Genetic Analysis of Cotton Fiber Traits by Molecular Markers

1.Development of EST-SSRs derived from G.barbadense:One hundred and nineteen EST-SSRs were developed based on 98 unique ESTs from a cDNA library constructed in our laboratory using developing fibers from G.barbadense cv.3-79.Among the SSRs,trinucleotide AAG appeared

Genetic Diversity of Main Inbred Indica Rice Varieties Applied in Guangdong Province as Revealed by Molecular Marker

Genetic diversity of 299 inbred indica rice varieties, including 33 introduced varieties, applied in Guangdong Province of China were assessed using 20 ILP （intron length polymorphism） and 34 SSR （simple sequence repeat） markers. Totally, 154 loci were screened for the 299 varieties, with the average number of alleles （Na）, rare alleles （Nr）, and polymorphism information content （PIC） scored at 3.4, 0.7 and 0.32, respectively. The Nei＇s genetic distance （GD） was estimated ranging from 0 to 0.7529 with an average of 0.4797. There was no significant difference of Na, Nr, PIC or GDs between the introduced and local varieties. Neighbor-joining （N J） analysis showed that the 299 varieties failed into three main distinct groups, and the 33 introduced varieties were distributed over all the groups or subgroups. Model-based cluster analysis demonstrated that only 73 （24.4%） of the 299 varieties and 7 （21.2%） of the 33 introduced varieties could be distinctly classified into the three groups. Analysis of molecular variance showed that within the groups divided by NJ analysis, the genetic variations revealed by ILP, SSR and these two combined were 7.7%, 5.6% and 6.6%, and within the groups divided by region （Guangdong local and the introduced varieties）, the genetic variables were 2.1%, 4.6%, 5.4%, respectively. These results suggested that the genetic diversity of the 299 inbred rice varieties in Guangdong Province was low, simultaneously relationship among varieties was poor and close in all kind of groups. Hence, it is very necessary to extend the genetic diversity during the breeding and selection practical procedure.

Assessing spatial genetic structure from molecular marker data via principal component analyses: A case study in a <i>Prosopis</i>sp. forest

Advances in genotyping technology, such as molecular markers, have noticeably improved our capacity to characterize genomes at multiple loci. Concomitantly, the methodological framework to analyze genetic data has expanded, and keeping abreast with the latest statistical developments to analyze molecular marker data in the context of spatial genetics has become a difficult task. Most methods in spatial statistics are devoted to univariate data whereas the nature of molecular marker data is highly dimensional. Multivariate methods are aimed at finding proximities between entities characterized by multiple variables by summarizing information in few synthetic variables. In particular, Principal Component analysis (PCA) has been used to study genetic structure of geo-referenced allele frequency profiles, incorporating spatial information with a posteriori analysis. Conversely, the recently developed spatially restricted PCA (sPCA) explicitly includes spatial data in the optimization criterion. In this work, we compared the results of the application of PCA and sPCA in the study of the spatial genetic structure at fine scale of a Prosopis flexuosa and P. chilensis hybrid swarm. Data consisted in the genetic characterization of 87 trees sampled in Córdoba, Argentina and genotyped at six microsatellites, which yielded 72 alleles. As expected, principal components explained more variance than sPCA components, but were less spatially autocorrelated. The maps obtained by the interpolation of sPC1 values allowed a better visualization of a patchy spatial pattern of genetic variability than the PC1 synthetic map. We also proposed a PC-sPC scatter plot of allele loadings to better understand the allele contributions to spatial genetic variability.

Genetic analysis of fertility restoring genes for AL-type male sterility in wheat

In order to screen molecular markers linked to fertility restoring genes and further improve the breeding efficiency of restorer lines, in this study, wheat varieties 18A, 18B and 99AR144-1 were used as experimental materials to establish F2 fertility-segregating population. Plant quantitative trait ＂major gene ＋ polygene mixed mo- del＂ separation analysis method and simple sequence repeat （SSR） molecular markers were adopted for genetic analysis of four generations, including the parents （P~ and P2）, and hybrid （G and G） populations. The results show that AL-type fertility restoring gene is controlled by two pairs of additive-dominant-epistatic genes and addi- tive-dominant polygene; two primers linked to fertility restoring genes were selected by SSR molecular markers, including Xgwm95 on chromosome 2A and Barc61 on chromosome 1B, with the linkage distance of 15.0 cM and 18.0 cM, respectively. Based on verification, these two markers are reliable for distinguishing AL-type wheat ste- rile lines and restorer lines.

Characterization and Genetic Analysis of Rumpled and Twisted Leaf Mutant(rtl1) in Rice

A rumpled and twisted leaf 1(rtl1) mutant was generated from a japonica cultivar Nipponbare by ethyl methanesulfonate treatment,which was characterized as rumpled and twisted leaf at the seedling stage.The F2 populations were constructed by crossing with indica cultivars TN1 and Zhefu 802,respectively.Genetic analysis demonstrated that the phenotype was controlled by a single recessive nuclear gene.The closely linked simple sequence repeat(SSR) marker RM1155 was obtained from bulked segregant analysis.Subsequently,sequence tagged site(STS) markers were developed using the published rice genome sequence.Finally,RTL1 was located between an STS marker T1591 and an SSR marker RM1359,at the distances of 0.48 cM and 0.96 cM,respectively.These results will facilitate the cloning of the target gene in further studies.

云南大理白族带绦虫mtDNA-Cytb序列测定及分析

目的利用分子遗传标记对采自云南大理白族地区人体带绦虫标本进行生物多态性的研究。方法从云南大理采集人体带绦虫标本株成虫节片,抽提虫体基因组DNA,PCR扩增线粒体DNA细胞色素B(mtDNA-Cytb)序列部分片段,测序;结合GenBank中已知猪带绦虫、牛带绦虫和亚洲带绦虫mtDNA-Cytb序列,经DNAMAN软件处理后计算遗传距离并构建系统发育树状图。结果大理白族带绦虫标本系统发育树显示大理(B1,B2,B5,B6)株带绦虫标本与亚洲带绦虫的遗传距离最接近,距牛带绦虫标本较远,与猪带绦虫则更远。大理(B3,B4)株带绦虫标本与猪带绦虫的遗传距离最接近,距牛带绦虫和亚洲带绦虫标本远。结论云南大理(B1,B2,B5,B6)株带绦虫标本属于亚洲带绦虫,而(B3,B4)株带绦虫标本属于猪带绦虫;mtDNA-Cytb序列分析可以用于带绦虫生物多态性研究。

From Markers to Genome Based Breeding in Horticultural Crops: An Overview

Molecular markers,genome sequencing and genome editing are considered as efficient tools to accomplish demands of plant breeders for crop improvement programs.Morphological and biochemical markers have not been extensively used as these are greatly influenced by environmental factors.Different molecular markers and sequencing techniques are routinely used in evaluation of genetic diversity and evolutionary relationship,accurate classification or taxonomy,characterization of germplasm,identification of hybrids and phylogenetic studies.Desired and undesired traits controlled by genes can be identified through different molecular markers technology all over the globe.These molecular markers are well established and have successfully been used for genetic analysis of different plants during last two decades.Recently,advanced techniques of molecular markers have been developed,which provide advance genotypic platform and tends to merge valuable properties of many basic systems.New class of markers also includes little modifications in basic methods to enhance the sensitivity and resolution.Biotechnologists,plant breeders and strong investment are strongly linked for crop improvement purposes.Current review provides detailed description of different markers,genome sequencing and genome editing that have been utilized for different genetic analyses of horticultural crops.Genome editing technologies based on CRISPR/Cas are now successfully applied in horticultural crops.Moreover,current review encourages the use of molecular marker technology for DNA fingerprinting,bar coding,sequencing,re-sequencing QTL mapping,genome association mapping and genome editing.It is need of time that diverse germplasm should be identified with different molecular techniques and further utilized in breeding purposes to achieve higher yielding and resistant cultivars against biotic and abiotic stresses.

Identification of SSR Marker Linked to a Major Dwarfing Gene in Common Wheat

A segregating population with 410 F2 individuals from the cross MERCIA （Rht-Bla）×Dwarf 123 was made to identify a new major dwarfing gene carrying by novel wheat germplasm Dwarf 123. Combination of bulk segerant analysis method was used. A total of 145 SSR markers were tested for polymorphisms among parental lines and DNA bulks of F2 population. Out of 145 primer pairs only three markers revealed corresponding polymorphism among parental lines and F2 DNA bulks. The marker Barc20 was close to the dwarfing gene with a genetic distance of 1.8 cM, and markers Gwm513 and Gwm495 were linked to the gene with genetic distance of 6.7 and 13 cM, respectively. Linkage analysis mapped the dwarfing gene to the long arm of chromosome 4B with the order of Barc20-dwarfing gene-Gwm513-Gwm495. The Comparision between the new gene and the known Rht-B1 alleles showed that dwarfing gene Rht-Ai123 was different from the others. The identification of the new dwarfing gene and its linked markers will greatly facilitate its utilization in wheat high yield breeding for reducing plant height.

白三叶杂交F1代群体的表型鉴定及SSR分析

早期快速鉴定白三叶(Trifolium repens L.)F1杂交子代,获取真杂种对白三叶优良品系的培育和遗传学研究具有重要的意义。本文针对两个白三叶亲本及55个杂交F1的6个表型性状进行分析,绘制聚类热图,再选用3对特异性SSR引物鉴定杂交F1代的真实性。结果表明,在聚类热图中57个株系可以根据亲本的表型性状划分为父本型和母本型。筛选出的19对SSR引物共扩增共得到清晰可辨条带281条,多态性条带137条,多态位点占比为48.41%,每个SSR位点的PIC在18.49%~43.58%之间,平均值为34.73%。其中3对特异性引物在55个杂交后代中共鉴定出53个真杂种,真杂种比率为96.36%,与UPGMA聚类分析结果基本一致。19对SSR分子标记引物具有较高的多态性,可直接用于白三叶遗传多样性分析、杂种鉴定等相关研究,鉴定到的白三叶F1代真杂种为后续育种工作奠定重要基础。

玉米籽粒皱缩突变体sh2019的分子标记初步定位

玉米籽粒作为光合产物的重要贮藏器官,其发育直接影响百粒重和产量。本研究以玉米籽粒皱缩突变体sh2019、野生型玉米自交系Mo17及两者的杂交F_(2)代为材料,进行表型分析、遗传分析和分子标记初步定位。结果表明,突变体sh2019籽粒干瘪,种皮皱缩,百粒重和出苗率均比野生型显著下降,分别下降43.55%和69.56%。遗传分析发现突变体sh2019的籽粒皱缩表型受1对隐性核基因控制。利用F_(2)分离群体借助集团分离分析法进行的分子标记定位结果表明,sh2019基因被定位于玉米3号染色体上约30.18 Mb的物理距离内。本研究结果可为开展sh2019基因的精细定位及分子标记辅助育种奠定基础。

基于转录组测序的玫瑰及其近缘种遗传多样性分析与指纹图谱构建

【目的】分析玫瑰及其近缘种之间的遗传多样性并构建指纹图谱,为玫瑰种质资源鉴定与开发利用奠定基础。【方法】在玫瑰的传统品种、杂交繁育品种和国内外引进品种中各选择1种,取其鲜嫩叶片进行转录组测序;基于测序得到的玫瑰转录组数据,使用MISA在reads覆盖的基因组数据中查找玫瑰的SSR位点,并根据SSR位点两端的保守序列使用Primer 3.0设计引物。选取10种玫瑰的DNA作为试验材料,筛选设计、合成后的引物。以48份玫瑰及其近缘种的DNA作为试验材料,利用筛选出的峰值较好的引物进行TP-M13-SSR PCR,并对其扩增产物进行毛细管电泳检测,应用GeneMarker 2.2.0(SoftGenetics,USA)读取毛细管电泳数据并用Excel进行整理;使用POPGEN VERSION 1.32计算筛选引物的观测杂合度、期望杂合度、Nei’s遗传多样性指数、观测等位基因数、有效等位基因数、Shannon信息指数,并用CERVUS version 3.0计算多态性信息含量。利用Powermarker计算玫瑰及其近缘种各种质之间的遗传距离;采用NTSYSpc 2.10e计算每2个种质之间的遗传相似性系数,并绘制UPGMA聚类树状图。最后采用引物与基因型组合的方式构建玫瑰及其近缘种的指纹图谱。【结果】基于玫瑰样品转录组测序数据,使用MISA共检测出48796个SSR位点,分布于139712条Unigene中,碱基重复类型数量最多的为二核苷酸重复和三核苷酸重复,分别为20628和12828个。使用Primer 3.0以SSR位点两端的保守序列为依据初步设计并合成了144对引物;以10个玫瑰品种的DNA作为模板筛选引物,共筛选出峰值较好的28对引物。以48份玫瑰及其近缘种的DNA为试验材料,28对引物在48份试验材料中均能扩增出峰型良好、多态性高的DNA片段;28对引物的观测杂合度、期望杂合度、Nei’s遗传多样性指数、观测等位基因数、有效等位基因数、Shannon信息指数和多态性信息含量的平均值分别为0.4101,0.7505,0.7011,4.607个,3.5116个,1.3442和0.6526。大多数供试样品间的遗传距离为0.6000~0.8000;聚类分析结果显示,在遗传相似系数为0.571时,48份玫瑰及其近缘种被分为两类。运用核心引物法筛选出的4对核心引物可将48份试验材料全部区分开,并构建了其指纹图谱。【结论】开发并筛选出28对多态性较好的SSR引物,可用于后续玫瑰的遗传多样性分析、遗传图谱构建、遗传稳定性鉴定等方面。

应用STR荧光标记分析烟台地区草莓种质资源遗传多样性

本研究以烟台地区1份野生草莓种质和6份常规栽培品种为试材,选取已发表具有扩增多态性的11对STR荧光标记引物进行扩增,采用多重荧光毛细管电泳检测,分析了该地区草莓种质的遗传多样性,并构建了其分子身份证.结果表明,用这11对引物从7份草莓种质中共检测到60个STR等位基因位点,平均每对引物5.45个,扩增片段长度在90~270 bp之间,多态信息含量平均为0.676,可用于草莓种质的多态性检测.聚类分析显示7份草莓种质间的遗传相似系数为0.077~0.842,在遗传相似系数为0.257时,7份种质被分为3个类群,W1(野生草莓)与S2(丰香种质)同源性较高.对7份草莓种质进行不同等位基因编码,构建了分子身份证.本研究结果可为烟台地区草莓种质资源鉴定、保护和开发利用提供重要依据.

31份藜麦种质农艺性状及ISSR遗传多样性分析

【目的】筛选西北干旱及半干旱地区不同利用价值藜麦种质,为藜麦种质资源的保护与利用奠定基础。【方法】以种植于甘肃临夏东乡县的31份藜麦种质资源为材料,分析其农艺性状,利用ISSR引物进行分子标记PCR扩增,阐明其遗传多样性及特点。【结果】株高、茎粗、鲜干比、茎叶比、单株产量5个农艺性状的变异系数在14.41%~63.30%,其中株高与茎粗、鲜干比呈极显著正相关,与单株产量呈显著正相关。茎粗与单株产量呈极显著正相关,与鲜干比呈显著正相关。鲜干比与单株产量呈极显著正相关。筛选出8条多态性高且清晰的ISSR引物,扩增出63条条带,其中多态性条带55条,多态性位点比率为83.70%,有效等位基因数(Ne)为1.4515,基因多样性(H)为0.2731,香农信息指数(I)为0.4174。根据UPGMA聚类分析结果,在遗传相似系数为0.72时,31份藜麦种质可分为5个类群。第1类群为已选育的陇藜1号、陇藜7号,抗倒伏性、抗病虫害好;第2类群株高较低,可作为抗倒伏材料进一步选育;第3类群株高高、单株产量大、鲜干比适中、茎叶比小,可作为鲜喂材料进一步选育;第4类群鲜干比最大,且与台湾红藜LQ-223的亲缘关系相近;第5类群具有茎叶比最大、中熟品种的特性。【结论】31份藜麦种质资源具有较高的遗传多样性,可为藜麦种质资源创新、遗传育种提供优质材料和科学依据。

一粒系小麦遗传多样性分析及抗条锈菌CYR34鉴定

一粒系小麦(Einkorn wheat,AA)作为小麦的基础物种,在形成普通小麦的过程中染色体组部分位点丢失,评价一粒系小麦的遗传多样性及对病害抗性的水平对普通小麦育种和遗传改良具有重要的理论意义和育种价值。本研究利用15对条带清晰、多态性高的SSR引物对170份一粒系小麦材料进行遗传多样性分析,并接种条锈菌流行生理小种CYR34进行抗病性评价。结果表明,SSR分析获得71个等位变异,引物平均多态性信息含量为0.6540;聚类分析和群体结构分析均将170份供试材料分为两个类群,两类群内的平均遗传距离分别为0.4732和0.5404;抗病性评价获得19份抗性较好的材料,其中免疫材料3份,近免疫材料2份,高抗1份,中抗13份,占供试材料的11.17%;有3对SSR引物与一粒系小麦抗条锈病显著相关。综上所述,一粒系小麦存在较多的等位基因变异,含有优异的抗条锈病基因,具有提高小麦抗条锈病的育种潜力。

水芹SSR分子标记开发与遗传多样性分析

水芹是伞形科水芹属多年生草本植物,是一种重要的药食两用蔬菜作物。在中国,水芹的种植区域十分广泛,然而目前对其种质资源的鉴定、培育及遗传信息的研究较少。本研究利用溧阳白芹基因组开发水芹简单重复序列(SSR)分子标记,分析55份水芹的遗传多样性并用非加权组平均法(UPGMA)构建系统进化树,同时用SSR扩增条带数据构建DNA指纹图谱。结果显示,共鉴定到325699个SSR位点,其中单核苷酸SSR重复单元、二核苷酸SSR重复单元、三核苷酸SSR重复单元、四核苷酸SSR重复单元、五核苷酸SSR重复单元、六核苷酸SSR重复单元的出现频率分别为33.94%、54.62%、9.31%、1.66%、0.17%、0.29%,其中二核苷酸SSR重复单元数最多,有177887个,且A/T(占比为29.98%)和AT/AT(占比为35.70%)是较丰富的重复类型。UPGMA分析结果表明,33对高多态性引物[多态信息含量(PIC)>0.25]可将55份水芹材料分为4组。利用筛选出的4对引物(Oj-084、Oj-110、Oj-112、Oj-156)可以将55份水芹材料完全区分开,并且可构建指纹图谱。研究结果可为水芹种质资源鉴定、保护及分子遗传育种提供有力依据。

基于表型与分子标记对浙贝母不同育种群体的分子鉴定与亲缘关系研究

为了对浙贝母种质资源评价、新品种选育提供理论支撑,该研究利用SCoT分子标记技术,对来源于宁波章水种植基地的146份浙贝母种质资源进行遗传多样性分析;利用Pearson's相关分析计算浙贝母种质资源表型及其与生物碱含量的相关性。结果显示,5条引物共扩增出111个位点,其中多态性位点96个,平均多态性位点比率为86.29%;在整体样本水平的遗传多样性分析中,Na、Ne、H、I分别为2.000、1.585 8、0.340 5、0.509 8,表明引物的多态性较高,能有效揭示146份浙贝母种质资源的多样性。聚类分析表明,所有样品的遗传相似系数为0.55~1.00,系统优选与种子辐照两组中后代表型性状基本遗传亲本的特点;杂交处理后代的亲缘关系与表型性状基本上偏向父本,与种质资源性状考察一致。Pearson's相关分析表明,花型与叶片数量、花朵颜色与叶片数量、叶片颜色与结籽程度呈极显著正相关,花型与叶片颜色呈显著正相关;花朵内壁颜色分别与叶片数量、花型,花色分别与茎秆粗细、结籽程度呈极显著负相关,叶片颜色与花色、叶片宽度与结籽程度、花型与结籽程度呈显著负相关;叶宽与贝母甲素、贝母乙素和总生物碱含量呈极显著负相关。综上,利用SCoT分子标记技术揭示了宁波章水的浙贝母种质资源的遗传多样性,可以有效地为浙贝母种质资源的优势育种提供依据,为浙贝母种质资源的分子辅助育种和开发利用提供参考。

基于SNP分子标记的新疆野生黄花苜蓿遗传多样性分析

为揭示新疆野生黄花苜蓿的遗传多样性,研究利用SLAF-seq技术对材料进行SNP开发。结果显示,材料测序平均Q30值为96.32%,平均GC值为37.99%。研究共开发了376 641个SLAF标签,多态性SLAF标签119 331个;SNP平均完整性为24.77%,平均杂合率5.53%。供试新疆野生黄花苜蓿品系的有效等位基因数、观测等位基因数、期望杂合度、观测杂合度和Shnnon Wiener指数的平均值分别为1.380、1.594、0.220、0.117和0.327。研究表明,聚类分析将材料分为7类,PCA将材料分为3类,但样品的来源为同一个祖先。

蜜蜂线粒体DNA在遗传分析中的应用

线粒体DNA是动物细胞核外唯一的遗传物质,具有结构简单、进化速度快、母系遗传和基因重组率小等特点。文章在介绍蜜蜂线粒体DNA的结构大小及其多态性的研究的基础上,对其在蜜蜂的种间多态性、亚种间及亚种内多态性、起源进化、群体遗传结构及基因流动、亚种及类型的分类等方面的研究应用进行阐述。

基于表型和分子标记分析24份巴戟天遗传多样性

【目的】广东省德庆县是道地药材巴戟天的产地,该文对广东德庆不同地区的24份巴戟天进行了种质资源的遗传多样性分析。【方法】以德庆县各地收集来的24份巴戟天资源为研究对象,使用主成分分析和SRAP、CDDP两种分子标记方法对24份巴戟天材料进行遗传多样性分析。【结果】在表型分析中,基于主成分分析的聚类图发现,官圩镇和高良镇、凤村镇和高良镇分别聚类至4个类群中。此外,18对SRAP引物组合和16条CDDP引物扩增后分别获得100条和98条总条带,其中SRAP多态性条带为50条,多态性比率达50%,平均遗传相似系数(GS)为0.87,遗传相似系数变化范围为0.71~0.97;CDDP多态性条带为80条,条带之间多态性比率达79.0%,各种质间遗传系数范围为0.71~0.96,平均遗传相似系数为0.86,且当系数为0.82时,两种分子标记结果均表明高良镇、官圩镇和凤村镇的种质之间具有一定的相似性。【结论】结合表型和分子标记聚类结果,高良镇和官圩镇、高良镇和凤村镇的亲缘关系最近,SRAP和CDDP两种分子标记方法对巴戟天遗传多样性的结果具有一定的差异,而联合分析可以更好地反映巴戟天遗传多样性研究及其资源的系统发育关系。

基于数量性状与SSR标记的白掌种质遗传关系分析

【目的】揭示白掌种质间表型信息及亲缘关系的遗传特性,为白掌种质资源的利用与遗传育种提供理论基础。【方法】以18份栽培种和16份杂种品系,共计34份白掌种质为研究对象,测定了株高、冠幅、叶长等13个表型数量性状。利用基于白掌株型突变转录组的微卫星(SSR)位点信息,筛选了16对SSR引物进行PCR扩增。利用SPSS、NT sys2.10e软件进行数量性状间相关性、主成分、聚类和遗传多样性分析。【结果】13个数量性状的变异系数为15.29%~31.48%,表明多样性水平较高。这些数量性状中,有76对呈现正相关关系(57对呈极显著相关,10对呈显著相关),2对呈负相关关系,说明白掌的生物学性状之间存在密切关联。主成分分析筛选出了2个特征值大于1的主成分,贡献率达86.62%。根据13个数量性状进行的表型聚类分析结果显示,在欧式距离为7.5时,这34份白掌种质分为5大类,可以有效区分形态差异明显的种质材料,从而反映白掌种质的株型差异。利用16对SSR引物共获得62个SSR位点,平均条带数为3.875条,多态信息含量0.291~0.853。当以相似系数0.74为阈值时,利用SSR的分子标记聚类将这34份白掌种质分为7大类,进一步揭示了它们之间的遗传差异和亲缘关系。【结论】两种分类结果并不一致,但均显示白掌种质丰富的遗传多样性。