用闭合三角形杂交群体检测QTL等位位点差异

本文简述QTL定位和数量性状分子标记辅助选择的基本原理、基本方法,以及在实际应用中存在的一些问题。将12个不同作图群体构建的刚UP或SSR分子标记连锁图,根据其大多数分子标记所在的染色体节,再按每条染色体在各自连锁图中的相对长度整合在一起,然后将所定位的玉米株高QTL转换成整合图上的相对位置。结果发现,12个作图群体定位的75个玉米株高QTL位点遍布整个染色体组,QTL定位的重演性不高。分析认为,这是数量性状受众多微效多基因控制的必然现象。最后,提出用闭合三角形杂交群体进行QTL定位,检测QTL等位点的多重差异,并设想用这种方法验证或提高不同作图群体定位同一数量性状QTL的重演性。     

大豆重组自交系群体NJRIKY遗传图谱的加密及其应用效果

作物基因组研究,包括基因或数量性状位点(QTL)定位、图位克隆以及物理图谱构建等,首先必须建立具有丰富标记信息的高密度遗传连锁图谱。由科丰1号和南农1138-2杂交组合衍生的重组自交系群体NJRIKY已经构建了4张大豆遗传连锁图谱,但由于遗传信息和标记数目不够充分,在基因和QTL作图时仍然存在精确度和准确度问题。为增加NJRIKY图谱密度,本研究在967对SSR引物中获得了401个多态性SSR标记。结合其他分子数据,使用作图软件Mapmaker/Exp3.0b,获得一张含有553个遗传标记,25个连锁群,总长2071.6cM,平均图距3.70cM的新遗传连锁图谱,其中SSR标记316个,RFLP标记197个,EST标记39个,形态标记1个。连锁群上大于20cM的标记间隔由原来42个减少到2个。原图谱的3个SMV抗性基因定位于D1b连锁群末端的开放区间上且仅与一个RFLP标记连锁,利用加密图谱对Rsc-3、Rsc-7、Rsc-9、Rsc-13、Rsa、Rn1和Rn3等7个SMV抗性基因重定位,全部位于D1b连锁群,与相邻分子标记距离均小于6cM,其中Rsc-9、Rn1、Rsa的距离小于1cM,Rsc-13与EST标记GMKF168a共分离。对本群体农艺性状进行QTL重定位,获得8个性状相关的42个主效QTL,其中20个QTL遗传贡献率大于10%,与原图谱比较,新定位的各QTL的标记区间明显缩短,与相邻标记的连锁更加紧密。     

Analysis of QTL for yield-related traits in cassava using an F<Subscript>1</Subscript> population from non-inbred parents

A cassava F₁ population raised from the cross SC6 × Mianbao was used to construct a genetic linkage map. The map incorporated 200 polymorphic amplified fragment length polymorphism, sequence-related amplified polymorphism, simple sequence repeat (SSR), and expressed sequence tag (EST)–SSR markers which fit a 1:1 segregation ratio. It comprised 20 linkage groups (LGs) and spanned a genetic distance of 1645.1 cM with an average marker interval of 8.2 cM. Fifty-seven repeatedly detected QTLs (rd-QTLs) for three phenotypic traits (fresh root yield, root dry matter content, and root starch content) were identified in the F₁ population in four trials of year 2003, 2004, 2005, and 2008 by inclusive composite interval mapping. Among the 57 rd-QTLs, 25 rd-QTLs were linked to SSR/EST–SSR markers, which will help to facilitate marker-assisted selective breeding in cassava, and 15 marker intervals on ten LGs showed pleiotropic effects.     

Identification of QTLs for alpha acid content and yield in hop (Humulus Lupulus L.)

Amplified fragment length polymorphism (AFLP) and microsatellite (SSR) markers were applied to a segregation population of 111 genotypes derived from a pseudo-testcross of hop (Humulus lupulus L.) in order to detect quantitative trait loci (QTLs) for alpha-acid content and yield traits. A total of 199 markers (150 AFLPs, 43 SSRs, one hypothetical sex marker, five chs genes) were located on the 20 linkage groups (LGs) of the maternal and paternal maps, covering 706 and 616 cM, respectively. Due to the presence of 16 common biparental SSR markers, homology of seven LGs between parental maps could be inferred. The progeny segregated quantitatively for alpha-acid content and yield determined in the years from 2002–2006. A total of 13 putative QTLs for alpha acid content, 13 for dry cone weight and 18 for harvest index were identified on the two maps across years. Possible homologies between the detected QTLs on the two maps as well as in different years were established for all three traits. The most promising QTL for alpha acid content was identified on LG03 flanked by two AFLP markers (E-ACC-M-CAA103F*/P-ACA-M-CAC412F). From 13.80 to 36.64% higher content of alpha acids than the averages obtained in different years was observed in plants having both flanking markers. The candidate region for further characterization of QTLs for yield traits was located on LG01 where the putative QTLs for harvest index were detected on both maps in each of the 5 years. The QTLs identified represent an important improvement in alpha acids MAS and the first step towards marker-assisted breeding for hop yield.     

甘蓝型油菜籽粒含油量、蛋白质、纤维素及半纤维素含量QTL分析

以甘蓝型黄籽油菜GH06和甘蓝型黑籽油菜P174为亲本,通过单粒法连续自交8代构建重组自交系群体,应用SSR标记绘制31个连锁群(LGs)的遗传连锁图谱,图谱总长1437.1 cM,相邻标记间的平均距离为3.89 cM。对4个不同环境下RIL8群体中每个株系籽粒含油量、蛋白质、纤维素和半纤维素含量进行了近红外分析,性状相关性表明含油量与其他3个性状均表现负相关,蛋白质含量与纤维素和半纤维素分别表现负相关和正相关。结合构建的遗传图谱采用复合区间作图法分析4个性状QTL,共检测到26个QTL,分布在N2、N3、N8、N9、N11、N13、N16和N17连锁群上,其中8个含油量QTL可解释表型变异的4.96%~21.83%;6个蛋白含量QTL,可解释表型变异的3.12%~14.28%;4个纤维素含量QTL,可解释表型变异的4.60%~17.29%;8个半纤维素含量QTL,可解释表型变异率的6.66%~16.68%。在N8上,发现有含油量QTL与半纤维素含量QTL重叠的区段。在N9上,发现有纤维素含量QTL与半纤维素含量QTL重叠的区段,上述2个区段重叠QTL加性效应方向相反。本研究认为油菜种子含油量、蛋白质、纤维素和半纤维素属于典型的数量性状,受环境影响较大,与这些QTL紧密相关的分子标记可为下一步分子标记辅助育种提供一定技术支撑。     

QTL mapping of agronomically important traits in sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> L.)

Sorghum is one of the most important cereal crops; it is used to produce feed, sugar, and biofuel. To investigate genetic tradeoffs between grain and stem sugar production, we evaluated plant height, Brix (the percentage of soluble solids in stalk juice), 100-grain weight and flowering time over 3 years in a recombinant inbred line (RIL) population consisting of 189 individuals derived from a cross between the sweet sorghum cultivar ‘Rio’ and grain sorghum ‘BTx623’. We constructed a genetic linkage map (total length, 1418.71 cM; average distance between markers, 11.26 cM), which consisted of 118 simple sequence repeat (SSR) and 8 insertion-deletion (INDEL) markers. A total of 14 QTLs were detected on chromosomes 1, 3, 6, 7, and 9, which included 6 QTLs for plant height; 4 for Brix; and 2 QTLs for each 100-grain weight and flowering time. Eight QTLs were detected at least in 2 years. These results will be useful for future QTL fine mapping and gene mining for these traits, and useful for the improvement of sorghum through molecular marker-assisted selection.     

陆地棉光合相关性状的QTL定位分析

光合作用是棉花产量的主要物质来源。本研究以高光效陆地棉冀优861和低光效陆地棉新陆早25号为亲本组配的196个F₂单株为作图群体,利用SSR（Simple Sequence Repeat）标记构建陆陆杂交遗传连锁图谱,共有30个标记位点连锁,包含4个连锁群,全长244.4cM。利用QTL IciMapping 4.1软件的完备区间作图法对冀优861×新陆早25号F_2:3家系的光合相关性状进行QTL作图分析,共定位到光合相关5个性状的10个QTLs,其中1个光合速率QTL和1个胞间CO₂浓度QTL分别定位在D3和D7染色体上。本研究为棉花光合相关性状QTL的精细定位及分离克隆打下基础,为聚合棉花高光效分子标记辅助育种提供理论依据。     

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.     

Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton

Genetic mapping is an essential tool for cotton (Gossypium hirsutum L.) molecular breeding and application of DNA markers for cotton improvement. In this present study, we evaluated an RI population including 188 RI lines developed from 94 F₂-derived families and their two parental lines, ‘HS 46’ and ‘MARCABUCAG8US-1-88’, at Mississippi State, MS, for two years. Fourteen agronomic and fiber traits were measured. One hundred forty one (141) polymorphic SSR markers were screened for this population and 125 markers were used to construct a linkage map. Twenty six linkage groups were constructed, covering 125 SSR loci and 965 cM of overall map distance. Twenty four linkage groups (115 SSR loci) were assigned to specific chromosomes. Quantitative genetic analysis showed that the genotypic effects accounted for more than 20% of the phenotypic variation for all traits except fiber perimeter (18%). Fifty six QTLs (LOD > 3.0) associated with 14 agronomic and fiber traits were located on 17 chromosomes. One QTL associated with fiber elongation was located on linkage group LGU01. Nine chromosomes in sub-A genome harbored 27 QTLs with 10 associated with agronomic traits and 17 with fiber traits. Eight chromosomes in D sub-genome harbored 29 QTLs with 13 associated with agronomic traits and 16 with fiber traits. Chromosomes 3, 5, 12, 13, 14, 16, 20, and 26 harbor important QTLs for both yield and fiber quality compared to other chromosomes. Since this RI population was developed from an intraspecific cross within upland cotton, these QTLs should be useful for marker assisted selection for improving breeding efficiency in cotton line development. Paper number J1116 of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

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.     

Fine mapping of major QTLs for alkaline tolerance at the seedling stage in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) through genetic linkage analysis combined with high-throughput DNA sequencing

Exploiting genes and quantitative trait loci (QTLs) related to maize (Zea mays L.) alkaline tolerance is helpful for improving alkaline resistance. To explore the inheritance of maize alkaline tolerance at the seedling stage, a mapping population comprising 151 F_2:3 lines derived from the maize cross between Zheng58, tolerant to alkaline, and Chang7-2, sensitive to alkaline, was used to establish a genetic linkage map with 200 SSR loci across the 10 maize linkage groups, with an average interval of 6.5 cM between adjacent markers. QTLs for alkaline resistant traits of alkaline tolerance rating (ATR), germination rate (GR), relative conductivity (RC), weight per plant (WPP) and proline content (PC) were detected. The obtained results were as follows: Five QTLs on chromosomes 2, 5 and 6 (GR and WPP: chr. 2; PC and ATR: chr. 5; and RC: chr. 6) were mapped. For precise mapping of the QTLs related to alkaline resistance, two bulked deoxyribonucleic acid (DNA) pools were constructed using individual DNAs from the most tolerant 30 F₂ individuals and the most sensitive 30 F₂ individuals according to the ATR and used to establish a high density map of SLAF markers strongly associated with the ATR by specific locus amplified fragment sequencing (SLAF-Seq) combined with super bulked segregant analysis (superBSA). One marker-intensive region involved three SLAFs at 296,000–6,203,000 bp on chromosome 5 that were closely related to the ATR. Combined with preliminary QTL mapping with superBSA, two major QTLs on chromosome 5 associated with alkaline tolerance at the maize seedling stage were mapped to marker intervals of dCap-SLAF31521 and dCap-SLAF31535 and phi024 and dCap-SLAF31521, respectively. These QTL regions involved 9 and 75 annotated genes, respectively. These results will be helpful for improving maize alkaline tolerance at the seedling stage by marker-assisted selection programs and will be useful for fine mapping QTLs for maize breeding.     

Developing new markers and QTL mapping for greenbug resistance in sorghum [Sorghum bicolor (L.) Moench]

Greenbug is a major damaging insect to sorghum production in the United States. Among various virulent greenbug biotypes, biotype I is the most predominant and severe for sorghum. To combat with the damaging pest, greenbug resistant sources were obtained from screening sorghum germplasm collection. This experiment was conducted to identify the genomic regions contributing resistance to greenbug biotype I in a sorghum accession, PI 607900. An F₂ mapping population consisting of 371 individuals developed from a cross of the resistant line with an elite cultivar, BTx623 (susceptible) were tested and scored for their response to greenbug feeding in the greenhouse. Significant differences in resistance were observed between the two parental lines and among their F₂ progeny in response to greenbug feeding at 7, 10, 14 and 21 days after infestation. A linkage map spanning a total length of 729.5 cM across the genome was constructed with 102 polymorphic SSR markers (69 genomic and 33 EST SSRs). Of those microsatellite markers, 48 were newly developed during this study, which are a useful addition for sorghum genotyping and genome mapping. Single marker analysis revealed 29 markers to be significantly associated with the plant response to greenbug feeding damage. The results from interval mapping, composite interval mapping and multiple interval mapping analyses identified four major QTLs for greenbug resistance on chromosome 9. These QTLs collectively accounted for 34–82 % of the phenotypic variance in greenbug resistance. Minor QTLs located on chromosome 3 explained 1 % of the phenotypic variance in greenbug resistance. The major allele for greenbug resistance was on chromosome 9 close to receptor-like kinase Xa21-binding protein 3. These markers are useful to screen more resistant genotypes. Furthermore, the markers tagged to QTL regions can be used to enhance the sorghum breeding program for greenbug resistance through marker-assisted selection and map-based cloning.     

烤烟6个农艺性状的QTL定位

由于烟草的分子标记开发和遗传图谱构建十分困难,迄今烟草中有关数量性状基因座(QTL)的定位研究仍非常有限。本研究利用一个由207个株系组成的烤烟DH群体及基于该群体所构建的含有24个连锁群、611个SSR标记,总长为1 882.1 cM的遗传图谱,采用复合区间作图方法,对株高(PH)、茎围(SG)、节距(IL)、叶片数(LN)、最大腰叶长(LWL)和最大腰叶宽(WWL) 6个与叶片产量有关的农艺性状进行QTL定位分析。共检测到69个QTL,大部分QTL的效应值较小,仅有4个具有较大的效应值,可解释大约15%~20%的表型变异。6个性状之间大多彼此相关。与此相符,在基因组中发现存在许多小区域,每个区域包含两个或两个以上紧密连锁的不同性状的QTL。     

栽培种花生遗传图谱的构建及主茎高和总分枝数QTL分析

栽培种花生是异源四倍体,基因组大,构建花生的分子遗传连锁图谱并对相关性状进行QTL定位研究的工作缓慢。本研究以遗传差异大的亲本组配杂交组合富川大花生×ICG6375构建F2作图群体,采用公开发表的2653对SSR引物,构建了一张含有234个SSR标记、分布于20个连锁群的栽培种花生遗传图谱。该图谱覆盖基因组的长度为1683.43c M,各个连锁群长度在36.11~131.48 c M之间,每个连锁群的标记数在6~15个之间,标记间的平均距离为7.19 c M。结合F3在湖北武汉和阳逻环境下的主茎高和总分枝数鉴定结果,应用Win QTLCart 2.5软件采用复合区间作图法进行了QTL定位和遗传效应分析。共检测到17个与主茎高和总分枝数相关的QTL位点,贡献率在0.10%~10.22%之间,分布于8个连锁群上。综合分析武汉和阳逻环境的鉴定结果,获得重复一致的与主茎高相关的6个QTL,其中q MHA061.1和q MHA062.1位于连锁群LG06上TC1A2~AHGS0153标记区间,贡献率为5.49%~8.95%;q MHA061.2和q MHA062.2位于LG06上AHGS1375~PM377标记区间,贡献率为2.93%~5.83%;q MHA092.2和q MHA091.1位于连锁群LG09上GM2839~EM87标记区间,贡献率为0.53%~9.43%。     

Genetic mapping for resistance to gray leaf spot in maize

The molecular marker technology has been used on mapping of quantitative trait loci (QTLs) associated with plant resistance. The objectives of this research were to estimate genetic parameters and to map genomic regions involved in the resistance to gray leaf spot in maize. Ninety F₃ families from the BS03 (susceptible) and BS04 (resistant) cross were used. Field trials were performed using a 10 × 10 square lattice design with three replications. Data from 62 SSR markers were used for linkage analysis. The locations of the QTLs on the linkage groups were determined by composite interval mapping method and the phenotypic variance explained by each marker was determined by regression analysis. Several QTLs associated to disease resistance were identified in the population BS03 × BS04. Some QTLs showed significant effects over the different environments studied. The existence of significant QTLs in common among different environments indicates these genomic regions as possible new tools for marker-assisted selection in maize breeding programs.     

Identification of QTLs for agronomic traits using association mapping in lentil

A diverse panel of 96 genotypes of lentil was used in this study to identify QTL for nine agronomic traits through marker-trait association analysis. This study showed significant genetic variability among the lentil genotypes for nine agronomic traits and had medium to large broad sense heritability estimates (h² =?0.58–0.95). Screening of 534 SSR markers resulted in 266 polymorphic loci that generated 697 alleles ranging from 2 to 16 alleles per locus across the genotypes. The model-based population structure analysis identified two distinct subpopulations among lentil genotypes and each subpopulation did not show any admixture. Marker trait association (MTA) analysis following ML model resulted in the identification of 24 MTAs for nine traits at P?<?0.01. The per cent of phenotypic variation explained by each associated marker with particular agronomic trait ranged from 7.3 to 25.8%. The highest proportion of total phenotypic variation (23.1–25.8%) was explained by the QTLs controlling the primary branches/per plant. In the present study, few EST-SSR markers showed significant association with days to maturity, pods/plant, secondary branches/plant, 100 seed weight, yield/plant and reproductive duration and explained large phenotypic variation (7.3–23.8%). Hence, these markers can be used as functional markers in lentil breeding program for developing improved cultivars.     

陆地棉重组近交系产量及其构成因素的QTL分析

利用爱字棉1517×德州047重组近交系(recombinant inbred lines, RIL)中G6群体构建的SSR遗传连锁图谱及基于混合线性模型的复合区间作图法对QTL进行定位,并对主效QTL,加性×加性上位性QTL及与环境互作效应进行分析,为利用分子聚合方法提高产量提供理论依据。对2006年、2008年以及2009年的产量性状进行分离分析,检测到24个不同年份的主效QTL,其中相关于单株籽棉、单株皮棉、衣分、子指以及单株铃数的分别检测到1个不同年份稳定存在的主效QTL;对3年的产量性状作环境因子联合分析,检测到14个主效QTL,其中6个与环境互作,检测到20对加加上位性QTL,其中7对与环境互作。不同年份检测的稳定且受环境影响小或不受环境影响的与近处标记紧密连锁的主效QTL可用于分子标记辅助选择,以提高育种的效率。     

海陆渐渗系棉花吐絮期叶绿素含量、荧光参数及相关性状的QTL定位分析

以海陆渐渗系13-1×辽棉12组配的195个单株的F2群体为作图群体,利用SSR(Simple sequence repeat)标记和Join Map3.0软件构建遗传连锁图谱,构建的遗传连锁图谱包含39个多态性标记、13个连锁群,该图谱总长1174.4 c M,覆盖棉花基因组的26.7%,利用Ici Mapping完备区间作图法对F2:3家系进行相关性状的QTL定位,共检测到30个叶绿素荧光参数、7个叶片干物质含量、6个叶面积指数、1个叶绿素含量的QTL位点,分布在8条染色体上,在同一染色体共标记区间内存在多个性状的QTL,部分位点加性遗传效应来自同一亲本,与干物质含量、最大光化学效应相关的QTL位点在3条染色体上不同标记区间内重复出现,与叶面积指数、最大光化学效应相关的QTL位点在4条染色体上不同标记区间内重复出现,表现出遗传上的一因多效或基因连锁效应,可用于高光效聚合育种。     

利用重组自交系群体对水稻产量相关性状的QTL分析

利用水稻(Oryza sativa L．)珍汕97和SLG组合的重组自交系群体和177个微卫星标记,采用复合区间作图法对产量相关性状进行了数量性状基因(QTL)定位,共得到38个QTLs。单个QTL解释这些性状6．6％～32．9％的性状变异,各性状QTL的累积表型贡献率达21．3％～79．5％。大多数性状之间具有显著的表型相关性,相关性较高的性状之间常具有较多共同或紧密连锁的QTL。