艺性状和2个黄曲霉抗性性状共有63个增效等位变异和47个减效等位变异,并发掘了ICG6022等携有优良等位变异的载体品种。     

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。     

大豆遗传群体选择与品质QTL的获得

本文以高油品种哈交97-5404-1为母本,以哈交99-5448-4为父本,建立重组自交系群体.应用SSR技术,对不同世代F2∶3,F2∶6、F2∶9遗传群体中的油份QTL定位进行了分析,不同世代大豆分离遗传群体中油份含量均接近于正态分布,油份含量性状表达偏向于母本哈交97-5404-1,F2∶3代获得了对油份贡献率较高的QTL,F2∶9代则获多个与油份相关的QTL,大豆F2∶3和F2∶9代的遗传群体适宜用做品质性状的QTL定位,不同世代定位的油份QTL,均与SSR位点Satt193有关,通过对来自全国不同品种的SSR进行了分析和方差分析证实,Satt193在第一等位变异下(即DNA片段长度为270 bp)做为油份的筛选标记具有实用性,而在第三等位变异下(即DNA片段长度为220 bp)做为蛋白质材料的筛选标记具有应用性.     

大豆杂种产量相关的位点及等位变异分析

选用来源于中国黄淮和美国的熟期组II~IV的8个大豆品种, 按Griffing方法II设计, 配成28个双列杂交组合, 包括8个亲本共计36份材料。选用300个SSR标记, 对8个大豆亲本进行全基因组扫描, 利用基于回归的单标记分析法, 对大豆杂种产量和分子标记进行相关性分析, 估计等位变异的效应和位点的基因型值, 剖析杂种组合的等位变异。结果表明, 300个SSR标记中有38个与杂种产量显著相关, 分布于17个连锁群上, 其中D1a和M等连锁群上较多, 有8个位于连锁定位的QTL区段内(±5 cM)。单个位点可分别解释杂种产量表型变异的11.95%~30.20%。杂种的位点构成中包括有增效显性杂合位点、增效加性纯合位点、减效加性纯合位点和减效显性杂合位点4部分, 其相对重要性依次递减。从38个显著相关的SSR标记位点中, 遴选出Satt449、Satt233和Satt631等9个优异标记基因位点, Satt449~A311、Satt233~A217和Satt631~A152等9个优异等位变异, 以及Satt449~A291/311、Satt233~A202/207和Satt631~A152/180等9个优异杂合基因型位点。这些结果为理解杂种优势的遗传构成和大豆杂种产量聚合育种提供了依据。     

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。     

亚洲地区中、外大豆品种幼苗期耐淹性与SSR标记的关联分析

利用自然群体进行关联分析是检测目标性状QTL、揭示其遗传基础的有效方法。对国内黄淮和南方地区和东亚、东南亚、南亚291份大豆品种幼苗期耐淹性和64个SSR标记的关联分析结果表明,整个群体由国内和国外2个不同的亚群体组成,2个亚群均存在连锁不平衡。在群体1(国内)中分别检测到相对死苗率、相对失绿率、相对萎蔫率的关联位点3、7和12个,群体2(国外)中相应位点6、3和5个;多个位点兼与2个或者3个耐淹性状关联;部分关联位点与连锁定位结果一致。在2个群体中分别筛选出3个耐淹性状减效最大(最耐淹)的优异等位变异24个和22个。相对死苗率优异等位变异在黄淮、南方地区5个主要系谱中分布不同,育种轮次间有波动。结合基因型和耐性表现,从国内材料中优选出合豆2号、黔豆3号、诱变31、南农493-1,从国外材料中优选出PI208432、PI377576、PI481690等耐淹载体材料,为耐淹育种奠定材料和标记辅助选择育种的基础。     

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。     

小麦南大2419及其衍生品种(系)主要农艺性状的关联分析

筛选与小麦重要农艺性状相关联的SSR标记,对小麦分子标记辅助育种有重要的实践意义.本研究利用多态性较高的80个SSR标记,对南大2419及其71份衍生后代品种(系)进行基因型分析,采用TASSEL软件的MLM (Mixed linear model)方法对籽粒产量、千粒重、有效穗、穗粒数等8个主要农艺性状进行SSR标记...     

Quantitative trait loci for agronomic traits in soybean

There continues to be improvement in seed yields of soybean by conventional breeding, but molecular techniques may provide faster genetic gains. The objective of this study was to identify quantitative trait loci (QTL) associated with the agronomic traits seed yield, lodging, plant height, seed filling period and plant maturity in soybean. To achieve this objective, 101 F₆‐derived recombinant inbred lines (RIL) from a population developed from a cross of N87‐984‐16 × TN93‐99 were used. Experiments were conducted in six environments during 2002–2003. Heritability estimates on an entry mean basis from data combined across environments ranged from 0.12 to 0.65 for seed yield and seed filling period, respectively. Composite interval mapping detected one QTL for yield (near Satt076), two for lodging (near Satt225 and Satt593) and four for maturity (near Satt263, Satt292, Satt293 and Satt591) in this population. Additional environmentally sensitive QTL for these traits, and for seed filling period and plant height are also reported. The QTL associated with agronomic traits that we report and the recently released germplasm (PI 636460) from this population may be useful in soybean breeding programmes.     

棉花品种资源群体结构与连锁不平衡分析

用基因组扫描的方法,利用棉花9个连锁群上的79个微卫星标记(Simple sequence repeat,SSR),对收集的204份陆地棉品种(系)组成的品种资源群体进行群体结构和连锁不平衡(Linkage disequilibrium,LD)分析.结果表明:本研究群体可划分为3个群体,其中两个群体分别由3个亚群体组成...     

A quantitative trait locus influencing tolerance to Phytophthora root rot in the soybean cultivar ‘Conrad’

‘Conrad’, a soybean cultivar tolerant to Phytophthora root rot (PRR), and ‘OX760-6-1’, a breeding line with low tolerance to PRR, were crossed. F₂ derived recombinant inbred lines were advanced to F₆ to generate a population through single-seed descent. This population was used to identify quantitative trait loci (QTLs) influencing PRR tolerance in ‘Conrad’. A total of 99 simple sequence repeat (SSR), or microsatellite, markers that were polymorphic and clearly segregated in the F₆ mapping population were used for QTL detection. Based on the data of PRR in the field at two planting locations, Woodslee and Weaver, for the years 2000 and 2001, one putative QTL, designated as Qsatt414-596, was detected using MapMaker/QTL. Qsatt414-596 was flanked by two SSR markers from the linkage group MLG J, Satt414 and Satt596. Satt414 and Satt596 were also detected to be significantly (P < 0.005) associated with PRR using the SAS GLM procedure and were estimated to explain 13.7% and 21.5% of the total phenotypic variance, respectively.     

SSR-tagged breeding scheme for allogamous crops: a trial in bunching onion (<Emphasis Type="Italic">Allium fistulosum</Emphasis>)

In several autogamous and vegetatively propagated crops, DNA markers have been used for cultivar identification. However, allogamous crops such as bunching onion (Allium fistulosum L.) are recalcitrant to marker-aided cultivar identification, as well as hybrid seed purity tests, due to the high degree of genetic heterogeneity within each cultivar. To aid cultivar identification and ensure its accuracy in bunching onion, we proposed the “SSR-tagged breeding” scheme in our previous study. The feasibility of this scheme was investigated here using a landrace of bunching onion with two populations tagged with two or four selected SSR markers. Compared with a control population, no significant differences were detected in the agronomic traits of the SSR-tagged populations. The targeted SSR loci were genetically uniform within each population whereas other loci maintained high heterogeneity. These results demonstrate that the SSR-tagged breeding scheme, even with a very small number of markers, is efficient for the identification of newly bred cultivars, and consequently for F₁ purity tests, in allogamous crops in which inbreeding depression is as severe as in bunching onion.     

Association analysis of sugar yield-related traits in sorghum [Sorghum bicolor (L.)]

Association mapping is widely used for detecting QTLs in higher plants. In the present study a synthetic sorghum population containing 119 representative samples, including 43 sweet and 76 grain sorghum accessions originating mainly from China, USA and India, were genotyped using 51 simple-sequence repeat (SSR) markers. Linkage disequilibrium (LD) of pair-wise loci and population structure were analyzed, followed by association analysis of SSR loci and 3 sugar yield related traits using the TASSEL general linear model program. Results showed that: (i) different degrees of LD occurred among syntenic markers and also among nonsyntenic markers, indicating historical recombination among sorghum linkage groups; (ii) significant LD extended up to 7.31 cM; (iii) the collection of accessions was composed of three subgroups; (iv) four marker loci were associated with stalk sugar concentration, fresh stalk weight and stalk juice weight measured in different growing environments and could be used, therefore, in future marker assisted breeding programs. Several loci were also associated with two or more traits simultaneously, which might be due to tight linkage between different genes affecting these traits and/or pleiotropy. In addition, some associated markers were located close to QTLs previously mapped in family-based linkage mapping analyses.     

Identification of population-specific QTLs for flowering in soybean

Flowering is an important stage in plant development and crucial for adaptation of plant species to different environments. Two soybean mapping populations were used to identify quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) by genotyping simple sequence repeat (SSR) markers. Single-factor analysis of variance detected association of phenotypic data with SSR markers in each population. DF QTLs were identified on four chromosomes (chrs.); two QTLs located on chrs. 2 and 13 with Satt041 and Satt206 in the Jinpumkong 2 × SS2-2 population and other two DF QTLs were detected on chrs. 6 and 19 with Satt100 and Satt373 in the Iksannamulkong × SS2-2 population. The major QTLs associated with Satt100 explained 30.3% of maximum phenotypic variation. Especially, all DF QTLs included QTLs for DM, except Satt206 on chr. 13. Moreover, two additional DM QTLs were mapped on chrs. 10 and 11 with Satt243 and Satt359, respectively. DF QTL on chr. 2 with Satt041 was the newly identified QTL only in the Jinpumkong 2 × SS2-2 population and explained 10.3% of the phenotypic variation. The single locus of Satt100 on chr. 6 and Satt373 on chr. 19 were located on soybean genomic regions of the known flowering gene loci E1 and E3, respectively. These population-specific QTLs (Satt100 and Satt373) are the major QTLs for flowering time, putatively, they may be related to maturity QTLs with large effect. Additionally, these QTLs are valuable for marker-assisted approaches and could be widely adopted by soybean breeders.