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后基因组时代下作物的SNP分型方法 总被引：4，自引：0，他引：4
单核苷酸多态性(single nucleotide polymorphisms,SNPs)是生物体最普遍的一种多态差异,在植物功能基因组研究和作物遗传改良方面有着广泛的应用。利用全基因组水平SNP标记谱进行遗传变异的研究、群体结构分析、关联性分析、作物分子设计育种,以及对大规模SNP数据进行验证、评估等,都迫切需要发展和利用各种不同的SNP分型手段实现。本文综述了目前常用的一些SNP分型方法,简要介绍了检测原理及操作流程,并对后基因组时代下作物的高通量SNP数据的分析进行了讨论。 相似文献
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单核苷酸多态性（SNPs）和插入-删除标记（InDels）日益成为主要作物的重要遗传标记。本研究中，我们想证明这两种标记在将指纹重叠群定位到遗传图谱上的实用性。为了得到SNP和InDcl标记，我们扩增了12个玉米品系中与3000个单基因相对应的基因组区域，其中194个单基因（6．4％）在琼脂凝胶上表现出B73和Mo17间的大小多态性InDels。 相似文献
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《华北农学报》2018,(Z1)
为研究蓝狐GH基因多态性及其与生长性状的关系,为蓝狐的选种及选育提供一定的理论依据。选取体质量、体长具有明显差异的芬兰狐和地产狐构建DNA池,采用PCR产物直接测序法对GH基因的全长进行单核苷酸多态性(Single nucleotide polymorphism,SNPs)位点的检测,并将发现的SNPs位点与生长性状进行关联分析。结果检测到2个SNPs,GH基因A306G和C1144T位点在芬兰狐和地产狐群体中存在多态性。遗传多样性分析表明,2个位点在芬兰狐中多态信息含量为0. 057 9,属于低度多态位点,地产狐多态信息含量为0. 573 1,属于高度多态位点。2个SNPs位点的遗传多样性参数、基因型频率和基因频率在同一群体中高度一致,说明这2个SNPs位点之间完全连锁,形成了AACC、ABCD和BBDD 3种单倍型。方差分析表明,芬兰狐和地产狐多态位点的基因型频率差异极显著(P 0. 01)。关联分析表明,公狐AACC基因型个体体质量显著高于ABCD基因型(P 0. 05),但与体长差异不显著(P 0. 05);母狐AACC基因型个体体质量极显著高于ABCD基因型个体(P 0. 01)且体长显著高于ABCD基因型个体(P 0. 05)。结果提示:2个SNPs与其生长性状可能相关。 相似文献
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《分子植物育种》2015,(1)
nyc3基因在叶绿素降解过程中起关键作用。本研究通过分析nyc3基因在533份水稻核心种质材料中存在的自然变异,发现了nyc3基因序列具有非常丰富的单核苷酸多态性,并在基因的转录区域共找到了28个SNPs,其中在启动子区域检测到10个SNPs,在5'UTR检测到2个SNPs,在3'UTR检测到16个SNPs。利用生物信息学软件,将核心种质中nyc3分为14个单倍型,筛选其中6个主要单倍型进行染色体画图,明确了各单倍型之间存在的SNP差异,同时确定28个SNPs在基因转录区域的分布。通过实验室构建的全基因组范围内水稻全生育期表达谱数据库,找到在不同时期、不同组织中nyc3的表达量,通过分析可以发现,nyc3的表达量伴随着水稻的生长在不断的升高,在水稻成熟期,叶片中nyc3的表达量达到最高值,充分说明nyc3在调控叶绿素降解上起到作用。 相似文献
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为揭示中国野生型大麻和栽培型大麻基因组之间的差异,本研究通过全基因组重测序技术对一种野生型大麻(ym606)和一种栽培型大麻(ym224-B)进行全基因组重测序,测序深度10×,通过与参考基因组(Cansat3_genome)进行比对,共检测到2 264 150个单核苷酸多态性位点(SNPs)。ym606和ym224-B的杂合度分别为0.12%和0.11%,两个个体之间的二等位多态性SNP可分为aa×bb、lm×ll、nn×np和hk×hk等4类,其中aa×bb型标记有988 575个,占多态性SNP总数量的46.32%,lm×ll、nn×np和hk×hk分别占比25.17%、22.59%和5.71%。研究结果能在一定程度上反映中国野生大麻和栽培大麻在基因组水平的差异,可为下一步构建野生型和栽培型大麻遗传分离群体及开发重要性状分子标记提供理论基础和参考。 相似文献
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五种热带水果乙烯受体基因的SNP分析 总被引：17，自引：6，他引：11
根据乙烯受体基因的保守序列设计引物，分别从荔枝、香蕉、木瓜、芒果和莲雾等五种热带水果的基因组DNA中克隆出的乙烯受体基因的保守序列，序列长度分别为1440bp、1441bp、1439bp、1440bp和1440bp，序列分析表明，与栽培稻的ers基因相似性最高。五种热带水果乙烯受体基因保守序列存在明显的单核苷酸变异，在19个核苷酸位点存在SNPs(single nucleotide polymorphisms)，其中12个SNPs存在于内含子中，7个SNPs存在于编码序列区。在编码序列区的SNPs，荔枝与其他4种热带水果相比具有较高的单核苷酸多态性，荔枝有4个核苷酸的变异，其余4种热带水果仅有一个核苷酸变异。编码区序列中的单核苷酸的改变，除了第783位核苷酸的不同没有引起氨基酸改变外，其余均导致编码氨基酸的改变。 相似文献
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HRM及其在植物育种中的应用展望 总被引：1，自引：0，他引：1
HRM（high resolution melting,高分辨率熔解曲线）分析基于监测双链DNA升温变性解链的熔解曲线,是新发展起的一种基因突变扫描及SNPs（single nucleotide polymorphisms,单核苷酸多态性）鉴定技术。由于在灵敏度和准确性上具有突出的优点,HRM近几年来在突变扫描、基因分型、DNA甲基化研究中得到广泛应用。本文简述了HRM的原理及特点,同时结合HRM分析植物群体的实例,对HRM在植物育种中的应用进行了展望。 相似文献
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DNA指纹图谱技术及其在作物品种资源中的应用 总被引：17，自引：0，他引：17
随着各种新型DNA分子标记的出现,带动了DNA指纹图谱技术的快速发展。本文简要阐述了几种常见DNA指纹鉴定技术,如限制性片段长度多态性(restrictionfragmentlengthpolymorphism,简称RFLP)、随机扩增多态性DNA(randomamplifiedpolymorphicDNA,简称RAPD)、扩增片段长度多态性(am-plifiedfragmentlengthpolymorphism,简称AFLP)、简单重复序列或微卫星标记(simplesequencerepeat,简称SSR)、内部简单重复序列(inter-simplesequencerepeat,简称ISSR)和单核苷酸多态性(singlenucleotidepoly-morphisms,简称SNPs)等的基本原理、在技术上的优缺点及其在作物品种资源中的应用,包括品种的鉴定、纯度的检测、品种亲缘关系与分类的研究及品种专利权的正当维护等。同时,对DNA指纹图谱技术在应用中的存在问题及相应的解决途径进行了简单的讨论,如目前DNA的提取方法与育种应用的大规模群体不相适应和大多数DNA指纹图谱检测技术仍比较繁琐,限制了该技术在育种中的大规模应用等。 相似文献
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TLR4基因SNP检测及在中外鸡种中的群体变异分析 总被引：2，自引：0，他引：2
摘要：以9个地方鸡种（北京油鸡、白耳鸡、溧阳鸡、河南斗鸡、泰和乌骨鸡、大骨鸡、狼山鸡、仙居鸡、茶花鸡）和3个引进品种（隐性白羽肉鸡、科宝鸡、来航蛋鸡)为素材,利用DNA直接测序技术对Toll样受体4（TLR4）蛋白基因（登陆号为AY064697）的全部外显子、部分内含子及5`调控区共4373bp的序列进行单核苷酸多态性检测,共检测到36个SNPs,其中19个SNPs位于编码区（cSNPs）,12个集中于第三外显子的特定区域上（蛋白的TRR结构域）;10个为错义突变,21个为新发现的SNPs。对集中于第三外显子上的12个SNP位点,在十二个品种的688个个体进行了PCR-SBT检测,这些SNPs 产生的不同基因型及等位基因在12个品种鸡间分布存在显著的差异,推测与该基因的功能存在相关。 相似文献
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Several SNP (single nucleotide polymorphism) genotyping methods have been developed in the past most of which require sophisticated instrumentation and large initial investments. We describe here a high-throughput SSCP (single strand conformation polymorphism) system on our HEGS (high efficiency genome scanning) platform, which is simple, accurate, cost effective and requires neither restriction digestion of the amplification products nor elaborate post-PCR processing detection. Several parameters critical to SSCP analysis were optimized viz., gel matrix and concentration, gel running temperature, buffer composition, running conditions and PCR primer design so as to identify SNPs in amplicons ranging from 100 to 750 bp in size. A simple post-PCR processing system was developed using fluorescent dye for quick and easy detection of SNP polymorphism. HEGS-SSCP was also found to be useful in uncovering simple sequence repeat differences between different genotypes that differ by one or few di/tri nucleotide repeats. The practical utility of this system is illustrated with two successful efforts towards construction of high resolution linkage maps of a lesion mimic locus on chromosome 7 and a major quantitative trait locus conditioning field blast resistance on chromosome 4 in rice. 相似文献
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N. Dixit P. Dokku S. V. Amitha Mithra S. K. Parida A. K. Singh N. K. Singh T. Mohapatra 《Euphytica》2013,192(1):55-61
GW2, a grain weight quantitative trait locus (QTL) in rice encodes a ring type E-3 ubiquitin ligase. A single nucleotide deletion at the 346th nucleotide position in the ligase domain of GW2 was earlier reported to result in higher grain weight in rice. The present study aimed at validating the known functional polymorphism and identifying additional natural genetic variation if any, in the region that included the functional domain of GW2 in a set of indica and aromatic genotypes for which ninety three rice genotypes were phenotyped for grain length, grain width and 100 grain weight. A wide range of variation was observed for these traits. PCR amplification and sequencing of GW2 target region revealed absence of insertion/deletion (InDel) at the 346th position which suggested that the genetic variation in grain weight in Basmati and non-Basmati indica genotypes was not explained by this InDel. However, four new single nucleotide polymorphisms (SNPs) were discovered at nucleotide positions 406, 461, 466 and 501 in the fifth exon and one InDel each in second and fourth introns. Only two of these SNPs, at positions 461 and 501 led to amino acid substitutions. A total of 10 haplotypes were constructed based on these four SNPs which could be regrouped into four categories based on their amino acid substitutions. Association genetic analysis of these haplotypes with different grain traits revealed a moderate association with grain width (R2 = 0.18 at P < 0.05). Thirteen haplotypes constructed using both intronic and exonic polymorphisms did not have any association with grain traits. 相似文献
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José Marcelo Soriano Viana Fabyano Fonseca e Silva Gabriel Borges Mundim Camila Ferreira Azevedo Hikmat Ullah Jan 《Euphytica》2017,213(1):13
The efficiency of quantitative trait locus (QTL) mapping methods needs to be investigated assuming high single nucleotide polymorphism (SNP) density and low heritability QTLs. This study assessed the efficiency of the least squares, maximum likelihood, and Bayesian approaches for QTL mapping assuming high SNP density and low heritability QTLs. We simulated 50 samples of 400 F2 individuals, which were genotyped for 1000 SNPs (average density of one SNP/centiMorgan) and phenotyped for three traits controlled by 12 QTLs and 88 minor genes. The genes were randomly distributed in the regions covered by the SNPs along ten chromosomes. The QTL heritabilities ranged from approximately 1–2% and the sample sizes were 200 and 400. The power of QTL detection ranged from 30 to 60%, the false discovery rate (FDR) ranged from only 0.5–1.2%, and the bias in the QTL position ranged from 4 to 6 cM. The QTL mapping efficiency was not influenced by the degree of dominance. The statistical approaches were comparable regarding the FDR. Regression-based and simple interval mapping methods showed equivalent power of QTL detection and mapping precision. Compared to interval mapping, the inclusive composite interval mapping provided slightly greater QTL detection power and mapping precision only for the intermediate and high heritability QTLs. By maximizing the prior number of QTLs, the Bayesian analysis provided the greatest power of QTL detection. No method proved to be superior. 相似文献
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Discovery of single nucleotide polymorphisms (SNPs), including small insertions and deletions (indels), is one of the hot topics in genetic research. SNPs were surveyed using nine soybean genotypes from Korea. Sequence variations in a total of 110 genes from GenBank among the nine genotypes were studied using genomic DNA as a template. Direct fluorescent dideoxynucleotide sequencing data of PCR products from primers designed from soybean ESTs were analyzed by SeqScape software to ensure high accuracy. Approximately 70% of the primer sets produced a single PCR product from which reliable sequence data were obtained, and 23.6% of these had at least one SNP. Overall, a total of 110 ESTs for SNPs were screened in 33,262 bp, consisting of 16,302 bp from coding regions and 16,960 bp from adjacent non-coding regions (5 UTR, 3 UTR and introns). SNPs in coding and non-coding regions occurred at a frequency of 1 per 3,260 bp, corresponding to a nucleotide diversity () of 0.00011, and 1 per 278 bp ( = 0.00128), respectively. This suggested that the higher level of sequence variation in non-coding regions would make them good regions in which to search for SNPs. The SNPs in partial cDNA sequences could be valuable for gene-targeted map construction in soybean. 相似文献
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As the majority of methods for single nucleotide polymorphism (SNP) identification are highly cost-prohibitive, it is necessary
to develop new strategies that are more suitable for small and medium-scale laboratories. In this paper, we investigate the
potential of degenerate oligonucleotide primed PCR (DOP-PCR) for SNP discovery in soybean. PCR fragments were amplified from
two soybean cultivars, ‘Pureunkong’ and ‘Jinpumkong 2,’ shotgun cloned and sequenced. The sequences of both cultivars were
then assembled and examined for occurrence of SNPs. The effectiveness of SNP discovery was much lower than expected. Over
1,300 analyzed sequences were grouped in 144 contigs, but only 51 putative SNP sites were found in 18 of these contigs. About
50% of the contigs contained identical sequences and in more than one-third (35.4%), putative paralogous fragments were assembled.
Subsequent validation of SNPs allowed the confirmation of only eight SNP sites. The failure to validate the remaining SNPs
was mostly due to amplification of duplicated or multiplicated genomic regions. A relatively high proportion of chloroplast
and mitochondrial DNA sequences was another limitation of effective SNP detection. Although the DOP-PCR technique was not
efficient enough for SNP discovery because of the degree of soybean genome complication, the relatively large number of paralogous
sequences in our data collection can be used for further detailed analysis of the genome structure of this species. 相似文献
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西瓜和黄瓜乙烯受体ETR1基因片段的克隆与序列比较分析 总被引：2，自引：0，他引：2
乙烯受体基因ETR1是乙烯信号转导过程中的关键调控基因.研究根据ETR1基因的保守序列设计引物,以西瓜(Citrullus lanatus (Thunb.) Matsum & Nadai var.lanatus)和黄瓜(Cucumis sativus L.)的基因组DNA为模板进行PCR扩增,获得序列长度分别为1 633 bp和1 491 bp的基因片段CLETR1和CSETR1.序列分析表明,CLETR1和CSETR1与Genebank中收录的多条ETR1基因的核苷酸序列同源性在80%～98%,氨基酸序列同源性在75%～98%.西瓜和黄瓜ETR1基因片段的编码序列存在明显的单核苷酸变异,共23个核苷酸位点存在SNPs(Single nucleotide polymorphisms),其中5个SNPs导致4个编码氨基酸的改变. 相似文献
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Yunfei Jiang Marwan Diapari Rosalind A. Bueckert Bunyamin Tar’an Thomas D. Warkentin 《Euphytica》2017,213(9):215
Field pea (Pisum sativum) is an important pulse crop globally for human consumption and livestock feed. A panel of 92 diverse pea cultivars was evaluated across nine environments and genotyped using 1536 single nucleotide polymorphisms (SNPs) arranged in a GoldenGate array. Population structure analysis revealed three subpopulations roughly consistent with the cultivar origin. Phenotyping included days to flowering (DTF), duration of flowering (DOF), number of reproductive nodes, number of pods on the main stem, percentage of pods set, percentage of pods retained with seed and pollen germination reduction due to heat stress. Association analyses identified a total of 60 SNPs significantly associated (?log10 p ≥ 4.3) with these seven reproductive development-related traits. Among these 60 marker-trait associations, 33 SNPs were associated with the onset of flowering, 8 SNPs with pod development and 19 SNPs with the number of reproductive nodes. No SNP marker was significantly associated with in vitro pollen germination reduction caused by high temperature stress. We found that 12 SNPs associated with DTF and 2 SNPs associated with DOF overlapped with the SNP markers associated with the number of reproductive nodes. Genomic regions associated with variation for reproductive development-related traits identified in this study provide grounds for future genetic improvement in pea. 相似文献