玉米RFLP连锁图谱构建及大斑病QTL定位

玉米大斑病菌存在有生理小种分化的现象,目前5个已定名的生理小种在我国均已发现,还有一些尚未定位名的新类群也出出现,提高玉米对大斑病的抗性,只有提高数量抗性才能达到目的,为了弄清楚玉米对大斑病数量抗性的基因数目及效效应,利用抗病自交5系P138和感病自交系缩3为亲本构建了F2：3家系群体,采用RFLP标记构建了包含了124个标记的玉米RFLP连锁图,覆盖玉米基因组1999．8cM,标记间平均距离为16．5cM,定位了玉米大斑病的病斑长,病斑宽和病斑面积的QTL分别为3、3、2个,其联合贡献率分别为58．1％、71．5％和27．5％,没有检测到病斑数／叶的QTL,其表现为单基因或者寡基因控制的性状,研究结果增加了对玉米大斑病的认识,对玉米抗大斑病育种具有重要的指导意义。     

水稻叶绿素含量的QTL定位

利用由两个籼稻品种Acc8558和H359杂交构建的一个包含131个株系(F19)的重组自交系群体,及其相应的包含147个RFLP和78个AFLP标记的遗传图谱,采用多性状复合区间定位方法,对控制水稻叶绿素含量的QTL进行了定位分析。对叶绿素a和叶绿素b含量各检测到6个QTL,其中5个QTL在两性状问是相同的。这些QTL主要分布在第1和第4染色体上,因此这两条染色体对叶绿素含量是重要的。QTL qChlAlc／qChlBlb(二者位置相同)在4个观测时期均表现较大效应,且在最后的剑叶期贡献最大,因此对叶绿素含量最为重要。另两个QTL(qCh-LA4a／qChlB4a和qChlA4b／qChlB4b)只在第2次观测时期效应显著,表明它们只在特定发育阶段发挥作用。     

水旱条件下小麦叶面积指数和叶绿素含量QTL定位

利用春小麦Worrakatta×Berkut重组自交系(RIL,recombinant inbred line)的309份家系为材料,在正常灌溉和干旱胁迫两个处理下,分别对小麦开花期、灌浆期和成熟期的叶面积指数(LAI,leaf area index),抽穗期、开花期和灌浆期的旗叶叶绿素含量(CC,chlorophyl...     

玉米抗南方锈病基因的QTL定位

为发掘新的抗南方锈病基因资源,本研究以感病自交系黄早四为母本、抗病自交系W456为父本,构建F2群体并开展抗病基因定位研究。采用人工接种鉴定的方法对两个亲本、F1、F2群体及对照材料进行表型鉴定和遗传分析。利用均匀覆盖10条染色体的200个SSR标记,分析240个F2单株的基因型并构建含有200个SSR位点的遗传连锁图,连锁图总长度3331 cM,标记间平均距离16.6 cM。使用QTL IciMapping V4.1软件中的完备区间作图法对抗病QTL进行分析,共检测到6个控制南方锈病的QTL:qSCR3、qSCR7、qSCR8-1、qSCR8-2、qSCR9和qSCR10,邻近标记分别为umc2105和umc1729、umc1066和bnlg2271、umc1904和umc1984、umc1984和bnlg1651、umc1957和bnlg1401、umc2034和umc1291,分别位于3、7、8、9和10号染色体上,其中8号染色体上有两个位点,标记区间长度在5～19 cM之间。单个QTL的表型贡献率在2.61%～24.19%之间,可以解释表型总变异的62.3%,其中3个QTL贡献率大于10%,位于10号染色体上的qSCR10贡献率最大,可解释表型变异的24.19%。通过对目标区间标记加密,将该位点的定位区间进一步缩小到2.51 cM内,与两侧标记的距离分别是2.15 cM和0.36 cM。初步定位得到10号染色体上存在抗南方锈病的主效QTL,可为抗病品种的培育提供参考。     

四倍体栽培棉种产量和纤维品质性状的QTL定位

陆地棉和海岛棉是两个不同的四倍体栽培种 ,但在生产上各有其特点 ,陆地棉丰产性强 ,海岛棉纤维品质优良 ,利用其种间杂交群体定位产量和品质性状的QTL ,对于分子标记辅助的海岛棉优质纤维向陆地棉转移很有意义。以SSR和RAPD为分子标记 ,陆地棉与海岛棉杂种 (邯郸 2 0 8×Pima90 )F2 群体为作图群体 ,构建了一张含 12 6个标记的遗传图谱 ,包括 6 8个SSR标记和 5 8个RAPD标记 ,可分为 2 9个连锁群 ,标记间平均距离为 13 7cM ,总长1717 0cM ,覆盖棉花总基因组约 34 34% ;以遗传图 12 6个标记为基础 ,对F2 :3 家系符合正态分布的 10个农艺性状及纤维品质性状进行全基因组QTL扫描 ,结果发现 2 9个QTL分别与产量和品质性状有关。其中与衣指、籽指、皮棉产量、子棉产量、衣分等产量性状相关的QTL分别有 1、3、5、6和 1个 ,与纤维长度、整齐度、强度、伸长率和马克隆值等品质性状相关的QTL分别有 2、4、2、4和 1个。各QTL解释的变异量在 12 4 2 %～ 47 0 1%之间。其中比强度有关的 2个QTL能够解释的表型变异率分别为 34 15 %和 13 86 %。     

玉米5个农艺性状的QTL定位

利用“豫玉22”构建的266个玉米F2：3家系为材料,通过一年两点的随机区组田间试验和分子标记分析,研究了玉米穗位高、雄穗分支数、茎粗、抽雄期、吐丝期5个重要农艺性状。相关分析表明,穗位高、雄穗分支数、茎粗与单株产量显著正相关,抽雄期与吐丝期高度正相关,雄穗分支数与茎粗显著正相关。采用复合区间作图法,通过500次排列测验分别确定各性状的LOD阈值,在武汉和襄樊两地共定位了7个穗位高QTL、9个雄穗分支数QTL、8个茎粗QTL、9个抽雄期QTL和7个吐丝期QTL;这些QTL在染色体上分布不均匀,具有集中分布的特点。研究表明,数量性状间的表型相关可能源于控制数量性状的QTL位点间的相关。     

玉米籽粒重金属铅(Pb2+)含量的QTL定位

铅(Pb²⁺)是现存环境最大量的有毒重金属污染元素,在我国特别是西南地区种植的玉米受重金属Pb²⁺污染日益严重,已严重影响到食物安全。文章利用玉米籽粒Pb²⁺低富集自交系178和籽粒Pb²⁺高富集自交系9782杂交衍生的重组自交系群体为作图群体,利用165对SSR多态性标记,构建了总长度为1499.85 cM、标记间平均距离为9.07 cM的分子遗传图谱,对玉米籽粒Pb²⁺含量性状进行了QTL定位分析,以期为选育籽粒低富集Pb²⁺的玉米新品种提供参考。结果表明,在Pb²⁺浓度为333.32 mg/kg胁迫下,共检测到2个与籽粒Pb²⁺含量相关的QTL,分别位于玉米第1、第4号染色体,其中qPC1位于标记区间umc1661~phi002h之间,表型贡献率为11.13%,加性效应为0.062;qPC4位于umc1117~nc005之间,表型贡献率为5.55%,加性效应为-0.044。性状相关分析结果表明,籽粒中Pb²⁺含量与穗长、穗粗、行粒数、穗重和百粒重等产量性状间均未达到显著水平,表明选育玉米籽粒Pb²⁺低富集的新自交系或杂交种不一定会影响到产量性状,而且籽粒Pb²⁺含量是一个相对独立的遗传性状。     

正常与水分胁迫下水稻叶片叶绿素含量的QTL分析

随着分子标记技术的发展,利用不同的遗传群体对叶绿素的分子遗传机理进行了一些探索,定位了一些控制叶绿素含量的数量性状基因座(Quantitative trait loci, QTL)。该研究着眼于当前干旱严重影响农业生产的形势,以水稻重组自交系‘珍汕97B’בIRAT109’ F₉代群体195个株系为材料,在正常与水分胁迫环境下研究叶片叶绿素含量与光合速率的变化及相关性,定位不同水分条件下影响叶绿素含量的QTL,为阐明干旱环境下水稻叶绿素含量的分子遗传机理、分子标记辅助育种和节水抗旱稻培育提供理论基础和依据。研究表明叶绿素含量与光合速率在正常供水下呈极显著正相关(r=0.185 7^**),但在干旱下则表现无关(r=0.076 6)。QTL定位共检测到13个影响叶绿素含量的主效QTL,分别位于第1、2、3、4、5、6、10染色体:其中在干旱处理下检测到6个,其联合贡献率为47.39%;在正常供水下检测到7个,联合贡献率达56.19%。检测到显著互作效应位点16对:其中干旱处理下有4对显著互作,联合贡献率为18.57%;正常供水下有12对显著互作,联合贡献率达38.49%。     

水稻籽粒锌含量的QTL定位

锌元素的营养失衡已成为影响人类健康的最重要因素之一,籽粒锌含量的QTL（quantitative trait loci）定位对研究富锌水稻的遗传育种具有重要的意义。以水稻（Oryzasativa L．）亲本奉新红米和明恢100杂交的145个株系的F2群体为实验材料,利用92个SSR（simple sequence repeat）标记对水稻籽粒锌含量进行了QTL定位,共检测到3个QTLs,分别定位于第3、6和11染色体上,对表型变异的贡献率分别为4．97％、12．75％和7．74％。其中位于第3染色体上的分子标记RM186和RM168之间的QZN3对表型变异的贡献率最大,其增效等位基因来自亲本明恢100,表现为部分显性。3个QTLs的联合贡献率为25．46％。具有基因累加效应。该研究结果有利于深入理解水稻锌含量的遗传基础,为锌含量的QTL精细定位、基因克隆和分子标记辅助选择提供依据。     

水稻籽粒锌含量的QTL 定位

锌元素的营养失衡已成为影响人类健康的最重要因素之一, 籽粒锌含量的QTL(quantitative trait loci)定位对研究富锌水稻的遗传育种具有重要的意义。以水稻(Oryza sativa L.)亲本奉新红米和明恢100杂交的145个株系的F2群体为实验材料, 利用92个SSR(simple sequence repeat)标记对水稻籽粒锌含量进行了QTL定位, 共检测到3个QTLs , 分别定位于第3、6和11染色体上, 对表型变异的贡献率分别为4.97%、12.75%和7.74%。其中位于第3染色体上的分子标记RM186和RM168之间的QZN3对表型变异的贡献率最大, 其增效等位基因来自亲本明恢100, 表现为部分显性。3个QTLs 的联合贡献率为25.46%, 具有基因累加效应。该研究结果有利于深入理解水稻锌含量的遗传基础, 为锌含量的QTL精细定位、基因克隆和分子标记辅助选择提供依据。     

QTL mapping for resistance of maize to grey leaf spot

Grey leaf spot (GLS) is a global maize leaf disease that seriously endangers maize production. Discovering and utilizing genetic loci for GLS resistance would be useful for breeding new varieties with improved resistance. In this study, 233 F_2:3 families (produced from the susceptible inbred line 08‐641 × the resistant inbred line 446) were used for quantitative trait locus (QTL) mapping of resistance to GLS. Five GLS resistance QTLs were detected on chromosomes 1, 2, 3, 4, and 6, which explained 6.7%‐21.3% of the phenotypic variation. The QTLs, qRgls.CH‐4, qRgls.CH‐1, qRgls.CH‐2, and qRgls.CH‐6, were stably expressed in the four environments, and all loci for GLS resistance were derived from the resistant parent, 446. The additive effects of qRgls.CH‐4, qRgls.CH‐1, and qRgls.CH‐6 were significantly greater than their single dominant effects, which may be beneficial for GLS resistance breeding. The QTL qRgls.CH‐6, located in bins 6.02–6.05, did not overlap with any previously reported resistance QTL and thus was identified here for the first time. QTL analysis of PI (leaf performance index) detected three leaf function QTLs on chromosomes 4, 8, and 9 were related to GLS resistance and explained 4.8%‐6.2% of the phenotypic variation. Among them, qPI.CH‐4 was significantly stronger expressed in several environments; this allele associated with increased leaf function came from the resistant parent, 446, and its interval overlapped with that of qRgls.CH‐4. Furthermore, both qRgls.CH‐4 and qPI.CH‐4 were located in a hotspot area for GLS resistance in bins 4.05‐4.06, indicating that GLS resistance was significantly related to leaf performance and that GLS significantly reduced leaf photosynthetic performance.     

玉米SSR连锁图谱构建及叶面积的QTL定位

叶片是玉米进行光合作用的主要器官,叶面积的大小(尤其是穗三叶面积)对于玉米干物质的积累及产量形成起着至关重要的作用。研究玉米叶面积的遗传基础对于指导玉米高产育种具有理论意义。文章以两个叶面积差异显著的亲本478×武312为基础材料所构建的218个F8代的重组自交系为作图群体,构建了一张包含184个SSR标记的遗传连锁图谱,图谱总长度为2084.1cM,平均图距为11.3cM。通过两年的田间试验对玉米叶面积(穗三叶)进行了QTL定位分析。两年共定位到7个和叶面积相关的QTL位点,2006年定位到4个QTL位点;2007年定位到3个QTL位点。在第2染色体umc1542-umc1518标记区间发现一个主效QTL位点,该位点可以在两年同时检测到,两年分别解释12.5%和17.3%的表型变异。该位点能稳定地检测到且具有较大的贡献率,可能会在玉米叶面积分子标记辅助选择上有所应用。     

QTL mapping of resistance to Sporisorium reiliana in maize

We mapped and characterized quantitative trait loci (QTL) for resistance to Sporisorium reiliana. A population of 220 F₃ families produced from the cross of two European elite inbreds (D32, D145) was evaluated with two replications at a French location with high natural incidence of S. reiliana and at a Chinese location employing artificial inoculation. The 220 F₃ families were genotyped with 87 RFLP and seven SSR markers. Using composite interval mapping, we identified two different sets of 3 and 8 QTL for the French and the Chinese locations explaining 13% and 44% of respectively. Individual QTL explained up to 14% of σ^² _p. The 11 QTL mapped to eight maize chromosomes and displayed mostly additive or partial dominant gene action. Significant digenic epistatic interactions were detected for one pair of these QTL. Only a few QTL for S. reiliana were in common with QTL for resistance to Ustilago maydis and Puccinia sorghi, identified at a German location for the same population. Consequently, in our materials resistance to these three fungal pathogens of maize seems to be inherited independently. Received: 14. December 1998 / Accepted: 30 January 1999     

QTL mapping of resistance to Fusarium ear rot using a RIL population in maize

Fusarium ear rot is a prevalent disease in maize, reducing grain yields and quality. Resistance breeding is an efficient way to minimize losses caused by the disease. In this study, 187 lines from a RIL population along with the resistant (87-1) and susceptible (Zong 3) parents were planted in Zhengzhou and Beijing with three replications in years 2004 and 2006. Each line was artificially inoculated using the nail-punch method. Significant genotypic variation in response to Fusarium ear rot was detected in both years. Based on a genetic map containing 246 polymorphic SSR markers with average genetic distances of 9.1 cM, the ear-rot resistance QTL were firstly analyzed by composite interval mapping (CIM). Three QTL were detected in both Zhengzhou and Beijing in 2004; and three and four QTL, respectively, were identified in 2006. The resistant parent contributed all resistance QTL. By using composite interval mapping and a mixed model (MCIM), significant epistatic effects on Fusarium ear rot as well as interactions between mapped loci and environments were observed across environments. Two QTL on chromosome 3 (3.04 bin) were consistently identified across all environments by the two methods. The major resistant QTL with the largest effect was flanked by markers umc1025 and umc1742 on chromosome 3 (3.04 bin), explaining 13–22% of the phenotypic variation. The SSR markers closely flanking the major resistance QTL will facilitate marker-assisted selection (MAS) of resistance to Fusarium ear rot in maize breeding programs.     

Spurious linkage between markers in QTL mapping

Selective genotyping of extreme progeny is a powerful method to increase the information content per individual when looking for quantitative trait loci (QTLs) using molecular markers for which a map is known. However, if marker information from the selected individuals is used to construct the map of the markers, this can lead to distorted segregation of the markers that in turn can lead to the estimation of a spurious linkage between independently inherited markers. The mistaken estimation of linkage between independently inherited markers will occur when there are two (or more) independently inherited QTLs linked to two (or more) markers and the same individuals are used to estimate the map of the markers and to do the QTL estimation. The incorrect linkage occurs because in selecting individuals from the tails of the phenotypic distribution we will also be selecting certain combinations of the markers instead of obtaining a random sample of the true distribution of the marker genotypes. Analytical results are outlined and the analyses of a simulated data set illustrate the problems that could arise when data from individuals chosen by selective genotyping are incorrectly employed to construct a marker map. A strategy is proposed to remedy this problem.     

Genome-wide analysis of maize cytoplasmic male sterility-S based on QTL mapping

Three types of sterile cytoplasm in cytoplasmic-male-sterility (CMS) maize, T, C and S, can be identified according to their fertility-restoration and mitochondrial DNA RFLP patterns. CMS-S, which is the least stable among the three types of CMS, is controlled by sterile cytoplasm interactions with certain nuclear-encoded factors. We constructed a high-resolution map of loci associated with male-restoration of CMS-S in BC1 populations of maize. The map covers 1730.29 cM, including 32 RFLP, 51 SSR 62 RAPD and 21 AFLP markers. Genome-wide QTL analysis detected 6 QTLs with significant effects on male fertility as assessed by their starch-filled pollen ratios. Four QTLs out of six were located between the SSR markers MSbnlg1633-Mrasg20, MSbnlg1662-Msume1126, MSume1230-MSumc1525, and RAPD marker MraopQ07-2-MraopK06-2 on chromosome 2. Two other minor loci were mapped between MraopK16-1-Mraopi4-1, on chromosome 9, and between Msuncbnlg1139-MraopR10-2, on chromosome 6. The Rf3 nuclear restoring gene was precisely located on the chromosome 2, 2.29 cM to the left of umc1525 and 8.9 cM to the right of umc1230. The results provide important markers for marker-assisted selection of stable CMS-S maize.     

玉米杂交种掖单13号的SSR连锁图谱构建与叶夹角和叶向值的QTL定位与分析

为了增加单位面积产量, 玉米育种者已经开始了更密植更紧凑株型的选育。叶夹角和叶向值是评价玉米株型的重要指标。本研究以掖478×丹340的500个F2单株为作图群体, 构建了具有138个位点的SSR标记连锁图谱, 图谱总长度为1 394.9 cM, 平均间距10.1 cM。利用397个F2：3家系对叶夹角和叶向值进行QTL定位分析, 结果表明: 叶夹角和叶向值分别检测到6和8个QTL, 累计解释表型变异41.0%和60.8%, 单个QTL的贡献率在2.9%~13.6%之间。与叶夹角和叶向值有关的基因主要作用方式为加性和部分显性。此外两个性状共检测到9对上位性互作位点, 表明上位性互作在叶夹角和叶向值的遗传中也起较重要的作用。     

Statistical methods for QTL mapping in cereals

This paper gives an overview of the statistical theory suitable for mapping quantitative trait loci in experimental populations derived from inbred parents, with a particular emphasis on methodology for cereal crops. The basic theory is described, and some new areas of statistical research appropriate for mapping in cereal crops are discussed.     

QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum

Capsaicinoids are unique compounds produced only in peppers (Capsicum spp.). Several studies using classical quantitative trait loci (QTLs) mapping and genomewide association studies (GWAS) have identified QTLs controlling capsaicinoid content in peppers; however, neither the QTLs common to each population nor the candidate genes underlying them have been identified due to the limitations of each approach used. Here, we performed QTL mapping and GWAS for capsaicinoid content in peppers using two recombinant inbred line (RIL) populations and one GWAS population. Whole‐genome resequencing and genotyping by sequencing (GBS) were used to construct high‐density single nucleotide polymorphism (SNP) maps. Five QTL regions on chromosomes 1, 2, 3, 4 and 10 were commonly identified in both RIL populations over multiple locations and years. Furthermore, a total of 109 610 SNPs derived from two GBS libraries were used to analyse the GWAS population consisting of 208 C. annuum‐clade accessions. A total of 69 QTL regions were identified from the GWAS, 10 of which were co‐located with the QTLs identified from the two biparental populations. Within these regions, we were able to identify five candidate genes known to be involved in capsaicinoid biosynthesis. Our results demonstrate that QTL mapping and GBS‐GWAS represent a powerful combined approach for the identification of loci controlling complex traits.     

QTL mapping with near-isogenic lines in maize

A set of 89 near-isogenic lines (NILs) of maize was created using marker-assisted selection. Nineteen genomic regions, identified by restriction fragment length polymorphism loci and chosen to represent portions of all ten maize chromosomes, were introgressed by backcrossing three generations from donor line Tx303 into the B73 genetic background. NILs were genotyped at an additional 128 simple sequence repeat loci to estimate the size of introgressions and the amount of background introgression. Tx303 introgressions ranged in size from 10 to 150 cM, with an average of 60 cM. Across all NILs, 89% of the Tx303 genome is represented in targeted and background introgressions. The average proportion of background introgression was 2.5% (range 0–15%), significantly lower than the expected value of 9.4% for third backcross generation lines developed without marker-assisted selection. The NILs were grown in replicated field evaluations in two years to map QTLs for flowering time traits. A parallel experiment of testcrosses of each NIL to the unrelated inbred, Mo17, was conducted in the same environments to map QTLs in NIL testcross hybrids. QTLs affecting days to anthesis, days to silking, and anthesis-silk interval were detected in both inbreds and hybrids in both environments. The testing environments differed dramatically for drought stress, and different sets of QTLs were detected across environments. Furthermore, QTLs detected in inbreds were typically different from QTLs detected in hybrids, demonstrating the genetic complexity of flowering time. NILs can serve as a valuable genetic mapping resource for maize breeders and geneticists. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.