豇豆SNP高密度遗传图谱构建及重要农艺性状QTL定位

为促进豇豆种质资源的高效利用和新基因发掘,本研究基于豇豆F2群体,利用重测序技术构建了包含2984个bin标记(142,146个SNP)的遗传连锁图谱。该图谱共11个连锁群,总长1333.48cM,平均图距0.45cM。不同连锁群的长度从84.63～183.15 cM不等,平均图距从0.27 cM至0.89 cM不等。根据F₂、F₃的表型调查,利用该图谱共检测到15个QTL,分别与百粒重、花色、荚长、荚形、荚质、籽粒颜色等14个性状相关。其中荚质、荚长、主茎分枝数等分别检测到1个主效QTL区间,其余性状检测到多个QTL区间。通过对区间内的基因注释分析,分别确定了与荚长、单株荚数、籽粒颜色构成等性状相关的候选基因。本研究中QTL分析结果将为豇豆属重要性状的标记辅助选择奠定基础,而候选基因筛选则有助于深入解析这些性状的遗传机理,提高豇豆分子遗传学研究水平。     

大豆株高QTL的定位与整合分析

株高是影响大豆产量的主要性状之一,本研究利用Charleston×东农594重组自交系构建的SSR遗传图谱,采用WinQTLCartographer Ver.2.5软件的CIM和MIM分析方法对2006-2008年连续3年的大豆株高数据进行QTL定位,检测到了15个控制株高的QTLs,分别位于LGB1、LGD1a和LGG等。另外,利用BioMercator2.1的映射功能将国内外常用的大豆图谱上的株高QTLs通过公共标记映射整合到大豆公共遗传连锁图谱soymap2上,将搜集到78个株高QTLs和本研究得到QTLs进行整合分析,最终得到12个大豆株高的"通用"QTL,分别位于LGB1、LGC2、LGD1a、LGF、LGG、LGK和LGM,其置信区间最小可达到0.24cM,为今后对大豆株高QTL精细定位,提供有利指导。     

基于高密度遗传图谱的蓖麻种子大小性状QTL定位

蓖麻种子大小直接影响产量,不同的蓖麻材料间种子大小差异较大,深入研究蓖麻种子大小性状的遗传机制对蓖麻种子产业的发展具有重要意义。本研究以蓖麻两性自交系SL1为父本,雌性系HCH1为母本1(组合1)、雌性系HCH3为母本2(组合2),分别构建F₂、BC₁群体。首先,分析2组遗传群体种子大小性状间的相关性。其次,利用全基因组测序技术(whole genome sequencing,WGS)对组合1的F₂群体中的150个单株进行测序分析,构建高密度遗传图谱并结合种子大小性状表型数据进行数量性状座位(quantitative trait locus, QTL)定位分析。最后,对QTL区间包含的基因进行BLAST同源比对和KEGG通路富集分析确定候选基因。结果表明,不同组合群体的种子大小各性状间的相关性有差异,种子的长度和宽度相关性最显著。共检测到种子大小性状相关QTL位点18个,其中种子长度2个QTLs、种子宽度5个QTL、种子厚度4个QTL、百粒重7个QTL,分别分布在连锁群1、4、7、8、9、10上, LOD值介于3.77～...     

玉米株高QTL定位研究进展

株高作为玉米的重要农艺性状,对产量、耐肥性、抗倒伏影响显著。随着分子生物学的发展,针对玉米株高性状开展了大量研究工作。总结玉米株高相关的QTL定位和基因克隆研究进展,并采用元分析技术对187个信息完整的玉米株高QTL定位结果进行整合分析,获得10个一致性QTL,并在一致性QTL置信区间内发掘可能参与玉米株高调控的候选基因。     

基于高密度遗传图谱定位大豆蛋白质含量相关的QTL

大豆是重要的粮食作物和经济作物,其籽粒蛋白约为40%,是优质植物蛋白主要来源之一。挖掘控制大豆高蛋白数量性状位点(Quantitativetraitloci,QTL)以及分子标记育种对高蛋白大豆培育具有重要的意义。本研究利用蛋白含量存在明显差异的中黄35 (Zhonghuang 35, ZH35)和中黄13 (Zhonghuang 13, ZH13)杂交构建的包含192个株系的重组自交系群体为供试材料,通过对两亲本及RIL群体重测序,构建了包含4879个bin标记的高密度遗传图谱,总遗传距离为3760.71 cM,相邻标记间的遗传距离为0.77 cM。RIL群体及亲本分别于北京顺义和河南濮阳种植, 2个环境共检测到15个蛋白含量相关QTL位点,分布于5号、12号、15号、17号、18号、19号和20号染色体,贡献率为4.36%～11.39%。其中,北京顺义和河南濮阳检测到qPro-20-1和qPro-20-3, 2个QTL贡献率分别为7.65%和7.58%,重叠区域包括33个基因。本研究有助于精细定位和图位克隆大豆蛋白含量相关基因,并为进一步培育高蛋白大豆品种提供基因资源。     

利用BSA法定位大豆全基因组株高QTL及候选基因分析

株高是影响大豆单株产量的重要性状,明确调控大豆株高的主效基因对利用分子辅助育种手段提高大豆产量具有重要意义。选用株高差异显著的东农594(高秆)为父本,Charleston(矮秆)为母本,杂交构建F₂群体和RIL群体,然后选取F₂群体的1 500个单株中极高和极矮单株各40株和RIL群体的高矮秆单株各20株,分别建立2套高矮秆池;进而利用二代DNA测序技术对亲本进行50×测序,高矮秆池进行20×测序并筛选read读数大于4的高质量可信SNP位点,在F₂群体筛选到20 187个符合要求的SNP位点、RIL群体筛选到20 285个符合要求的SNP位点;最后采用混合群体分离分析(Bulked segregant analysis, BSA)的SNP-index关联分析法和Euclidean distance(ED)关联分析法计算2个群体和株高关联的染色体区间,进而重新计算株高关联染色体的阈值,并筛选2个群体2种方法共同定位到的10个染色体区间作为候选区间,此结果显著降低了全基因组单一阈值鉴定到的染色体区间,提高了定位结果的准确...     

大豆遗传图谱的构建和抗胞囊线虫(Heterodera glycines Ichinohe)的QTL分析

大豆胞囊线虫1号和4号生理小种是黄淮地区的优势小种,ZDD2315是我国特优抗源。本文旨在定位ZDD2315对1号和4号生理小种抗性的QTL。试验以Essex为母本,ZDD2315为父本和轮回亲本,创建了一个包含114个单株的BC1群体。采用250个SSR标记和1个形态标记通过MAPMAKER 3.0构建了包含25个连锁群的遗传图谱,覆盖大豆基因组2 963.5 cM     

栽培种花生单仁重QTL定位分析

花生(ArachishypogaeaL.)是我国重要的油料作物和经济作物,单仁重是决定花生产量和商品性的重要性状之一。本研究以大粒品种山花15号(母本)与小粒品种中花12号(父本)杂交构建的RIL群体为材料,基于高密度遗传图谱,在6个种植环境下进行单仁重QTL定位。在A04、A06、A07、B05、B07、B09和B10等7个染色体上共检测到9个与单仁重相关的QTL,这些QTL的LOD值为3.01～33.97、表型贡献率为2.61%～34.28%、加性效应值为-0.03～0.15 g、定位的物理区间为0.03～4.32 Mb,其中, qSSWA07.1是在6个种植环境下重复检测的单仁重主效QTL,qSSWA06.1和qSSWB09.1均在4个种植环境下重复检测到。qSSWA07.1和qSSWA06.1的加性效应为正,增效位点来自山花15号,qSSWB09.1的加性效应为负,增效位点来自中花12号,利用与qSSWA06.1、qSSWA07.1和qSSWB09.1紧密连锁的3个bin标记(A06:Block3344、A07:Block3373和B09:Block10032)的基因型分析了3...     

Soybean plant height QTL mapping and meta‐analysis for mining candidate genes

Plant height is closely related to seed yield of soybean. The goal of this study was to identify important loci affecting soybean plant height using meta‐analysis based on a reference physical map. Plant height related to QTLs was mapped across eight years with a RIL population by WinQTLCart v2.5. 182 QTLs related to plant height of soybean from database and our research were collected, and each QTL was projected onto the soybean physical map by software BioMercator v2.1. The confidence interval of meta‐QTL ranged from 0.09 to 5.07 Mb, and the mean phenotypic variance ranged from 4.9% to 73.0%. Furthermore, 4,259 candidate genes were located in these consensus QTLs, and 40 of them were involved in the plant growth and stem elongation and annotated as plant hormone signal transduction (pathway ID ko04075) in KEGG pathway. These results would lay a foundation for fine mapping of QTLs/genes related to plant height and marker‐assisted selection for breeding in soybean.     

Dynamic QTL mapping for plant height in Upland cotton (Gossypium hirsutum)

Plant height served as one of model traits to analyse dynamic development. The objective of this research was to investigate quantitative trait loci (QTL) and dynamic QTL for plant height trait using an intraspecific recombinant inbred line (RIL) population and a constructed genetic map in Upland cotton (Gossypium hirsutum L.). Totally, 41 QTL and 23 conditional QTL controlling plant height were detected at two experimental environments, respectively. Four stable QTL were identified simultaneously in both environments. Some QTL identified at the early stage could not be detected at the final stage at plant maturity. Conditional QTL with different genetic effects were identified at certain stages, demonstrating that the expression of QTL had temporal characteristic during plant growth. Therefore, the study of dynamic QTL could unravel temporal genetic patterns controlling complex developmental quantitative traits.     

Cultivar identification and genetic map of mango (Mangifera indica)

Amplified Fragment Length Polymorphism (AFLP) information was used for identification of mango (Mangifera indica L.) cultivars, for studying the genetic relationship among 16 mango cultivars and seven mango rootstocks and for the construction of a genetic linkage map. Six AFLP primer combinations produced 204 clear bands and on the average 34 bands for each combination. The average Band-Sharing between cultivars and rootstocks was 83% and 80%, respectively. The average Band-Sharing for mango is 81%. The probability of obtaining a similar pattern for two different mango cultivars and rootstocks is 6 × 10⁻³and 2 × 10⁻³, respectively. A preliminary genetic linkage map of the mango genome was constructed, based on the progeny of a cross between ‘Keitt’ and ‘Tommy-Atkins’. This linkage map consists of 13 linkage groups and covers 161.5 cm defined by 34 AFLP markers. This revised version was published online in August 2006 with corrections to the Cover Date.     

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...     

Construction of high-density linkage map and identification of QTLs associated with resistance to black rot in radish (Raphanus sativus) by RAD sequencing

High-density marker-based QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped an F₂ population (KB12-1 × PP12-1) using a RAD-seq approach and constructed a high-density linkage map for radish. After a series of filtering procedures were performed, 17,124 SNPs and 3,336 indels with aa × bb genotyping were retained to obtain bin markers. Then, a linkage map comprising a total of 1,221 bin markers in nine linkage groups spanning 1,467.3 cM with an average marker interval of 1.2 cM was constructed. We evaluated the resistance of the F₂ mapping population to black rot using F₃ progeny, and two major QTLs related to black rot resistance were identified based on this map. Among these QTLs, qBRR2 on Chr.2 explained 26.97% of the phenotypic variation with a LOD score of 11.93, and qBRR7 on Chr.7 accounted for 27.06% of the phenotypic variation with a LOD score of 11.83. The additive effect of qBRR2 was positive (14.97); however, qBRR7 had the opposite effect (−11.99). The high-density linkage map and the major QTLs qBRR2 and qBRR7 provide new important information for disease resistance gene discovery and utilization in genetic improvement.     

GBS高密度遗传连锁图谱定位甘蓝型油菜粉色花性状

甘蓝型油菜花瓣颜色是重要的观赏性状,花瓣颜色的选育和改良已成为材料创制的主要研究方向。目前对甘蓝型油菜粉色花性状定位研究未见报道。本研究以甘蓝型油菜纯系黄花62和甘蓝型油菜纯系粉花77为亲本构建双单倍体(doubled haploid,DH)群体。利用简化基因组测序技术(genotyping-by-sequencing,GBS)筛选出3253个单核苷酸多态性(single nucleotide polymorphism,SNP)标记,构建了全长1766.06 cM甘蓝型油菜连锁图谱,标记间平均遗传距离为0.54 cM;使用WinQTL Cartographer复合区间作图方法对粉色花性状进行数量性状座位(quantitative trait locus,QTL)定位,检测到位于A07和C03染色体上各1个QTL;将定位区间内基因与甘蓝和白菜同源基因进行线性比对,在这些区间中找到了一些存在于3个物种的同源基因;对粉色花定位区间内基因进行可变剪切分析发现,2个花色相关基因BnaA07g15980D和BnaA07g17500D在亲本粉色花瓣中发生内含子保留可变剪切。上述研究结果为甘蓝型油菜粉色花相关基因精细定位和分子连锁标记开发提供了更多线索。     

Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.)

A genetic linkage map with 70 loci (55 SSR, 12 AFLP and 3 morphological loci) was constructed using 117 F₂ plants obtained from a cross between two upland cotton cultivars Yumian 1 and T586, which have relatively high levels of DNA marker polymorphism and differ remarkably in fiber-related traits. The linkage map comprised of 20 linkage groups, covering 525 cM with an average distance of 7.5 cM between two markers, or approximately 11.8% of the recombination length of the cotton genome. The present genetic linkage map was used to identify and map the quantitative trait loci (QTLs) affecting lint percentage and fiber quality traits in 117 F_2:3 family lines. Sixteen QTLs for lint percentage and fiber quality traits were identified in six linkage groups by multiple interval mapping: four QTLs for lint percentage, two QTLs for fiber 2.5% span length, three QTLs for fiber length uniformity, three QTLs for fiber strength, two QTLs for fiber elongation and two QTLs for micronaire reading. The QTL controlling fiber-related traits were mainly additive, and meanwhile including dominant and overdominant. Several QTLs affecting different fiber-related traits were detected within the same chromosome region, suggesting that genes controlling fiber traits may be linked or the result of pleiotropy.     

Detection and characterization of epistasis between QTLs on plant height in rice using single segment substitution lines

Hua-jing-xian 74 and its 12 single segment substitution lines (SSSLs) in rice were used as crossing parents to construct a half diallel crossing population. A total number of 91 materials were grown under three planting densities. By analysis of average plant height (PH) over all environments 10 SSSLs were detected with significant additives and 6 SSSLs with significant dominances. These SSSLs were further tested under different densities respectively, indicating that some of single locus effects were sensitive to densities and the conditions under the density of 16.7 cm × 16.7 cm maybe inhibited the expressing of these PH QTLs. Qualitative and quantitative analyses of each four participating genotypes indicated that digenic interactions among these QTLs were prevalent. Of 66 tested interactions, about 42.4% were epistatic (P < 5%). Although some QTLs hadn’t single locus effects, they were possible to form digenic interactions. A significant finding was that the detected epistases were mostly negative. Additionally, these epistases were also found being sensitive to planting densities, the conditions under the density of 10 cm × 16.7 cm perhaps promoted the expressing of epistatic interactions among PH QTLs.     

Construction of a genetic linkage map for witloof (Cichorium intybus L. var. foliosum Hegi)

A genetic linkage map based on an intraspecific cross between two inbred lines of witloof‐chicory (Cichorium intybus L. var. foliosum Hegi) has been constructed. In total, 129 RAPD markers were scored in 565 F₂ plants. Grouping of these markers at a LOD of threshold 4.0 resulted in nine linkage groups, which is equal to the chicory haploid genome. The nine linkage groups covered 609.6 cM. All 129 RAPD markers were linked to one of the nine groups. Three RAPD markers could not be mapped. Out of the 126 remaining RAPD markers, 18 showed segregation distortion with significance value of P < 0.01.