中国明对虾AFLP分子标记遗传连锁图谱的构建

以中国明对虾抗WSSV(白斑综合症病毒,WhiteSpotSyndromeVirus)选育群体第四代为母本,野生中国明对虾为父本,采用单对杂交方式产生F1代,F1代个体姊妹交产生F2代共42个个体为做图群体。62对AFLP选择性引物组合共产生529个分离位点,符合1∶1孟德尔分离类型位点共253个,3∶1孟德尔分离类型位点共276个。利用拟测交理论分别构建中国明对虾雌虾、雄虾的遗传连锁图谱,利用F2自交模型构建共同的AFLP分子标记连锁图谱。三张连锁图上分别有31、25和44个连锁群,图谱分辨率为分别为2.4cM、2.4cM和2.1cM。标记间隔距离分别为12.20cM、11.45cM和11.12cM图谱覆盖率分别达到50.21%、51.93%和48.08%。能够基本满足进行QTL(数量性状位点,QuantitativeTraitLocus)定位的需要。将该图谱和其他对虾类遗传连锁图谱进行了比较分析,探讨了利用相关分子标记将已有图谱进行整合的可能。     

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。     

家蚕高密度AFLP连锁图谱的构建

为了进行家蚕Bombyx mori数量性状的QTL定位研究,以白色茧系品种C₁₀₀ (♀)和近交系大造(P50)(♂)杂交得到F₁,用F₁(♂)与双隐性标记的C₁₀₀ (♀)回交,得到回交一代(BC₁),用改进的AFLP分子标记方法,经96组选择性扩增引物扩增,获得分离比为1∶1(P≤0.05)的1 744个AFLP位点。用Map Manager QTXb19（Version 0.29）连锁图谱构建软件,构建了具有814个标记,36个连锁群的家蚕高密度AFLP分子标记连锁图谱。该连锁图谱覆盖的家蚕基因组长度为13 005 cM,连锁群长度变化范围为109.0～1 573.7 cM,连锁群的平均长度为361.25 cM,其标记间平均图距15.98 cM,最小图距2.3 cM,最大图距47.7 cM,标记间大于30 cM的gap共有39个。该连锁图平均每个连锁群23个标记,最多一个连锁群有92个标记,最少8个标记。该连锁图谱确定了与经典实验遗传图谱第15连锁群和W染色体连锁群相对应的两个连锁群。     

桃''秦光2号''×''曙光''F1代SSR遗传连锁图谱的构建

以桃品种‘秦光2号’和‘曙光’及其90株F1代群体为试验材料,依据SSR标记构建桃的遗传连锁图谱。构建的图谱覆盖桃基因组640cM,包含16个连锁群、73个标记,标记间平均图距为11.7cM;桃的白/黄肉性状(Y/y)、离/粘核性状(F/f)被分别定位在第8连锁群和第9连锁群上,距其相邻的分子标记距离分别为4和5cM。所构建的遗传连锁图谱可用于进一步研究。     

利用杉木的F1代群体构建遗传连锁图谱

对于杉木11分离的分子标记位点,提出了一种新的构建遗传连锁图谱的策略.通过二点连锁分析,任意两个位点的连锁相和重组率可以得到推断和估计.对于一个连锁群中的最优排序,采用隐马尔可夫链模型的方法进行多位点的连锁分析.该作图方法比通常林木上所用的"拟测交"作图方法更有效.采用该作图策略,利用句容0号无性系(♀)×柔叶杉(♂)的F1代群体的AFLP分子标记数据重建了句容0号无性系和柔叶杉的遗传连锁图谱.在句容0号无性系的连锁图谱中,有101个标记分布在11个连锁群上,图谱的总长度为2 282.6 cM,平均图距为22.6 cM,单个连锁群上最多含有17个标记,最少含有5个标记;在柔叶杉的连锁图谱中,有94个标记分布在11个连锁群上,图谱的总长度为2 565.8 cM,平均图距为27.3 cM,单个连锁群上最多含有16个标记,最少含有4个标记.构建的句容0号无性系和柔叶杉的遗传连锁图谱比原有的图谱分别增加了26个标记和28个标记,双亲的图谱共增加了54个AFLP标记,使图谱上的分子标记总数达到195个,双亲遗传图谱的跨度均超过了2 000 cM,基本上达到了杉木基因组的长度,图谱的覆盖率接近于100%.利用新的作图方法可以较大提高分子标记在图谱上的分辨率,得到可认为是覆盖了整个基因组的遗传连锁框架图.     

利用杉木的F1代群体构建遗传连锁图谱

对于杉木 1∶1分离的分子标记位点 ,提出了一种新的构建遗传连锁图谱的策略。通过二点连锁分析 ,任意两个位点的连锁相和重组率可以得到推断和估计。对于一个连锁群中的最优排序 ,采用隐马尔可夫链模型的方法进行多位点的连锁分析。该作图方法比通常林木上所用的“拟测交”作图方法更有效。采用该作图策略 ,利用句容0号无性系 (♀ )×柔叶杉 (♂ )的F1代群体的AFLP分子标记数据重建了句容 0号无性系和柔叶杉的遗传连锁图谱。在句容 0号无性系的连锁图谱中 ,有 10 1个标记分布在 11个连锁群上 ,图谱的总长度为 2 2 82 6cM ,平均图距为 2 2 6cM ,单个连锁群上最多含有 17个标记 ,最少含有 5个标记 ;在柔叶杉的连锁图谱中 ,有 94个标记分布在 11个连锁群上 ,图谱的总长度为 2 5 6 5 8cM ,平均图距为 2 7 3cM ,单个连锁群上最多含有 16个标记 ,最少含有 4个标记。构建的句容 0号无性系和柔叶杉的遗传连锁图谱比原有的图谱分别增加了 2 6个标记和 2 8个标记 ,双亲的图谱共增加了 5 4个AFLP标记 ,使图谱上的分子标记总数达到 195个 ,双亲遗传图谱的跨度均超过了 2 0 0 0cM ,基本上达到了杉木基因组的长度 ,图谱的覆盖率接近于 10 0 %。利用新的作图方法可以较大提高分子标记在图谱上的分辨率 ,得到可认为是     

水稻籼粳交F2、F6群体遗传连锁图谱的比较分析

以部分基因组和全基因组测序水稻籼稻(O sativa L. indica)品种“培矮64S”(Pei’ai 64S♀)和粳稻(O sativa L. japonica)品种“日本晴”(Nipponbare♂)为构图亲本, 选取F2代180个株系为作图群体, 构建含138个微卫星位点的水稻遗传连锁图谱, 覆盖基因组2 046.2 cM, 平均图距17.1 cM, 即F2 图谱; 采用单粒传法获得F2:6 代330个株系, 用相同的多态性标记分析F6群体, 构建含92个标记连锁图谱, 覆盖基因组2 563.5 cM, 平均图距27.86 cM, 即F6图谱; F2、F6图谱在连锁群数、定位标记数、标记的位置顺序、遗传图距、平均图距等方面发生了较大变化, 并对产生这些差异的原因进行了初步分析。     

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。     

家蚕AFLP连锁框架图谱的构建

利用改进的AFLP分子标记方法,对家蚕Bombyx mori回交一代BC1群体进行连锁图谱的构建。经17组AFLP引物的选择性扩增,共得到430个多态位点,卡方检验后有253个为有效位点。利用Mapmaker/Exp (Version 3.0b)软件作连锁分析,其中163个标记分属28个连锁群,连锁群标记数变化范围是2～28个,平均每个连锁群标记数为5.8个,该图覆盖的基因组长度为2.998.9cM(图距单位),连锁群长度变化范围为4.5～652.8 cM,连锁群的平均长度为107.1 cM,平均图距为4.5～36.7 cM。     

虾夷扇贝遗传连锁图谱的初步构建

用AFLP标记首次构建了虾夷扇贝遗传连锁图谱。用56对引物组合对父母本和52个F^₁代个体进行遗传连锁分析, 共得到1 855个标记, 其中多态位点为598(32.2%)个, 而354个符合孟德尔1: 1分离比。用这些标记和23个偏分离标记(0.01相似文献   

A genetic linkage map for azuki bean [Vigna angularis (Willd.) Ohwi & Ohashi]

To make progress in genome analysis of azuki bean (Vigna angularis) a genetic linkage map was constructed from a backcross population of (V. nepalensis x V. angularis) x V.angularis consisting of 187 individuals. A total of 486 markers—205 simple sequence repeats (SSRs), 187 amplified fragment length polymorphisms (AFLPs) and 94 restriction fragment length polymorphisms (RFLPs) —were mapped onto 11 linkage groups corresponding to the haploid chromosome number of azuki bean. This map spans a total length of 832.1 cM with an average marker distance of 1.85 cM and is the most saturated map for a Vigna species to date. In addition, RFLP markers from other legumes facilitated finding several orthologous linkage groups based on previously published RFLP linkage maps. Most SSR primers that have been developed from SSR-enriched libraries detected a single locus. The SSR loci identified are distributed throughout the azuki bean genome. This moderately dense linkage map equipped with many SSR markers will be useful for mapping a range of useful traits such as those related to domestication and stress resistance. The mapping population will be used to develop advanced backcross lines for high resolution QTL mapping of these traits. O.K. Han, A. Kaga, T. Isemura have contributed equally to this paper.     

A first linkage map of olive (Olea europaea L.) cultivars using RAPD,AFLP, RFLP and SSR markers

The first linkage map of the olive (Olea europaea L.) genome has been constructed using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLP) as dominant markers and a few restriction fragment length polymorphisms (RFLP) and simple-sequence repeats (SSR) as codominant markers. Ninety-five individuals of a cross progeny derived from two highly heterozygous olive cultivars, Leccino and Dolce Agogia, were used by applying the pseudo test-cross strategy. From 61 RAPD primers 279 markers were obtained - 158 were scored for Leccino and 121 for Dolce Agogia. Twenty-one AFLP primer combinations gave 304 useful markers - 160 heterozygous in Leccino and 144 heterozygous in Dolce Agogia. In the Leccino map 249 markers (110 RAPD, 127 AFLP, 8 RFLP and 3 SSR) were linked. This resulted in 22 major linkage groups and 17 minor groups with fewer than four markers. In the Dolce Agogia map, 236 markers (93 RAPD, 133 AFLP, 6 RFLP and 4 SSR) were linked; 27 major linkage groups and three minor groups were obtained. Codominant RFLPs and SSRs, as well as few RAPDs in heteroduplex configuration, were used to establish homologies between linkage groups of both parents. The total distance covered was 2,765 cM and 2,445 cM in the Leccino and Dolce Agogia maps, respectively. The mean map distance between adjacent markers was 13.2 cM in Leccino and 11.9 cM in Dolce Agogia, respectively. Both AFLP and RAPD markers were homogeneously distributed in all of the linkage groups reported. The stearoyl-ACP desaturase gene was mapped on linkage group 4 of cv. Leccino.     

A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies

A genetic linkage map for the ectomycorrhizal basidiomycete Laccaria bicolor was constructed from 45 sib-homokaryotic haploid mycelial lines derived from the parental S238N strain progeny. For map construction, 294 simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers were employed to identify and assay loci that segregated in backcross configuration. Using SNP, RAPD and SSR sequences, the L. bicolor whole-genome sequence (WGS) assemblies were aligned onto the linkage groups. A total of 37.36 Mbp of the assembled sequences was aligned to 13 linkage groups. Most mapped genetic markers used in alignment were colinear with the sequence assemblies, indicating that both the genetic map and sequence assemblies achieved high fidelity. The resulting matrix of recombination rates between all pairs of loci was used to construct an integrated linkage map using JoinMap. The final map consisted of 13 linkage groups spanning 812 centiMorgans (cM) at an average distance of 2.76 cM between markers (range 1.9-17 cM). The WGS and the present linkage map represent an initial step towards the identification and cloning of quantitative trait loci associated with development and functioning of the ectomycorrhizal symbiosis.     

Distribution of DArT, AFLP, and SSR markers in a genetic linkage map of a doubled-haploid hexaploid wheat population.

A genetic linkage mapping study was conducted in 93 doubled-haploid lines derived from a cross between Triticum aestivum L. em. Thell 'Arina' and a Norwegian spring wheat breeding line, NK93604, using diversity arrays technology (DArT), amplified fragment length polymorphism (AFLP), and simple sequence repeat (SSR) markers. The objective of this study was to understand the distribution, redundancy, and segregation distortion of DArT markers in comparison with AFLP and SSR markers. The map contains a total of 624 markers with 189 DArTs, 165 AFLPs and 270 SSRs, and spans 2595.5 cM. All 3 marker types showed significant (p < 0.01) segregation distortion, but it was higher for AFLPs (24.2%) and SSRs (22.6%) than for DArTs (13.8%). The overall segregation distortion was 20.4%. DArTs showed the highest frequency of clustering (27.0%) at < 0.5 cM intervals between consecutive markers, which is 3 and 15 times higher than SSRs (8.9%) and AFLPs (1.8%), respectively. This high proportion of clustering of DArT markers may be indicative of gene-rich regions and (or) the result of inclusion of redundant clones in the genomic representations, which was supported by the presence of very high correlation coefficients (r > 0.98) and multicollinearity among the clustered markers. The present study is the first to compare the utility of DArT with AFLP and SSR markers, and the present map has been successfully used to identify novel QTLs for resistance to Fusarium head blight and powdery mildew and for anther extrusion, leaf segment incubation, and latency.     

High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

A high-density linkage map was constructed for an F2 population derived from an Interspecific cross of cultivated allotetraploid species between Gossypium hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the Interspecific cross of ＂CRI 36 × Hal 7124＂ were genotyped at I 252 polymorphic loci Including a novel marker system, target region amplification polymorphism （TRAP）. The map consists of 1 097 markers, including 697 simple se- quence repeats （SSRs）, 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were Identified In tetraploid cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.     

Constructing a Genetic Linkage Map Using an F<Subscript>1</Subscript> Population of Non-inbred Parents in Cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz)

A genetic linkage map of cassava has been generated with total of 355 molecular markers, 231 amplified fragment length polymorphisms (AFLPs), 41 simple sequence repeats (SSRs), 48 sequence-related amplified polymorphisms (SRAPs), and 35 expressed sequence tag (EST)-SSRs segregating from an F₁ population of an intraspecific cross between SC6, as female parent, and Mianbao, as male parent. The genetic map consisted of 18 linkage groups and spanned a 1,707.9 cM genetic distance, with the average marker interval being 4.81 cM. Thirty-five EST-SSR markers that were developed by our laboratory were mapped onto this map. The genetic map generated in this study will enrich the information of structural genomics in cassava, facilitating to identify quantitative trait loci (QTL) of interest and to serve as a useful complement for construction of an integrated map in the future.     

QTL mapping ofFusarium moniliforme ear rot resistance in maize. 1. Map construction with microsatellite and AFLP markers

To map the QTLsof Fusarium moniliforme ear rot resistance inZea mays L., a total of 230 F₂ individuals, derived from a single cross between inbred maize lines R15 (resistant) and Ye478 (susceptible), were genotyped for genetic map construction using simple sequence repeat (SSR) markers and amplified fragment length polymorphism (AFLP) markers. We used 778 pairs of SSR primers and 63 combinations of AFLP primers to detect the polymorphisms between parents, R15 and Ye478. From the polymorphic 30 AFLP primer combinations and 159 SSR primers, we scored 260 loci in the F₂ population, among which 8 SSR and 13 AFLP loci could not be assigned to any of the linkage groups. An integrated molecular genetic linkage map was constructed by the remaining 151 SSR and 88 AFLP markers, which distributed throughout the 10 linkage groups of maize and spanned the genome of about 3463.5 cM with an average of 14.5 cM between two markers. On 4 chromosomes, we detected 5 putative segregation distortion regions (SDR_s), including 2 new ones (SDR₂ and SDR₇). The other 3 SDR_s were located near the regions where gametophyte genes were mapped, indicating that segregation distortion could be partially caused by gametophytic factors.     

Comparison of Linkage Disequilibrium in Elite European Maize Inbred Lines using AFLP and SSR Markers

Application of association mapping to plant breeding populations has the potential to revolutionize plant genetics. The main objectives of this study were to (i) investigate the extent and genomic distribution of linkage disequilibrium (LD) between pairs of amplified fragment length polymorphism (AFLP) markers, (ii) compare these results with those obtained with simple sequence repeat (SSR) markers, and (iii) compare the usefulness of AFLP and SSR markers for genomewide association mapping in plant breeding populations. We examined LD in a cross-section of 72 European elite inbred lines genotyped with 452 AFLP and 93 SSR markers. LD was significant (p < 0.05) for about 15% of the AFLP marker pairs and for about 49% of the SSR marker pairs in each of the two germplasm groups, flint and dent. In both germplasm groups the ratio of linked to unlinked loci pairs in LD was higher for AFLPs than for SSRs. The observation of LD due to linkage for both marker types suggested that genome-wide association mapping should be possible using either AFLPs or SSRs. The results of our study indicated that SSRs should be favored over AFLPs but the opposite applies to populations with a long history of recombination.     

Molecular linkage maps of Vitis vinifera L. and Vitis riparia Mchx

Two linkage maps for grape (Vitis spp.) have been developed based on 81 F(1) plants derived from an interspecific cross between the wine cultivar Moscato bianco (Vitis vinifera L.) and a Vitis riparia Mchx. accession, a donor of pathogen resistance traits. The double pseudotest-cross mapping strategy was applied using three types of molecular markers. The efficiency of SSRs to anchor homologous linkage groups from different Vitis maps and the usefulness of AFLPs in saturating molecular linkage maps were evaluated. Moreover, the SSCP technique was developed based on sequence information in public databases concerning genes involved in flavonoid and stilbene biosynthesis. For the maternal genetic map a total of 338 markers were assembled in 20 linkage groups covering 1,639 cM, whereas 429 loci defined the 19 linkage groups of the paternal map which covers 1,518 cM. The identification of 14 linkage groups common to both maps was possible based on 21 SSR and 19 AFLP loci. The position of SSR loci in the maps presented here was consistent with other published mapping experiments in Vitis.     

Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.).

A microsatellite-based high-density linkage map for oil palm (Elaeis guinensis Jacq.) was constructed from a cross between two heterozygous parents, a tenera palm from the La Mé population (LM2T) and a dura palm from the Deli population (DA10D). A set of 390 simple sequence repeat (SSR) markers was developed in oil palm from microsatellite-enriched libraries and evaluated for polymorphism along with 21 coconut SSRs. A dense and genome-wide microsatellite framework as well as saturating amplified fragments length polymorphisms (AFLPs) allowed the construction of a linkage map consisting of 255 microsatellites, 688 AFLPs and the locus of the Sh gene, which controls the presence or absence of a shell in the oil palm fruit. An AFLP marker E-Agg/M-CAA132 was mapped at 4.7 cM from the Sh locus. The 944 genetic markers were distributed on 16 linkage groups (LGs) and covered 1,743 cM. Our linkage map is the first in oil palm to have 16 independent linkage groups corresponding to the plants 16 homologous chromosome pairs. It is also the only high-density linkage map with as many microsatellite markers in an Arecaceae species and represents an important step towards quantitative trait loci analysis and physical mapping in the E. guineensis species.