镜鲤体长性状的QTL定位分析

以镜鲤良种后代为祖父母本所培育的杂交F2群体的68个个体为材料,利用553个分子标记(217个SSR和336个SNP标记)对其进行基因型检测,运用JoinMap4.0软件包对遗传连锁图谱进行构建。利用MapQTL5.0区间作图法(Interval mapping)进行QTL检测,通过置换实验(1 000次重复)确定连锁群显著性水平阈值。在对体长的区间定位中共检测到12个与体长性状相关的QTLs区间,分布在BL-1-1(SNP0137-SNP1481)、BL-4-1(SNP0092-HLJ797)、BL-5-1(SNP1268-HLJ423)、BL-7-1(HLJ870-SNP0702)、BL-12-1(SNP0922-HLJ639)、BL-16-1(HLJE351-SNP0674)、BL-25-1(SNP0394-SNP0862)、BL-35-1(HLJ668-SNP0832)、BL-43-1(SNP0389-SNP1425)、BL-47-1(HLJ057-HLJ1113)、BL-47-2(HLJ1439-HLJ1418)等11个连锁群上,解释表型变异范围是13.8%~64.9%,其中贡献率大于20%的主效QTLs有8个,是体长性状的主效QTLs区间。     

鲤鱼体长性状的QTL定位及其遗传效应分析

以大头鲤/荷包红鲤抗寒品系的重组自交系群体及其遗传连锁图谱, 利用Windows Map Manager 2.0的标记回归法进行QTL单标记定位分析和复合区间作图法进行QTL区间检测, 通过置换实验(1 000次重复)确定连锁群显著性水平阈值。在体长性状的标记回归研究中, 共7个标记达到显著水平(P<0.01), 对性状的贡献率为14.00%～27.00%, 其中3个标记达到极显著水平(P<0.001)。HLJ534, HLJ319, HLJ370座位可能与影响鲤鱼体长性状的主效基因连锁。在体长性状的QTL区间定位研究中, 共6个QTL达到连锁群显著水平(P=0.05), 对性状的贡献率为11.33.%～23.12%, 其中2个达到连锁群极显著性水平(P=0.01), 它们的加性效应方向并不一致。HLJ190-HLJ497区间和HLJ479-HLJ483区间是影响鲤鱼体长性状的主效QTL区间。     

猪2号染色体遗传连锁图谱的构建与QTL定位分析

构建了猪2号染色体的遗传连锁图谱,并进一步进行了重要生产性状数量性状位点的定位,结果表明,7个微卫星位点均为中高度多态性位点,多态信息含量为0．40182－0．58477,可以满足遗传连锁图谱构建的要求,构建的资源家系遗传连锁图谱总长152．9cM,位点的排列顺序与USDA结果一致,但除了Sw2516与Sw1201标记区间外,所有标记区间距离均大于USDA图谱,将连锁图谱与性状记忆结合起来,进一步进行了猪数量性状位点定位的研究,在2号染色体发现了显著影响活体估测瘦肉率等活体估测性状的QTLs,此外还发现眼肌高度和背最长肌大理石纹的QTLs,其中影响活体估测瘦肉率的QTL达到了染色体显著的水平（P＜0．01）,且解释性状的表型变异达21．55％,影响眼肌高度和背最长肌大理石纹的QTLs分别可以解释10．12％和10．97％的表型变异,影响活体估测性状的QTLs加性效应与显性效应作用方向相反,影响眼肌高度的QTL加性效应与显性效应相同,在大白猪中具有增效等位基因,定位的QTLs效应较大,为在群体中开展分子标记辅助育种奠定了理论基础。     

鲤鱼(Cyprinus carpio L.)头长、眼径、眼间距QTL的定位

用265个AFLP标记、127个微卫星分子标记、37个EST-SSR标记和16个RAPD标记对大头鲤/荷包红鲤抗寒品系的F2雌核发育群体44个个体进行基因型检测, 构建鲤鱼遗传连锁图谱。利用软件WinQTLCart2.5采用复合区间作图法对头长、眼径、眼间距3个性状进行了QTL分析。结果显示, 共检测到5个与头长性状相关的QTL, 分别定位于鲤鱼连锁图谱的LG2(qHS-2-1)、LG3 (qHS-3-1)、LG40(qHS-40-1)和LG4 (qHS-4-2和qHS-4-3) 上。其中qHS-40-1拥有最大的 LOD值, 为7.94, 可解释的表型变异为 34.29%。qHS-4-2的LOD值最小, 为5.03, 可解释的表型变异为11.52%。5个与头长性状相关的 QTL 加性效应值均为负值。检测到两个与眼径性状相关的QTL, 分别定位于鲤鱼连锁图谱的LG39连锁群(qED-39-1)和LG40连锁群(qED-40-1)上, 其中qED-40-1的LOD值比较大, 为2.76, 其加性效应值为负值, 可以解释5.62%的表型变异; qED-39-1的LOD值为2.72, 加性效应值为正值, 可以解释9.77%的表型变异。检测到两个与眼间距性状相关的QTL, 分别定位到鲤鱼连锁图谱的LG20连锁群(qEC-20-1)和LG28 连锁群(qEC-28-1)上。其中qEC-20-1的LOD值比较大, 为3.77, 加性效应值为正值, 可以解释8.29%的表型变异; qEC-28-1的LOD值为2.79, 对应的加性效应值为负值, 可以解释8.88%的表型变异     

镜鲤体重的QTL定位

本研究利用217个微卫星标记和336个SNPs标记对德国镜鲤F2代68个个体基因组DNA进行基因型检测.其中507个标记共组成62个连锁群,覆盖基因组总长度为2 805.85 cM,标记间平均距离为6.31 cM;利用软件MapQTL 4.0采用区间作图法对体重性状进行QTL定位分析.研究结果共检测到14个与体重性状有关的QTLs,分布于9个连锁群.其中BW-5-1有最大的LOD值,为4.46;BW-1-1的LOD值最小,为2.25.单个QTL平均解释表型变异介于14.10%~45.50%之间,其中贡献率大于20%的主效QTLs有9个.通过BLASTX与斑马鱼蛋白质序列数据库进行序列比对,找到了与斑马鱼酰基辅酶A脱氢酶蛋白、胰淀粉酶α2蛋白、Apoeb protein和甘油醛-3-磷酸脱氢酶蛋白同源的分子标记.本研究结果对分子标记辅助育种具有重要应用价值.     

海岛棉(Gossypium barbadense L.)产量和早熟性状QTL定位

对海岛棉产量和早熟性状进行QTL初步定位,为分子标记辅助育种提供依据.利用5200多对SSR引物筛选海岛棉品种新海3号和Giza82间的多态性引物,获得107对.以多态性引物检测新海3号×Giza82的190个F2∶3家系,获得120个多态性位点.利用JoinMap3.0分析软件构建了一个包含22个连锁群,74个标记,标记间平均距离12.06cM,全长893cM,覆盖海岛棉基因组20.12％的分子标记遗传连锁图谱.采用复合区间作图法检测到21个与海岛棉产量性状和早熟性状有关的QTL,其中早熟性状检测到12个QTL,分别位于1、3、5、6、11、17、22共7个连锁群上;产量性状检测到9个QTL,分别位于1、4、5、6、7、16、22共7个连锁群上.研究结果为海岛棉产量性状和早熟性状的分子设计育种提供了有用的信息.     

海岛棉产量和早熟性相关性状的QTLs定位

对海岛棉产量和早熟性状进行QTL初步定位,为分子标记辅助育种提供依据。利用5200多对SSR引物筛选海岛棉品种新海3号和Giza82间的多态性引物,获得107对。以多态性引物检测新海3号×Giza82的190个F2:3家系,获得120个多态性位点。利用JoinMap3.0分析软件构建了一个包含22个连锁群,74个标记,标记间平均距离12.06 cM,全长893 cM,覆盖海岛棉基因组20.12%的分子标记遗传连锁图谱。采用复合区间作图法检测到21个与海岛棉产量性状和早熟性状有关的QTL,其中早熟性状检测到12个QTL,分别位于1、3、5、6、11、17、22共7个连锁群上;产量性状检测到9个QTL,分别位于1、4、5、6、7、16、22共7个连锁群上。研究结果为海岛棉产量性状和早熟性状的分子设计育种提供了有用的信息。     

大豆遗传图谱的构建和若干农艺性状的QTL定位分析

大豆许多重要农艺性状都是由微效多基因控制的数量性状,对这些数量性状进行QTL定位是大豆数量性状遗传研究领域的一个重要内容.本研究利用栽培大豆科新3号为父本、中黄20为母本杂交得到含192个单株的F2分离群体,构建了含122 个SSR标记、覆盖1719.6cM、由33个连锁群组成的连锁遗传图谱.利用复合区间作图法,对该群体的株高、主茎节数、单株粒重和蛋白质含量等农艺性状的调查数据进行QTL分析,共找到两个株高QTL,贡献率分别为9.15%和6.08%;两个主茎节数QTL,贡献率分别为10. 1%和8.6%;一个蛋白质含量QTL,贡献率为9.8%;一个单株粒重QTL,贡献率为11.4% .通过遗传作图共找到与所定位的4个农艺性状QTL连锁的6个SSR标记,这些标记可以应用于大豆种质资源的分子标记辅助选择,从而为大豆分子标记辅助育种提供理论依据.     

小麦旗叶长、宽及面积的QTL分析

以小麦品种‘小偃81’和‘西农1376’构建的含236个家系的自交重组系(RIL)群体(F2:7、F2:8代)为研究材料,采用完全随机区组设计,连续2年在陕西杨陵、河南驻马店和山东济南于灌浆期(花后20d)随机取每个株系10株测量旗叶长、宽,并利用172个SSR标记构建了遗传连锁图谱,通过基于完备区间作图法的QTL IciMapping V3.2软件,对控制小麦旗叶长、宽和面积的数量性状位点(QTL)进行了加性效应分析。结果发现:(1)9个旗叶长QTLs位于1A、4A、3B、5D和7D染色体上,单个QTL可解释5.10%~16.44%的表型变异;10个旗叶宽QTLs位于1A、3A、5A、7A、3B和5D染色体上,单个QTL可解释4.63%~14.24%的表型变异;12个旗叶面积QTLs位于1A、4A、3B、2D和5D染色体上,单个QTL可解释4.25%~22.67%的表型变异。(2)控制小麦旗叶长、宽和面积的QTLs存在差异,同一QTL在不同性状中的遗传贡献率也不同。(3)同一性状在同一年份,不同地点和在不同年份,相同地点下检测到的QTLs有的相同,但有的差异明显。(4)有些控制不同性状的QTLs在染色体的同一标记区间,表现一因多效。研究表明:位于1A和5D染色体上的2个加性QTLs都同时控制旗叶长、宽和面积,且前者为主效基因,后者遗传贡献率也较大,可用于标记辅助育种和分子聚合育种。     

绿豆产量相关农艺性状的QTL定位

绿豆育种的目标性状大多是受多基因控制的数量性状,表现型受环境影响很大。为深入分析绿豆复杂数量性状的遗传特征,本试验以绿豆Berken/ACC41 F10重组近交系群体为作图群体,利用该群体已经构建的包含79个RFLP标记的分子连锁图谱对北京和广西2个种植环境下考察的11个绿豆产量相关农艺性状进行QTL定位。结果表明,2个环境下共检测到产量相关性状QTL 63个（其中北京25个,广西38个）,分布于除第13连锁群以外的12条连锁群。大部分QTL只在单一环境下被检测到,说明产量相关QTLs与环境之间存在明显的互作。2个环境均能检测到的QTL仅有6个,分别为控制荚长、百粒重、生育期的QTLs,这6个在不同生态环境下同时发挥效应的QTLs对于绿豆分子标记辅助育种具有特殊的意义。研究还发现2个QTLs富集区域和若干成束分布的QTLs,它们可能是发掘通用QTL的候选位点。     

Mapping quantitative trait loci (QTL) for body weight, length and condition factor traits in backcross (BC1) family of Common carp (Cyprinus carpio L.)

Body weight and length are economical important traits in aquaculture species influenced by quantitative trait loci (QTL) and environmental factors. In this study, a backcross (BC1) common carp family, with 86 progeny, was utilized to construct genetic map for preliminary QTL mapping. The genetic map was constructed with 366 markers, including 191 SNP from gene, coverage 50 linkage groups with an average marker distance of 18.5 cM. A total of fourteen QTLs associated with body weight (BW), body length (BL) and condition factor (K) were detected on ten linkage groups (LGs). Among these QTLs detected, three (qBW8, qBL8 and qK8) were associated with BW, BL and K respectively, were mapped on LG8. qBW8 and qK8 were identified on similar interval neared locus HLJ2394 explained 14.9 and 20.9 % of the phenotype variance, while qBL8 was identified on separate nearby locus HLJ571 with 30.8 % of phenotype variance. Two QTLs, qBW13 and qK13, related with BW and K separately, were found on LG13 at different locus with phenotype variance of 25.3 and 20.9 %. Other two QTLs, qBW19 and qBL19, associated to BW and BL were mapped on same region near SNP0626 on LG19, and explained 10.3 and 15.6 % of phenotype variance. While other seven QTLs related with BW and BL were located on different LGs. Confidential interval was ranged from 1.1 to 10 cM in the present study. These markers, with lower QTL interval, have great influence on the body weight and length. Therefore, these QTLs will be helpful to find out the genes related with specific trait.     

Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay

Understanding genetic characteristics in rice populations will facilitate exploring evolutionary mechanisms and gene cloning. Numerous molecular markers have been utilized in linkage map construction and quantitative trait locus (QTL) mappings. However, segregation-distorted markers were rarely considered, which prevented understanding genetic characteristics in many populations. In this study, we designed a 384-marker GoldenGate SNP array to genotype 283 recombination inbred lines (RILs) derived from 93-11 and Nipponbare Oryza sativa crosses. Using 294 markers that were highly polymorphic between parents, a linkage map with a total genetic distance of 1,583.2 cM was constructed, including 231 segregation-distorted markers. This linkage map was consistent with maps generated by other methods in previous studies. In total, 85 significant quantitative trait loci (QTLs) with phenotypic variation explained (PVE) values≥5% were identified. Among them, 34 QTLs were overlapped with reported genes/QTLs relevant to corresponding traits, and 17 QTLs were overlapped with reported sterility-related genes/QTLs. Our study provides evidence that segregation-distorted markers can be used in linkage map construction and QTL mapping. Moreover, genetic information resulting from this study will help us to understand recombination events and segregation distortion. Furthermore, this study will facilitate gene cloning and understanding mechanism of inter-subspecies hybrid sterility and correlations with important agronomic traits in rice.     

微卫星DNA标记分析德国镜鲤的遗传潜力

结合体重、体长、体高等数量性状, 用30个微卫星分子标记, 评估了3个德国镜鲤群体的遗传潜力, 共检测到287个等位基因, 559种基因型, 片段长度109~400 bp, 有效等位基因数1.1014~6.4665, 观察杂合度0.0968~0.9892, 期望杂合度0.0926~0.8554, 位点多态信息含量0.08787~0.8559, 其中中度多态(0.25≤PIC≤0.5)13个, 高度多态(PIC≥0.5)13个。统计结果显示: 3个群体的遗传潜力处于中度水平, 双来养殖群体的遗传潜力比换新和松浦繁殖群体低。同时, 用30个基因座的不同等位基因和基因型与双来群体的体重、体长、体高进行了连锁分析, 得到2个与镜鲤体长相关的微卫星分子标记(HLJ319, HLJ693)和1个与体高相关的位点(HLJ677), 与体长相关的1个位点(HLJ693)还与体重连锁。将此遗传标记在鲤鱼重组自交系中验证, 结果显示: 主要经济性状相连锁的3个遗传标记中HLJ319与鲤鱼体长性状的QTL定位结果基本一致。     

Quantitative trait loci for morphometric traits in multiple families of common carp(Cyprinus carpio)

Quantitative trait locus(QTL) mapping is frequently used to understand the genetic architecture of quantitative traits.Herein,we performed a genome scanfor QTL affecting the morphometric characters in eight full-sib families containing 522 individuals using different statistical methods(Sib-pair and half-sib model).A total of 194 QTLs were detected in 25 different regions on 10 linkage groups(LGs).Among them,37 QTLs on five LGs(eight,13,24,40 and 45) were significant(5%genome-wide level),while the remaining 40(1%chromosome-wide level) and 117(5%chromosome-wide level) indicated suggestive effect on those traits.Heritabilities for most morphometric traits were moderate to high,ranging from 0.21 to 0.66,with generally strong phenotypic and genetic correlations between the traits.A large number of QTLs for morphometric traits were co-located,consistent with their high correlations,and may reflect pleiotropic effect on the same genes.Biological pathways were mapped for possible candidate genes on QTL regions.One significantly enriched pathway was identified onLG45,which had a P-value of 0.04 and corresponded to the "regulation of actin cytoskeleton pathway".The results are expected to be useful in marker-assisted selection(MAS) and provide valuable information for the study of gene pathway for morphometric and growth traits of the common carp.     

A consensus linkage map of common carp (Cyprinus carpio L.) to compare the distribution and variation of QTLs associated with growth traits

The ability to detect and identify quantitative trait loci (QTLs) in a single population is often limited. Analyzing multiple populations in QTL analysis improves the power of detecting QTLs and provides a better understanding of their functional allelic variation and distribution. In this study, a consensus map of the common carp was constructed, based on four populations, to compare the distribution and variation of QTLs. The consensus map spans 2371.6 cM across the 42 linkage groups and comprises 257 microsatellites and 421 SNPs, with a mean marker interval of 3.7 cM/marker. Sixty-seven QTLs affecting four growth traits from the four populations were mapped to the consensus map. Only one QTL was common to three populations, and nine QTLs were detected in two populations. However, no QTL was common to all four populations. The results of the QTL comparison suggest that the QTLs are responsible for the phenotypic variability observed for these traits in a broad array of common carp germplasms. The study also reveals the different genetic performances between major and minor genes in different populations.     

Mapping of QTLs for morpho-agronomic and seed quality traits in a RIL population of common bean (Phaseolus vulgaris L.)

The objective of this research was to determine the quantitative trait loci (QTLs) controlling phenological traits (days to flowering, days to end of flowering, days to harvest as green pod, and days to maturity), seed size traits (seed length, seed height, seed width, and seed weight), and seed quality traits (water absorption, and coat proportion), in common bean. A population of 104 F₇ recombinant inbred lines (RILs) derived from an inter-gene pool cross between Xana, and Cornell 49242, was used to develop a genetic linkage map including 175 AFLPs, 27 microsatellites, 30 SCARs, 33 ISSRs, 12 RAPDs, 13 loci codifying for seed proteins, and the four genes Fin,fin (growth habit); Asp,asp (seed coat shininess); P,p (seed color); and I,i (resistance to bean common mosaic virus). The map has a total length of 1,042 cM distributed across 11 linkage groups aligned to those of the core linkage map of bean using common molecular markers as anchor points. The QTL analyses were carried out over three environments using the mean environment data with composite interval mapping. Thirty-one QTLs for ten traits were found to be significant in at least one environment and in the mean environment data, the number of significant QTLs identified per trait ranging from two to five. Twenty-seven of these QTLs mapped forming clusters in eight different chromosomal regions. The rationale for this clustered mapping and the possible relationship between some QTLs for phenological traits and the genes Fin and I are discussed.     

Quantitative trait loci for morphometric traits in multiple families of common carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis>)

Quantitative trait locus (QTL) mapping is frequently used to understand the genetic architecture of quantitative traits. Herein, we performed a genome scan for QTL affecting the morphometric characters in eight full-sib families containing 522 individuals using different statistical methods (Sib-pair and half-sib model). A total of 194 QTLs were detected in 25 different regions on 10 linkage groups (LGs). Among them, 37 QTLs on five LGs (eight, 13, 24, 40 and 45) were significant (5% genome-wide level), while the remaining 40 (1% chromosome-wide level) and 117 (5% chromosome-wide level) indicated suggestive effect on those traits. Heritabilities for most morphometric traits were moderate to high, ranging from 0.21 to 0.66, with generally strong phenotypic and genetic correlations between the traits. A large number of QTLs for morphometric traits were co-located, consistent with their high correlations, and may reflect pleiotropic effect on the same genes. Biological pathways were mapped for possible candidate genes on QTL regions. One significantly enriched pathway was identified on LG45, which had a P-value of 0.04 and corresponded to the “regulation of actin cytoskeleton pathway”. The results are expected to be useful in marker-assisted selection (MAS) and provide valuable information for the study of gene pathway for morphometric and growth traits of the common carp.     

Genetic variation underlying pod size and color traits of common bean depends on quantitative trait loci with epistatic effects

Common bean is an important vegetable legume in many regions of the world. Size and color of fresh pods are the key factors for deciding the commercial acceptance of bean as a fresh vegetable. The genetic basis of important horticultural traits of common bean is still poorly understood, which hinders DNA marker-assisted breeding in this crop. Here we report the identification of single-locus and epistatic quantitative trait loci (QTLs), as well as their environment interaction effects for six pod traits, namely width, thickness, length, size index, beak length and color, using an Andean intra-gene pool recombinant inbred line population from a cross between a cultivated common bean and an exotic nuña bean. The QTL analyses performed detected a total of 23 QTLs (single-locus QTLs and epistatic QTLs): five with only individual additive effects and six with only epistatic effects, while the remaining twelve showed both effects. These QTLs were distributed across linkage groups (LGs) 1, 2, 4, 6, 7, 8, 9, 10 and 11; particularly noteworthy are the QTLs for pod size co-located on LGs 1 and 4, indicative of tight linkage or genes with pleiotropic effects governing these traits. Overall, the results obtained showed that additive and epistatic effects are the major genetic basis of pod size and color traits. The mapping of QTLs including epistatic loci for the six pod traits evaluated provides support for implementing marker-assisted selection toward genetic improvement of common bean.     

A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs

A genetic linkage map is a powerful research tool for mapping traits of interest and is essential to understanding genome evolution. The aim of this study is to provide an expanded genetic linkage map of common carp to effectively carry out quantitative trait loci analysis and conduct comparative mapping analysis between lineages. Here, we constructed a genetic linkage map of common carp (Cyprinus carpio L.) using microsatellite and single-nucleotide polymorphism (SNP) markers in a 159 sibling family. A total of 246 microsatellites and 306 SNP polymorphic markers were genotyped in this family. Linkage analysis using JoinMap 4.0 organized 427 markers (186 microsatellites and 241 SNPs) to 50 linkage groups, ranging in size from 1.4 to 130.1 cM. Each group contained 2-30 markers. The linkage map covered a genetic distance of 2,039.2 cM and the average interval for markers within the linkage groups was approximately 6.4 cM. In addition, comparative genome analysis within five model teleost fish revealed a high percentage (74.7%) of conserved loci corresponding to zebrafish chromosomes. In most cases, each zebrafish chromosome comprised two common carp linkage groups. The comparative analysis also revealed independent chromosome rearrangements in common carp and zebrafish. The linkage map will be of great assistance in mapping genes of interest and serve as a reference to approach comparative mapping and enable further insights into the comprehensive investigations of genome evolution of common carp.