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.     

甘蓝型油菜千粒重性状的QTL初步定位研究

千粒重是油菜重要的产量相关性状之一,构建油菜遗传连锁图谱是研究其产量性状基因的前提。本研究利用小孢子培养技术,选育出了甘蓝型油菜大粒品系(G-42)和小粒品系(7-9)的纯合DH系DH-G-42和DH-7-9,其千粒重分别为6.24 g和2.42 g,二者比值达2.58。以DH-G-42为母本、DH-7-9为父本,构建了含190个单株的F2遗传作图群体,利用SSR和SRAP标记技术绘制遗传连锁图谱,该图谱共包含20个连锁群,涉及128个SSR标记和100个SRAP标记,图谱总长1546.6cM,标记间平均图距为6.78cM。本研究共检测到3个与千粒重性状相关的QTL,分别位于A9和C1连锁群,其中qSW-A9-1和qSW-A9-2贡献率分别达到10.98%和27.45%,均可视为控制粒重的主效QTL。本研究为后续进行油菜千粒重性状QTL的精细定位分析、分子标记辅助选择育种及新基因的克隆等奠定了基础。     

基于SRAP分子标记的冰草遗传连锁图谱构建

构建高密度遗传连锁图谱是冰草抗性、品质、产量等重要性状QTL精细定位及标记辅助育种研究的基础。该试验以四倍体杂交冰草F2群体的202个分离单株及其亲本为材料,利用SRAP分子标记技术和Join Map 4.0作图软件对冰草的遗传连锁图谱进行了构建。结果表明:(1)共筛选出22对多态性好、标记位点清晰稳定的SRAP适宜引物,对冰草杂种F2分离单株的基因组DNA进行PCR扩增,共获得510个SRAP多态性标记位点,其比率占88.2%。(2)偏分离分析表明,偏分离标记比率仅为14.12%,符合遗传作图的要求。(3)成功构建了冰草的SRAP分子标记遗传连锁图谱,该图谱有14个连锁群、510个标记,连锁群间长度范围86.4～179.0cM,覆盖基因组总长度1 912.9cM,标记间平均间距3.75cM,为高密度遗传图谱。     

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 %。     

梨分子遗传图谱构建及生长性状的QTL分析

利用鸭梨和京白梨杂交得到的F1(145株)实生苗为作图群体,通过对AFLP和SSR两种分子标记的遗传连锁分析,应用Joinmap 3.0作图软件,368个AFLP标记、34个SSR标记构建了分属18个连锁群的梨分子遗传连锁图谱,各连锁群的LOD值在4.0～7.0范围之间,图谱总长度覆盖梨基因组1395.9cM,平均图距为3.8cM.采用区间作图法,对该群体与生长性状相关的调查数据进行QTL分析,检测到与新梢生长量、新梢茎粗、节间长度、节间数量、树干径、树高及皮孔密度7个农艺性状连锁的QTL位点35个,其中主效QTL位点11个(LOD≥3.5).与生长性状相关的农艺性状QTL位点多集中在LG16连锁群上.     

黄瓜SRAP遗传连锁图的构建及侧枝基因定位

在由黄瓜的两个自交系S06与S52杂交产生的F₂群体中, 应用SRAP(sequence-related amplified polymorphism)标记构建遗传连锁图谱, 检测控制黄瓜侧枝数(lbn)和侧枝平均长度(lbl)的数量性状座位(QTL). 使用筛选出的64个多态性引物组合对F2群体进行分析, 得到108个多态性位点. 经MAPMAKER/EXP3.0分析(LOD≥3.0), 获得由92个标记座位组成、覆盖7个连锁群的遗传图谱, 总长1164.2 cM, 标记平均间距12.6 cM. 应用QTLMapper1.6, 各检测到4个控制lbn和lbl的QTL, 其中, 对lbn贡献率最大的QTL位于第二连锁群的ME11SA4B-ME5EM5区间, 其S06基因型具有增效作用; 对lbl贡献率最大的QTL位于第二连锁群的DC1OD3-DC1EM14区间, 其S06基因型具有增效作用.     

南瓜遗传连锁图谱的构建及粒宽性状的QTL定位

以印度南瓜纯系大粒材料‘0515-1’和小粒材料‘0460-1-1’为亲本,获得193个南瓜F2单株群体,应用AFLP和SSR分子标记技术进行多态性筛选,构建了含84个标记位点的遗传连锁图谱。结果表明,整个图谱包含12个连锁群,全长683.50cM,标记平均间距为8.13cM。采用复合区间定位分析,共检测到控制南瓜籽粒宽度的4个数量性状位点(QTL),分别位于3个连锁群上,各QTL的贡献率在2.87%～29.68%之间。     

鲤饲料转化率性状的QTL 定位及遗传效应分析

数量性状(QTL)定位是实现分子标记辅助育种、基因选择和定位、培育新品种及加快性状遗传研究进展的重要手段。饲料转化率是鲤鱼的重要经济性状和遗传改良的主要目标, 而通过QTL 定位获得与饲料转化率性状紧密连锁的分子标记以及相关基因是遗传育种的重要工具。研究利用SNP、SSR、EST-SSR 等分子标记构建鲤鱼(Cyprinus carpio L.)遗传连锁图谱并对重要经济性状进行QTL 定位。选用174 个SSR 标记、41 个EST-SSR 标记、345 个SNP 标记对德国镜鲤F2 代群体68 个个体进行基因型检测, 用JoinMap4.0 软件包构建鲤鱼遗传连锁图谱。再用MapQTL5.0 的区间作图法(Interval mapping, IM)和多QTL 区间定位法(MQMMapping, MQM)对饲料转化率性状进行QTL 区间检测, 通过置换实验(1000 次重复)确定连锁群显著性水平阈值。结果显示, 在对饲料转化率性状的多QTL 区间定位中, 共检测到15 个QTLs 区间, 分布在9 个连锁群上, 解释表型变异范围为17.70%—52.20%, 解释表型变异最大的QTLs 区间在第48 连锁群上, 为52.20%。HLJE314-SNP0919(LG25)区间标记覆盖的图距最小, 为0.164 cM; 最大的是HLJ1439-HLJ1438(LG39)区间,覆盖图距为24.922 cM。其中区间HLJ1439-HLJ1438、HLJ922 -SNP0711 解释表型变异均超过50.00%, 可能是影响饲料转化率性状的主效QTLs 区间。与饲料转化率相关的15 个QTLs 的加性效应方向并不一致, 有3个区间具有负向加性效应, 平均为?0.027; 12 个正向加性效应, 平均值为0.06。研究检测出的与鲤鱼饲料转化率性状相关的QTL 位点可为鲤鱼分子标记辅助育种和更进一步的QTL 精细定位打下基础。       

大粒裸燕麦(Avena nuda L.)遗传连锁图谱的构建

以“元莜麦”和“555”杂交得到的281个F2单株为作图群体,利用20对AFLP引物、3对SSR引物和1个穗型性状构建了一张大粒裸燕麦遗传连锁图。该图谱全长1544.8cM,包含19个连锁群,其上分布有92个AFLP标记、3个SSR标记和1个穗型形态标记,不同连锁群标记数为2-14个,长度在23.7-276.3cM之间,平均长度为81.3cM,标记间平均距离为20.1cM。穗型标记分离比符合3：1,11个AFLP标记表现为偏分离,偏分离比为11.5%。该图谱符合遗传连锁框架图的要求,为今后大粒裸燕麦的QTL定位、分子标记辅助育种和比较基因组学等研究奠定基础。     

甘蓝分子连锁图的构建与品质性状的QTL定位

以两个不同生态型甘蓝(Brassica oleracea var．capitata)品种杂交得到的F2代为作图群体,用RAPD标记构建甘蓝分子连锁图。通过对520个随机引物进行筛选,236个引物在两亲本间表现多态性,多态性比例为47．7％。选取111个引物对群体进行分析,构建了一张含有135个标记位点,9个连锁群,覆盖长度为1023．7cM的分子连锁图。利用该图谱对甘蓝叶球紧实度和中心柱长两性状进行了QTL定位分析。检测到3个与叶球紧实度相关的QTL,总贡献率为62．5％;检测到4个与中心柱长相关的QTL,总贡献率为59．1％。     

Integration genetic linkage map construction and several potential QTLs mapping of Chinese shrimp (Fenneropenaeus chinensis) based on three types of molecular markers

In this study, totally 54 selected polymorphic SSR loci of Chinese shrimp (Fenneropenaeus chinensis), in addition with the previous linkage map of AFLP and RAPD markers, were used in consolidated linkage maps that composed of SSR, AFLP and RAPD markers of female and male construction, respectively. The female linkage map contained 236 segregating markers, which were linked in 44 linkage groups, and the genome coverage was 63.98%. The male linkage map contained 255 segregating markers, which were linked in 50 linkage groups, covering 63.40% of F. chinensis genome. There were nine economically important traits and phenotype characters of F. chinensis were involved in QTL mapping using multiple-QTL mapping strategy. Five potential QTLs associated with standard length (q-standardl-01), with cephalothorax length (q-cephal-01), with cephaloghorax width (q-cephaw-01), with the first segment length (q-firsel-01) and with anti-WSSV (q-antiWSSV-01) were detected on female LG1 and male LG44 respectively with LOD> 2.5. The QTL q-firsel-01 was at 73.603 cM of female LG1. Q-antiWSSV-01 was at 0 cM of male LG44. The variance explained of these five QTLs was from 19.7-33.5% and additive value was from -15.9175 to 7.3675. The closest markers to these QTL were all SSR, which suggested SSR marker was superior to AFLP and RAPD in the QTL mapping.     

Integration genetic linkage map construction and several potential QTLs mapping of Chinese shrimp (<Emphasis Type="Italic">Fenneropenaeus chinensis</Emphasis>) based on three types of molecular markers

In this study, totally 54 selected polymorphic SSR loci of Chinese shrimp (Fenneropenaeus chinensis), in addition with the previous linkage map of AFLP and RAPD markers, were used in consolidated linkage maps that composed of SSR, AFLP and RAPD markers of female and male construction, respectively. The female linkage map contained 236 segregating markers, which were linked in 44 linkage groups, and the genome coverage was 63.98%. The male linkage map contained 255 segregating markers, which were linked in 50 linkage groups, covering 63.40% of F. chinensis genome. There were nine economically important traits and phenotype characters of F. chinensis were involved in QTL mapping using multiple-QTL mapping strategy. Five potential QTLs associated with standard length (q-standardl-01), with cephalothorax length (q-cephal-01), with cephaloghorax width (q-cephaw-01), with the first segment length (q-firsel-01) and with anti-WSSV (q-antiWSSV-01) were detected on female LG1 and male LG44 respectively with LOD > 2.5. The QTL q-firsel-01 was at 73.603 cM of female LG1. Q-antiWSSV-01 was at 0 cM of male LG44. The variance explained of these five QTLs was from 19.7–33.5% and additive value was from −15.9175 to 7.3675. The closest markers to these QTL were all SSR, which suggested SSR marker was superior to AFLP and RAPD in the QTL mapping.     

Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

To facilitate marker assisted selection, there is an urgent need to construct a saturated genetic map of upland cotton (Gossypium hirsutum L.). Four types of markers including SSR, SRAP, morphological marker, and intron targeted intron–exon splice junction (IT-ISJ) marker were used to construct a linkage map with 270 F_2:7 recombinant inbred lines derived from an upland cotton cross (T586 × Yumian 1). A total of 7,508 SSR, 740 IT-ISJ and 384 SRAP primer pairs/combinations were used to screen for polymorphism between the two mapping parents, and the average polymorphisms of three types of molecular markers represented 6.8, 6.6 and 7.0%, respectively. The polymorphic primer pairs/combinations and morphological markers were used to genotype 270 recombinant inbred lines, and a map including 604 loci (509 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) and 60 linkage groups was constructed. The map spanned 3,140.9 cM with an average interval of 5.2 cM between two markers, approximately accounting for 70.6% of the cotton genome. Fifty-four of 60 linkage groups were ordered into 26 chromosomes. Multiple QTL mapping was used to identify QTL for fiber quality traits in five environments, and thirteen QTL were detected. These QTL included four for fiber length (FL), two for fiber strength (FS), two for fiber fineness (FF), three for fiber length uniformity (FU), and two for fiber elongation (FE), respectively. Each QTL explained between 7.4 and 43.1% of phenotypic variance. Five out of thirteen QTL (FL1 and FU1 on chromosome 6, FL2, FU2 and FF1 on chromosome7) were detected in five environments, and they explained more than 20% of the phenotypic variance. Eleven QTL were distributed on A genome, while the other two on D genome.     

Analysis of an intraspecific RIL population uncovers genomic segments harbouring multiple QTL for seed relevant traits in lentil (<Emphasis Type="Italic">Lens culinaris</Emphasis> L.)

Improving seed related traits remains key objective in lentil breeding. In recent years, genomic resources have shown great promise to accelerate crop improvement. However, limited genomic resources in lentil greatly restrict the use of genomics assisted breeding. The present investigation aims to build an intraspecific genetic linkage map and identify the QTL associated with important seed relevant traits using 94 recombinant inbreds (WA 8649090 × Precoz). A total of 288 polymorphic DNA markers including simple sequence repeat (SSR), inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) were assayed on mapping population. The resultant genetic linkage map comprised 220 loci spanning 604.2 cM of the lentil genome, with average inter-marker distance of 2.74 cM. QTL mapping in this RIL population uncovered a total of 18 QTL encompassing nine major and nine minor QTL. All major QTL were detected for seed related traits viz., seed diameter (SD), seed thickness (ST), seed weight (SW) and seed plumpness (SP) across two locations. A considerable proportion of the phenotypic variation (PV) was accounted to these QTL. For instance, one major QTL on LG5 controlling SW (QTL 15) explained 50% PV in one location, while the same QTL accounted for 34.18% PV in other location. Importantly, the genomic region containing multiple QTL for different seed traits was mapped to a 17-cM region on LG5. The genomic region harbouring QTL for multiple traits opens up exciting opportunities for genomics assisted improvement of lentil.     

QTL mapping of yield and fiber traits based on a four-way cross population in <Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.

Four-way cross (4WC) involving four different inbred lines frequently appears in the cotton breeding programs. However, linkage analysis and quantitative trait loci (QTL) mapping with molecular markers in cotton has largely been applied to populations derived from a cross between two inbred lines, and few results of QTL dissection were conducted in a 4WC population. In this study, an attempt was made to construct a linkage map and identify QTL for yield and fiber quality traits in 4WC derived from four different inbred lines in Gossypium hirsutum L. A linkage map was constructed with 285 SSR loci and one morphological locus, covering 2113.3 cM, approximately 42% of the total recombination length of the cotton genome. A total of 31 QTL with 5.1–25.8% of the total phenotypic variance explained were detected. Twenty-four common QTL across environments showed high stability, and six QTL were environment-specific. Several genomic segments affecting multiple traits were identified. The advantage of QTL mapping using a 4WC were discussed. This study presents the first example of QTL mapping using a 4WC population in upland cotton. The results presented here will enhance the understanding of the genetic basis of yield and fiber quality traits and enable further marker-assisted selection in cultivar populations in upland cotton.     

Linkage analysis and identification of quantitative trait loci associated with freeze tolerance and turf quality traits in St. Augustinegrass

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass commonly grown in the southern USA. In this study, the first linkage map for all nine haploid chromosomes of the species was constructed for cultivar ‘Raleigh’ and cultivar ‘Seville’ using a pseudo-F₂ mapping strategy. A total of 160 simple sequence repeat markers were mapped to nine linkage groups (LGs) covering a total distance of 1176.24 cM. To demonstrate the usefulness of the map, quantitative trait loci (QTL) were mapped controlling field winter survival, laboratory-based freeze tolerance, and turf quality traits. Multiple genomic regions associated with these traits were identified. Moreover, overlapping QTL were found for winterkill and spring green up on LG 3 (99.21 cM); turf quality, turf density, and leaf texture on LG 3 (68.57–69.50 cM); and surviving green tissue and regrowth on LGs 1 (38.31 cM), 3 (77.70 cM), 6 (49.51 cM), and 9 (34.20 cM). Additional regions, where QTL identified in both field and laboratory-based/controlled environment freeze testing co-located, provided strong support that these regions are good candidates for true gene locations. These results present the first complete linkage map produced for St. Augustinegrass, providing a template for further genetic mapping. Additionally, markers linked to the QTL identified may be useful to breeders for transferring these traits into new breeding lines and cultivars.     

Construction of a cucumber genetic linkage map with SRAP markers and location of the genes for lateral branch traits

Using SRAP (sequence-related amplified polymorphism) markers a genetic linkage map of cucumber was constructed with a population consisting of 138 F₂ individuals derived from a cross of the two cucumber lines, S06 and S52. In the survey of parental polymorphisms with 182 primer combinations, 64 polymorphism-revealing primer pairs were screened out, which generated totally 108 polymorphic bands with an average of 1.7 bands per primer pair and at most 6 bands from one primer pair. The constructed molecular linkage map included 92 loci, distributed in seven linkage groups and spanning 1164.2 cM in length with an average genetic distance of 12.6 cM between two neighboring loci. Based on this linkage map, the quantitative trait loci (QTL) for the lateral branch number (lbn) and the lateral branch average length (lbl) in cucumber were identified by QTLMapper1.6. A major QTL lbn1 located between ME11SA4B and ME5EM5 in LG2 could explain 10.63% of the total variation with its positively effecting allele from S06. A major QTL lbl1 located between DC1OD3 and DC1EM14 in LG2 could account for 10.38% of the total variation with its positively effecting allele from S₀₆.     

Development of SSR markers and construction of a linkage map in jute

Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources.We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute.     

An EST-SSR-based linkage map for Persea americana Mill. (avocado)

Recent enhancement of the pool of known molecular markers for avocado has allowed the construction of the first moderately dense genetic map for this species. Over 300 SSR markers have been characterized and 163 of these were used to construct a map from the reciprocal cross of two Florida cultivars 'Simmonds' and 'Tonnage'. One hundred thirty-five primer pairs amplified 163 usable loci with 20 primer pairs amplifying more than one locus. 'Tonnage' was heterozygous for 152 (93%) loci, whereas 'Simmonds' was heterozygous for 64 (39%). Null alleles were identified at several loci. Linkage maps were produced for both reciprocal crosses and combined to generate a composite linkage map for the F₁ population of 715 individuals. The composite map contains 12 linkage groups. Linkage groups ranged in size from 157.3 cM (LG2) to 2.4 cM (LG12) and the number of loci mapped per group ranged from 29 (LG1) to two (LG12). The total map length was 1,087.4 cM. Only seven markers were observed to have segregation distortion (α ≤ 0.05) across both sub-composite (reciprocal) maps. Phenotypic data from traits of horticultural interest are currently being collected on this population with the ultimate goal of identifying useful quantitative trait loci and the development of a marker-assisted selection program.