共查询到17条相似文献，搜索用时 203 毫秒
1.
海岛棉具有纤维品质好、抗病性强等优异性状,不仅为纺织工业提供优质棉纤维原料,也是陆地棉相关性状改良的重要供体材料。然而,与陆地棉相比,开展海岛棉的遗传多样性和基因分型研究相对较少。本研究基于CottonSNP80K芯片对282份不同来源的海岛棉品种/材料进行基因组SNP分型研究,以选择高效鉴别海岛棉材料的核心位点组合。按照检出率大于95%、具多态性、最小等位频率(MAF)大于0.01、杂合率小于0.05、无冗余位点等条件筛选,获得2594个高质量SNP位点。对上述位点设置不同数目梯度筛选,确定最优核心位点数。随着位点个数的增多,位点组合对海岛棉材料的识别率逐渐增加。当位点数为200时,识别率为89%;位点数提高到1500时,识别率可达99%。进一步增加位点数,识别率无显著变化。利用中选的1500个SNP位点检测供试材料,其平均MAF值0.14,平均杂合率0.007,平均多态信息含量0.21。SNP位点的聚丙烯凝胶电泳验证表明,SNP-PCR与芯片分型结果一致性达98.3%。本研究提供了适于海岛棉指纹图谱构建、含1500位点的一套核心SNP位点组合,可用于海岛棉遗传多样性分析和品种身份鉴定。 相似文献
2.
本研究基于前期对57份油橄榄种质资源的全基因组GBS-SNP分型结果开展核心SNP位点的筛选。统计分析73482个GPS-SNP位点发现,有68030个(92.58%)SNP位点的检出率达到100%,33979个(46.2%)位点的最小等位基因频率≥0.2,29647个(40.35%)位点的杂合率为0,其中同时符合上述3个条件(检出率=100%,最小等位基因频率≥0.2,杂合率=0)的位点有14125个(19.2%),其位置覆盖全基因组,既分布于基因区也位于基因间区,与73482个SNP位点的分布高度一致(R=0.997),多态信息量平均为0.43(0.33~0.67)。进一步以14125个SNP位点信息为依据,计算57个油橄榄品种间的遗传距离,并与基于全部位点(73482个SNPs)信息获得的对应品种间的遗传距离作比较,结果显示两者呈极显著的相关性(R=0.9),表明这些SNP位点具有多态性好、代表性广、可靠性高的特点,可作为油橄榄的核心SNP位点,适用于油橄榄品种鉴定、种质评价、基因定位和分子辅助育种。本研究对核心SNP位点在油橄榄品种鉴定中的具体应用进行了探讨,并指出至少需要11个核心SNP位点组合才能实现对57个油橄榄品种的完全区分。 相似文献
3.
基于单拷贝SNP标记的棉花杂交种纯度高通量检测技术 总被引：2，自引：1，他引：1
利用有代表性的材料进行SNP位点的全基因组扫描分析与综合评估,基于KASP技术开发1套适用于我国棉花杂交种纯度高通量检测的核心SNP组合。从63K的棉花全基因组芯片中筛选获得具有单拷贝特性的SNP标记分别为5474个(中棉所TM-1基因组版本)和1850个(南京农大TM-1基因组版本)。根据芯片扫描分析结果,权衡考虑位点多态性、分型效果、纯合率与杂合率等因素,最终从每条染色体上优选1个杂交种杂合率高且分型效果理想的核心SNP位点,合计26个。采用KrakenTM软件将SNP位点转化成KASP标记,利用SNPline平台进行SNP分型检测,实现了对大量样品的高通量基因分型,尤其适用于品种纯度快速检测,为SNP标记技术在棉花品种鉴定及指纹数据库构建等方面的应用奠定基础。 相似文献
4.
兼容型maizeSNP384标记筛选与玉米杂交种DNA指纹图谱构建 总被引：1，自引：0，他引：1
TIAN Hong-Li YANG Yang WANG Lu WANG Rui YI Hong-Mei XU Li-Wen ZHANG Yun-Long GE Jian-Rong WANG Feng-Ge ZHAO Jiu-Ran 《作物学报》2020,46(7):1006-1015
为加强玉米品种管理和知识产权保护,评估确定了一套兼容多技术平台,适于玉米分子鉴定的SNP位点组合,该组合包含384个位点;构建了335个玉米杂交种SNP-DNA指纹,幵针对位点和样品从各个角度迚行分析。384个位点全部分布在基因内区域,显示了较好的多态性; MAF、PIC、DP平均值分别为0.39、0.36、0.60, 384个位点中88%的位点MAF值高于0.30, 98%的位点PIC值高于0.30, 98%的位点DP值高于0.50。对335个玉米杂交种迚行遗传相似系数两两比较, GD (1-Nei遗传距离)的变异范围为0.60～0.99, GD≥0.98、0.95、0.90者分别占比0.10%、0.38%、1.40%;GS(相同等位基因比)的变异范围为0.50～0.99,GS≥0.98、0.95、0.90者分别占比0.03%、0.11%、0.35%。从384个位点中抽取最优位点组合, 12个位点组合时品种识别率为0.99, 20个位点组合能够识别335个品种。综上所述,本研究报道的384个核心SNP位点具有兼容多平台、高稳定性、高重复性、高品种区分能力,利用核心位点构建了335个玉米杂交种SNP-DNA指纹,为玉米品种分子鉴定、指纹数据构建以及分子育种提供了关键数据支撑。 相似文献
5.
基于高通量测序开发玉米高效KASP分子标记 总被引：2，自引：0，他引：2
SNP (Single Nucleotide Polymorphism)在基因组中数量多、分布广,适用于大规模、自动化基因型检测。本研究利用205份不同来源的玉米自交系全基因组重测序数据鉴定出一系列多态性高的二态性SNP位点并开发出700个KASP分子标记。其中, 202个在46个玉米代表系中得到验证的KASP标记进一步用于系统进化树构建及群体结构分析。结果显示,开发成功的KASP标记在染色体上分布均匀,平均PIC为0.463,平均MAF为0.451。基于KASP标记位点和总SNP位点的聚类分析结果高度吻合。KASP标记位点与总SNP位点的遗传距离相似性系数高达89.5%,能成功区分玉米的杂种优势群。该KASP标记可在玉米种质资源分析、连锁群构建以及杂种优势群划分等方面发挥重要作用。 相似文献
6.
为揭示湖南省油菜种质资源库中核心种质的遗传多样性,本研究利用油菜组60K基因芯片对266份甘蓝型油菜品系及其10份近缘种品系10份进行全基因组SNP位点分析,原始数据通过Visual Basic软件筛选,利用Powermarker软件计算SNP位点PIC值和供试材料的遗传距离、聚类分析。结果表明：根据SNP标记缺失率和染色体分布均匀度共筛选到24 593个SNP位点,平均每条染色体分布1 294个多态性位点,位点的Nei’s基因多样性指数(H)、主要等位基因频率(MAF)和多态性信息含量(PIC)平均值分别为0.401、0.688 3、0.316;276份供试材料间遗传距离在0.000 1～0.477之间,平均为0.329 6,Kinship值为0的占71.49%;供试材料可分成5个大类,其中最大类(含有250份种质)又可分为9个亚类,供试材料的类群分布与种质类型、地理来源一致。研究结果表明供试育种亲本种质遗传多样性丰富,可更客观反映供试材料的亲缘关系,为种质资源的育种利用提供理论依据。 相似文献
7.
基于SNP标记小麦自然群体遗传多样性及复合图谱的构建 总被引：2，自引：0，他引：2
《分子植物育种》2015,(7)
本研究利用Illumina i Select 90K(81 587个SNP)基因芯片对中国冬麦区205份小麦育成品种(系)构成的自然群体进行基因分型,分析中国冬麦区小麦的遗传多样性并整合群体的复合遗传图谱。用于检测的81 587个SNP标记位点中,利用32 432个具有品种间多态性的位点进行群体遗传多样性分析,检测到64 864个等位变异,每个位点平均2个等位变异,SNP位点的多态性信息含量(PIC)变化范围为0.05~0.38,平均为0.26;聚类分析将205份小麦材料按亲缘关系划分为4个类群。复合遗传图谱包含24 355个SNP标记位点,覆盖小麦全基因组3 674.16 c M,单个染色体长度为118.91~241.38 c M,标记间平均遗传距离为0.15 c M;小麦的3个染色体组中,B基因组中包含的SNP标记最多(12 321,50.60%),其次是A基因组(9 523,39.10%),D基因组含标记最少(2 511,10.31%)。研究结果为利用该群体进行标记/性状间的关联分析提供遗传信息,并为小麦杂交亲本的选择和新品种培育提供参考。 相似文献
8.
【目的】随着不同棉种序列数据库的逐步完善以及高通量测序技术的发展,棉花单核苷酸多态性(Single nucleotide polymorphism,SNP)标记开发可利用的公共数据资源逐步增加。【方法】本研究基于陆地棉祖先基因组的现代种亚洲棉表达序列标签(Expressed sequence tag,EST)数据库,利用CAP3对亚洲棉EST数据库进行拼接。拼接获得7 187个重叠群(Contig),再利用Quality SNP软件进行SNP位点分析。【结果】在807条含有4条以上EST序列的Contig中查找到2 690个SNP位点。通过筛选次要等位基因频率大于30%的位点,获得953个可靠度较高的候选SNP,通过电子筛选,最终获得可用于陆地棉分析的SNP 149个,利用位点特异性聚合酶链式反应以及酶切扩增多态序列验证了EST-SNP的准确性。【结论】本研究证实基于亚洲棉EST数据库挖掘用于陆地棉研究的EST-SNP切实可行,并有望将EST-SNP用于陆地棉遗传图谱构建、重要性状的基因定位以及分子标记辅助育种。 相似文献
9.
《分子植物育种》2015,(9)
异源四倍体花生(Arachis hypogaea L.)包含两套基因组,分别来自二倍体祖先A.duranensis(A基因组)和A.ipaensis(B基因组)。相对于二倍体,异源四倍体SNP的鉴定和分析面临更多挑战,因为在SNP的鉴定和分析过程中,通常需要同时分析两套基因组中相同位点的DNA序列。本研究以12个花生品种和2个二倍体祖先为材料,通过扩增子重测序EST和GSS(各100条序列)开发SNP。结果显示共检测出18个EST-SNPs和44个genomic-SNPs,出现频率分别为1 SNP/2 557 bp和1 SNP/1 011 bp。为了进一步评估和应用所开发的SNP,采用高分辨率溶解曲线方法对96个花生品种进行SNP基因分型。EST-SNP在供试品种中的多态性信息量介于0.021~0.413,平均为0.172。Genomic-SNP的多态性信息量介于0.08~0.478,平均为0.249。本研究表明采用扩增子测序和HRM方法能够从异源四倍体花生中准确鉴定SNP,且所开发的SNP信息量丰富,能够用于花生遗传育种研究。 相似文献
10.
基于SSR标记新疆陆地棉的DNA指纹图谱构建及遗传多样性分析 总被引：1，自引：0，他引：1
【目的】利用Simple sequence repeats(SSR)标记构建新疆近40年间审定的120个陆地棉品种的DNA指纹图谱并进行遗传多样性分析。【方法】从586对候选引物中筛选得到78对多态性高、扩增稳定且均匀分布于棉花染色体上的引物,并用这78对引物构建120个陆地棉品种的DNA指纹图谱。【结果】78对核心引物在120个材料中检测到392个等位位点,其中多态性位点324个,多态性比率达82.7%。24个标记位点在17个品种上具有特征谱带。采用12对引物组合即可鉴定120个棉花品种。聚类分析显示,120个陆地棉品种遗传相似系数变化范围为0.50~0.96,平均为0.73,遗传相似系数偏高,表明新疆陆地棉品种的遗传基础较狭窄。【结论】引物组合法是构建DNA指纹图谱最有效的方法。遗传相似系数矩阵将120个陆地棉品种分为三大类群,与系谱来源较为吻合。 相似文献
11.
Washington Gapare Warren Conaty Qian-Hao Zhu Shiming Liu Warwick Stiller Danny Llewellyn Iain Wilson 《Euphytica》2017,213(3):66
A genome-wide association study (GWAS) was conducted on a diversity panel of 103 cotton accessions over three seasons to determine genetic contributions to a range of cotton yield components including fibre quality, plant architecture and stomatal conductance traits. The accessions covered breeding lines, released cultivars and some obsolete cultivars that contributed significantly to modern breeding pools. They were genotyped with Illumina’s CottonSNP63 K single nucleotide polymorphism (SNP) assay. Broad-sense heritability was low for yield component traits (\(h_{B}^{2}\) = 0.14–0.43), except for gin turnout and boll weight (\(h_{B}^{2}\)) = 0.74 and 0.59, respectively), and low to high for fibre quality traits (\(h_{B}^{2}\) = 0.26–0.89). Population structure analysis revealed extensive admixture and cryptic relatedness amongst the accessions. Genome-wide linkage disequilibrium (LD) analyses showed LD decayed, on average, within a physical distance of 5 Mbp and reduced to 2 Mbp at r 2 ≥ 0.2, suggesting that few markers are necessary for association mapping in cotton. A mixed linear model accounting for population structure and cryptic relatedness identified 17 and 50 significant SNP associations for fibre length and micronaire, respectively. GWAS failed to detect significant associations in other traits, with the contribution of any single SNP to the phenotypic falling below 5%. This may be due to the low level of DNA polymorphism in cotton and/or insufficient resolution provided by the cotton SNP chip. Whole genome sequencing combined with whole genomic selection approaches that do not require prior knowledge about the effect or function of individual SNPs may be better suited than GWAS for trait dissection and prediction in cotton breeding. 相似文献
12.
Lei Jiejie Shao Panxia Guo Chunping Zhang Dawei Tang Binghui Nurimanguli Aini Peng Yajuan Cui Tianyu Zhang Aoshen Lin Hairong Lin Zhongxu You Chunyuan Nie Xinhui 《棉花学报》2013,32(3):185-198
[Objective] We completed anassociation analysis of economic traits for upland cotton using simple sequence repeat (SSR) markers. We then explored the allelic variation sites to analyze the genetic basis of economically important traits, studied the genetic mechanism of Xinjiang upland cotton, and aimed to accelerate efficient breeding of upland cotton. [Method] We carried out polymorphic scanning on 156 upland cotton varieties in Xinjiang by screening 73 pairs of SSR markers encompassing the whole cotton genome. We constructed boxplot maps using R statistical computing software and graphics language and used TASSEL software to correlate yield or fiber quality traits with significant allelic variation loci. [Results] We obtained 10 allelic variation loci related to yield traits using the correlation analysis of Xinjiang upland cotton varieties from six different environments. The interpretation rate of phenotypic variation ranged from 6.69% to 9.88% with an average of 8.43%. Twenty-three allelic variation loci associated with fiber quality traits and phenotypic variation interpretation rates ranged from 3.73% to 13.22% with an average of 7.52%. The 22 detected quantitative trait loci were reported in previous studies and 10 showed the same associated traits as previously reported. [Conclusion] The population genetic structure of Xinjiang upland cotton varieties is simple, the linkage disequilibrium level is low, and the phenotypic traits show a stable trend under six environments. Using association analysis, we discovered unique allelic variation genes related to yield and fiber quality and diverse allele loci. 相似文献
13.
Belayneh Ayalew Desalegne Kifle Dagne Gedil Melaku Boukar Ousmane Christian A. Fatokun 《Journal of Crop Science and Biotechnology》2017,20(2):107-128
The extent of genetic diversity and relatedness of cowpea germplasm from East Africa are poorly understood. A set of 13 microsatellites (SSR) and 151 single nucleotide polymorphisms (SNPs) markers were applied to assess the levels of genetic diversity in a sample of 95 accessions of local cowpea germplasm and inbred lines of Vigna unguiculata. The average genetic diversity (D), as quantified by the expected heterozygosity, was higher for SSR loci (0.52) than for SNPs (0.34). The polymorphic information content was 0.48 for SSR and 0.28 for SNP while the fixation index was 0.095 for SSR and 0.15 for SNPs showing moderate differentiation and high gene flow among cowpea accessions from East African countries. The results of data analysis of both SSR and SNP markers showed similar clustering patterns suggesting a substantial degree of association between origin and genotype. Principal coordinate analysis (PCoA) with SSR and SNP markers showed that accessions were grouped into two and three broad groups across the first two axes, respectively. Our study found that SNP markers were more effective than SSR in determining the genetic relationship among East African local cowpea accessions and IITA inbred lines. Based on this analysis, five local cowpea accessions Tvu-13490, Tvu-6378, Tvu-13448, Tvu-16073, and 2305675 were identified to be tightly clustered sharing several common alleles with the drought tolerant variety Danila when analyzed with SSR and SNP markers. The findings will assist and contribute to future genetic diversity studies aimed at the genetic improvement of local Eastern Africa cowpea accessions for improved overall agronomic performance in general and breeding for drought tolerant in particular. 相似文献
14.
陆地棉SSR标记遗传多样性及其与农艺性状的关联分析 总被引：6，自引：2，他引：4
分析陆地棉栽培种遗传多样性,通过关联分析寻找与棉花农艺性状相关联的分子标记,为分子标记辅助选择育种和提高棉花育种效率奠定基础。本文采用74个Simple sequence repeat(SSR)标记对172份陆地棉栽培种的基因组变异进行扫描,使用NTSYS-pc 2.20进行聚类,分析该群体遗传多样性;利用Structure 2.3.4软件分析群体结构,在此基础上结合田间表型数据,采用Tassel 2.1的一般线性模型(General linear model,GLM)进行关联分析,定位与农艺性状相关的QTLs。74个标记共检测到148个多态性位点,涉及246个等位变异,变异范围2~7个,平均等位变异数为3.32;引物的多态性信息含量(PIC)为0.0281~0.3733,平均值为0.2370;遗传相似系数变异在0.2816~1,平均值为0.5369,平均遗传相似系数为0.5369,表明我国陆地棉遗传基础狭窄,尽管国外及西北内陆棉区部分材料具有较丰富的遗传变异。聚类分析将该群体划分为12个亚群,不同棉区的材料交叉分布,且聚类结果基本与系谱吻合。群体结构分析却将172份供试材料划分为3个亚群;通过关联分析,发现30个位点与铃重、衣分、黄萎病抗性显著相关(P0.05),各位点对表型变异贡献率为2.24%~5.27%。 相似文献
15.
Wang Xinyi Li Xueyuan Gong Zhaolong Wang Junduo Fan Liping Zheng Juyun Liang Yajun Guo Jiangping Mamat Moming Ai Xiantao 《棉花学报》2018,30(4):308-315
[Objective] The aim of this study was to construct a DNA fingerprinting database of 120 upland cotton cultivars from Xinjiang and to analyze their genetic diversity based on SSR markers. [Methods] Seventy-eight evenly distributed SSR primer pairs with high polymorphism and good repeatability were successfully screened out from 586 candidates to construct the fingerprinting database. [Result] A total of 392 alleles from 120 varieties were screened using 78 pairs of core primers, 324 of which were polymorphic loci with a polymorphism rate of 82.7%. Seventeen cultivars had specific genotypes determined using 24 primer pairs and 120 upland cotton cultivars could be identified by only 12 primer combinations. Cluster analysis indicated that genetic similarity coefficient for the 120 upland cotton cultivars ranged from 0.50 to 0.96, with an average of 0.73, indicating that upland cotton resources possess high genetic similarity and have an accordingly narrow genetic basis. [Conclusion] The primer combination method is one of the most effective methods for constructing DNA fingerprinting. The 120 upland cotton varieties were divided into three types with the genetic similarity coefficient matrix; these groups were strongly consistent with their pedigrees. 相似文献
16.
[Objective] We explored the genetic diversity of early maturity upland cotton germplasm resources in Xinjiang, China. We discovered specific germplasm resources and elite allelic variation related to fiber quality. [Method] We used 219 early maturity upland cotton accessions in our experiments and investigated 15 agronomic traits in three environments. We used a total of 128 pairs of simple sequence repeat (SSR) primers to scan for polymorphism. We then used NTsys-pc2.1 software to analyze genetic diversity, and Structure2.3.1 and Tassle5.0 software to perform association analysis of fiber quality traits based on phenotypic effect values to identify elite allele variation and conventional materials. [Result] A total of 244 loci were amplified by 128 marker pairs in 219 samples with an average of 1.91 loci per marker. The polymorphic information content ranged from 0.13 to 0.86 with an average of 0.63. The distribution range of the genetic similarity coefficient between materials in this population was 0.42-0.99 with an average of 0.61. The genetic similarity coefficient was between 0.5 and 0.7 and accounted for 90.19%. Through association analysis, we detected 11 markers that were significantly (P<0.01) associated with fiber quality traits, and discovered seven typical materials with specific allele. [Conclusion] In total, 219 Xinjiang early-maturing upland cotton germplasm resources have low genetic diversity. Based on SSR association analysis, we discovered some specific allele variations and conventional materials related to fiber quality traits. 相似文献
17.
干旱是导致全世界棉花严重减产、纤维品质下降的重要因素,因此获得高产、优质、耐旱的棉花新品种一直是棉花的育种目标。本研究选取217份陆地棉栽培种组成的自然群体为研究对象,采用全生育期处理组灌水量为对照组50%的干旱胁迫处理,并在处理后期对217份材料的株高、衣分、单铃重等18个性状进行2年2点的表型鉴定,干旱胁迫后,群体间响应差异明显,多个表型性状在对照和处理间表现显著差异。通过BLUP分析表型数据并计算各性状的抗旱系数;全基因组范围选取的214对多态性SSR分子标记扫描群体,共检测到393个多态性位点,基因多样性系数平均值为0.402,范围为0.072~0.631,PIC值平均为0.329,范围为0.070~0.560;群体结构分析表明,该群体可分为2个亚群。用上述SSR标记分别对18个性状的抗旱系数进行关联分析,共关联到76个极显著位点(P<0.01),表型变异解释率为2.930%~7.218%,其中共有14个标记位点能同时被2种或以上性状检测到。研究结果可为后期棉花杂交育种亲本选择及抗旱分子标记辅助育种提供理论基础及参考依据。 相似文献