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1.
单核苷酸多态性的检测及应用 总被引：6，自引：1，他引：5
单核苷酸多态性（single nucleotide polymorphisms, SNPs）是近年来发展起来的一种高效便捷的分子标记。它是由单个碱基的转换、颠换、插入或缺失引起的点突变,使得群体之间和个体之间产生了差异。最初SNPs主要运用在与人体重要疾病的关联性研究中,随着检测技术不断提高以及多种生物SNP数据库的不断完善,单核苷酸多态性已经成为开展生物遗传进化及性状关联性分析等领域研究的重要工具。综合介绍了单核苷酸多态性的特点及主要检测方法,并简要概述了SNPs的应用领域和前景。 相似文献
2.
碱基插入/缺失(InDel)在基因组中的分布密度仅次于SNP且易于基因型分型,成为分子标记开发的主要来源。为了开发芥蓝品种间有多态性的分子标记,本研究利用2份芥蓝自交系重测序数据鉴定的InDel位点,在全基因组范围内设计了367对InDel候选标记。通过PCR检测比较8个芥蓝自交系的多态性,发现284对标记在至少2个芥蓝自交系间有多态性,阳性率为77.4%。本研究利用重测序技术开发芥蓝品种间InDel标记效率较高,为种质资源分析、基因定位、分子标记辅助育种等提供了便捷工具。 相似文献
3.
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
4.
遗传标记及其在园艺植物研究中的应用 总被引：4，自引：1，他引：4
评述了形态学标记（morphological markers）、细胞学标记(cytological markers)、生化标记(biochemical markers)、DNA分子标记(DNA molecular markers)等技术的发展现状,着重介绍了近年来DNA指纹图谱技术,即限制性片段长度多态性(Restriction Fragment Length Polymorphism,RFLP)、随机扩增片段长度多态性 (Random Amplified Polymophismic DNA,RAPD)、简单重复序列 (simple sequence repeats,SSR)、扩增片段长度多态性(Amplified Fragment Length Polymorphism,AFLP)、单核苷酸多态性 (single nucleotide polymorphism,SNP) 等标记技术的特点及其在园艺植物品种的分类鉴定、纯度的分析检测及品种间亲缘关系等研究中的应用。 相似文献
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DNA分子标记是继形态标记、细胞标记和生化标记之后发展起来的一种新的较为理想的遗传标记，在甘蔗育种方面发挥了重要作用。DNA分子标记包括：限制性片段长度多态性(RFLP)、随机扩增多态性DNA(RAPD)、扩增片段长度多态性(AFLP)、简单重复序列(SSR)、染色体或基因组原位杂交(GISH)、荧光原位杂交(FISH)等。本文对植物DNA分子标记的原理、特点及其在甘蔗种属鉴定、遗传多样性分析、分子图谱构建及病害分子诊断等方面的研究进行简要的概述。 相似文献
6.
DNA分子标记技术的研究与应用 总被引：1，自引：0，他引：1
DNA分子标记是继传统的形态学标记、细胞学标记、生化标记之后发展起来的以DNA为基础的遗传标记技术,因其独有的技术特点,迅速在各领域得到广泛的应用与发展。本研究总结概括了基于m RNA的表达序列标签(ESTs)、差异显示逆转录PCR (DDRT-PCR)、特征性差异分析(RDA)、基因表达系列分析(SAGE);基于目的基因的保守DNA衍生多态性(CDDP)、目标起始密码子多态性(SCoT)、保守区域扩增多态性(Co-RAP)和基于反转录转座子的反转录转座子位点间扩增多态性(IRAP)、反转录转座子-微卫星扩增多态性(REMAP)等几种新型DNA分子标记技术的原理、特点、优缺点,以及常见DNA分子标记技术的特点比较及其应用,以期在其基础上推动分子标记技术进一步融合、创新与发展。 相似文献
7.
马尾松基因组SSR标记在松属其他树种中的通用性分析 总被引：1，自引：0，他引：1
《分子植物育种》2015,(12)
SSR标记是林木种内遗传多样性及种质鉴别的重要分子工具,而通用性SSR标记可有效解决近缘物种标记不足、开发成本高等问题。本研究检测并分析了基于马尾松基因组测序结果开发的22个SSR多态性标记,在湿地松、白皮松及黄山松等7个松属树种中的通用性(可扩增性及多态性)。结果显示:参试标记在湿地松、白皮松、华山松、加勒比松、油松、黄山松及细叶云南松中的有效扩增率分别为68.18%、31.82%、36.63%、63.64%、100%、100%及100%;对以上7个树种各随机抽样6个植株(实生苗)进行扩增多态性初步检测,多态性标记占有效扩增标记的比例分别为86.67%、71.43%、25.00%、78.57%、90.91%、95.45%及100%。研究结果表明该22个标记绝大部分可应用于参试树种(尤其是油松,黄山松及细叶云南松)的遗传多样性及分子标记辅助育种研究中。 相似文献
8.
SNP及其在肉牛育种中的应用进展 总被引：1，自引：1，他引：0
单核苷酸多态性(Single nucleotide polymorphism,SNP)作为第三代分子标记,具有位点丰富、代表性强和遗传稳定等特点,已成为分子标记研究领域的焦点。本研究综述了SNP特点、检测方法及其在肉牛生长发育性状、繁殖性状、胴体与肉质性状的应用,作为分子标记辅助选择的候选基因,加快肉牛育种进程。 相似文献
9.
《棉花学报》2021,33(5)
【目的】L-D1基因调控陆地棉叶形。本研究设计特异分子标记精准鉴定L-D1等位基因,为其在陆地棉冠层结构改良中的应用提供支撑。【方法】利用具有鲁棉研28号遗传背景的L-D1等位基因近等基因系,分析不同等位基因组合对叶形的影响。根据4个等位基因的启动子和编码区的多态性设计特异分子标记,并对不同叶形中的等位基因进行检测。【结果】L-D1基因从3叶期开始调控叶片叶裂的形成,4～8叶期叶裂不断加深,从9叶期开始基本稳定;L-D1等位基因不同组合可形成相似叶形,仅从形态上难以准确辨别。克隆获得L-D1位点4个等位基因起始密码子前约4 kb的启动子片段,发现24个SNPs(Single nucleotide polymorphism,单核苷酸多态性)、1个133 bp及1个14 bp的插入缺失。根据等位基因启动子及编码区的SNP和缺失插入开发了1个Indel分子标记InDel＿8和2个衍生酶切扩增多态性序列标记dCAPS＿192、dCAPS＿519,分别为l2、L2o、L2s的特异分子标记。【结论】根据陆地棉中控制叶形的L-D1等位基因间的差异开发了3个特异性分子标记,可用来鉴定不同的L-D1等位基因。 相似文献
10.
脂肪型脂肪酸结合蛋白(A-FABP)属脂肪酸结合蛋白家族(FABPs)成员,参与调节哺乳动物细胞内脂肪浓度,进而影响肌肉内脂肪含量(IMF),因此A-FABP可作为影响IMF的候选基因。本研究采用PCR-SSCP技术检测甘南牦牛、青海牦牛、天祝白牦牛(Bos grunniens)A-FABP基因部分第3内含子、第4外显子及部分3’-UTR区单核苷酸多态性(SNPs),分析检测区域分子遗传特征。结果表明,3类群牦牛引物扩增区域发现5种等位基因A-E;同普通牛A-FABP基因序列比对发现6处SNPs,其中第4外显子区存在c.4222A>G的同义突变;3’-UTR区c.*94T>A只存在于牦牛群体,是其区别于普通牛的遗传特征之一。各等位基因在群体间分布差异较大,其中天祝白牦牛只发现3种等位基因,而青海牦牛发现4种等位基因,这可能与牦牛类群的地域分布及选育程度有关。3类群牦牛A-FABP基因检测位点表现为中度多态(PIC为0.29～0.36),有效等位基因数较高,可作为潜在的牦牛肉质性状分子标记位点。 相似文献
11.
Starch properties are major determinants of grain quality and food characteristics in rice (Oryza sativa L.). Control of starch properties will lead to the development of rice cultivars with desirable characteristics. We performed quantitative trait locus analysis and detected a putative region on chromosome 2 associated with phenotypic variation of starch properties in two glutinous rice varieties developed in the Hokkaido region of Japan: ‘Kitayukimochi’, which has a low pasting temperature and creates soft rice cakes, and ‘Shirokumamochi’, which has a high pasting temperature and creates hard rice cakes. Starch branching enzyme IIb (SbeIIb) was identified as a candidate gene within the region. Sequence analysis of SbeIIb in parental lines identified two single-nucleotide polymorphisms (SNPs) with non-synonymous mutations in the coding region of the ‘Shirokumamochi’ genotype (SbeIIbsr). We genotyped over 100 rice cultivars, including 28 rice varieties in the Honshu region of Japan, using the CAPS marker, which was designed using one of the SNPs. However, SbeIIbsr was not found in rice cultivars in Honshu. Distribution analysis indicated that SbeIIbsr was introduced to the rice breeding population in Hokkaido from the American variety ‘Cody’ via the Hokkaido cultivar ‘Kitaake’. As a result, SbeIIbsr was distributed only in progenies of ‘Kitaake’. 相似文献
12.
Erbao Liu Shangshang Zhu Siyuan Zeng Xiaoxiao Hu Dalu Li Guocan Wu Jie Ji Yang Liu Delin Hong 《Euphytica》2018,214(11):217
Improving the combining ability for grain quality traits of the parents is the key factor to enhance averaged bulk grain quality of hybrid japonica rice. Eight quality traits including brown rice rate, milled rice rate (MRR), head rice rate (HRR), chalkiness degree (CD), percentage of chalky grain (PCG), alkali spreading value (ASV), gel consistency (GC) and amylose content (AC) of the bulked sample of rough rice harvested from the 81 F1 hybrid plants were investigated in 2014 and 2015. By combining the phenotypic data of general combining ability (GCA) for the quality traits with genotypic data of single nucleotide polymorphism (SNP) obtained by genotyping by sequencing method, CAScreen1.0 program compiled by MATLAB language was conducted to identify the elite SNP genotype associated with combining ability of quality traits in parents. Totally 35 elite SNP genotypes involving 22 genes (genotypes) were detected associated with GCA of seven quality traits (P?<?0.05) in both 2014 and 2015. Seven and four SNPs were detected associated with combining ability for MRR and HRR, respectively. For PCG and CD, six and ten SNPs were detected associated with combining ability of parents, respectively. Six SNPs involving two genes were detected for combining ability of GC. Only two SNPs were detected which associated with combining ability for ASV. For combining ability of AC, six elite SNPs genotype were detected. Among them, elite SNP genotype of LOC_Os08g25220 (T/C) located on chromosome 8 could significantly reduce AC content in mixed rice samples of hybrid japonica rice. 相似文献
13.
Genotyping by sequencing of 270 Indica rice varieties revealed genetic markers probably related to heavy metal accumulation 
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下载免费PDF全文 Yuhu Liang Xiao Dong Xuemei Ni Qi Wang Sunil Kumar Sahu Junliang Hou Manzhong Liang Liangbi Chen Gengyun Zhang 《Plant Breeding》2018,137(5):691-697
Genotyping by sequencing (GBS) has been applied to identify genetic markers in crops for trait association and breeding purposes. Here, we applied GBS technology to study a natural population of 270 Indica rice strains, which resulted in identification of 79,545 genomewide single nucleotide polymorphisms. Using these SNPs, we found the close relationship between the 270 Indica rice strains. Furthermore, we tested the feasibility of using these 270 Indica strains in studying important rice traits by analysing the cadmium and other metal accumulation of these strains and correlating the traits with genetic markers. We identified 32 SNPs to be associated with cadmium (Cd) accumulation, explaining 61.25% of the Cd concentration variances in grains. The genetic markers provided here are valuable resources for future rice studies, and further characterization of the candidate loci identified in this study can also aid the development of low Cd‐accumulating rice varieties. 相似文献
14.
水稻抽穗期控制候选基因的SNP/InDel多态性分析 总被引：2，自引：0，他引：2
抽穗期是水稻的一种重要农艺性状，但其遗传控制机理还不清楚。本文利用数据库搜索的方法，搜索并分析了30个与拟南芥光周期调控途径花期控制基因同源的水稻基因。利用水稻多态性数据库，得到了发生在这些基因以及Hd6、Ehd1、OsSOCl上的820个SNP及191个InDel位点。分析表明，这些位点不是平均分布到每个基因上。SNP／InDel含量较高的基因存在SNP／InDel的热点片段。14．1％的SNP位点，及7％的InDel位点分布在基因的编码区。本文也分析了侯选基因侧翼5Kb范围内的SNP／InDel多态性位点。按照侧翼多态性位点数目的分布可以将侯选基因分成4种类型，即两侧保守型、两侧热点型、单侧热点型、一侧热点一侧保守型。 相似文献
15.
Xiaona Zhang Pingbo Li Peng Yun Lingqiang Wang Guanjun Gao Qinglu Zhang Lijun Luo Chunyu Zhang Yuqing He 《Plant Breeding》2019,138(6):820-829
Vitamin E (VE) is an important nutritional trait in rice grains. In order to dissect the genetic basis underlying VE content, a recombinant inbred lines population derived from 'Zhenshan 97B' and 'Nanyangzhan' was used for quantitative trait locus (QTL) analysis. Totally, 29 QTLs for six VE traits were identified in 2 consecutive years. Among those, five QTLs repeatedly detected in two years formed a cluster on chromosome 2, which was responsible for all five VE isomers. OsγTMT, the gene encoding γ‐tocopherol methyltransferase in rice, was located to the same region and treated as the candidate gene. Sequence analysis of alleles from two parents revealed many polymorphisms, including 19 single nucleotide polymorphisms (SNPs) and two insert/deletions (Indels) in the promoter region, two nonsynonymous SNPs in exons, and 25 SNPs and an Indel in introns. Besides, a QTL for δ‐tocotrienol and two QTLs for α‐tocopherol were repeatedly detected on chromosome 5 and 8, respectively, all three regions carrying no homologous genes involved in VE biosynthesis. These results could be useful in development of rice lines displaying desirable VE content. 相似文献
16.
以业已完成深度重测序的134份水稻地方种质资源为材料,在大田栽培条件下按不施氮(N0),施96kg hm^–2纯氮(N1)和施192kg hm^–2纯氮(N2)3种氮肥水平,检测了分蘖盛期植株的钾含量、植株干重和钾积累。结果表明,水稻钾含量、植株干重和钾积累在N0、N1、N2三种氮肥处理下均呈正态分布,表型变异丰富。植株干重和钾积累与施氮量呈极显著正相关,钾含量与施氮量相关性不显著;钾含量与植株干重呈负相关,钾含量与钾积累相关性不显著,而植株干重与钾积累呈极显著正相关。在3个施氮水平下,籼稻的钾含量极显著低于粳稻,籼稻的干重和钾积累都极显著高于粳稻。全基因组关联分析发现,在3个氮肥水平下检测到12个显著相关位点,其中钾积累、钾含量和植株干重的显著相关位点分别有2、5和5个。在N1水平下,位于第6染色体上与钾含量相关的SNP(Chr6_1,524,776)的显著性峰候选区包含与钾离子转运蛋白互作的RUPO基因。根据钾含量的差异,鉴定出3个钾含量与低氮响应有关的SNP位点,1个位点与高氮响应有关,而位于第10染色体上的显著性位点Chr10_2,822,026对低氮和高氮均有响应,该区域的4个候选基因的表达在不同氮水平间存在差异。 相似文献
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白叶枯病是水稻生产最严重的细菌性病害,挖掘新的白叶枯病抗性基因资源并培育抗病品种是控制该病害的重要方法。本研究利用父母本抗性差异较大的协优9308衍生的139个重组自交系群体作为遗传材料,人工接种不同白叶枯菌后的病斑长度作为连续型表型,结合经DNA深度测序获得的476,505个单核苷酸多态性(single-nucleotide polymorphism,SNP)标记进行全基因组关联分析(genome-wide associated study,GWAS)。结果表明在P<1×10–4下, 4个菌株处理后共鉴定到109个与白叶枯抗性显著关联的SNPs位点,解释表型变异率59.78%～63.29%。其中CR4接种发现了25个SNP位点其贡献率为61.00%,在这些SNP位点附近共筛选到19个基因,其中有2个为NBS-LRR抗病相关基因(LOCOs11g43420和LOCOs11g45930)。表达分析验证发现该2个基因在抗性亲本中恢9308的表达量分别为感病母本协青早B的4.42倍和8.86倍,表明其可能在正调控白叶枯病... 相似文献
19.
百粒重是大豆重要的产量性状之一,利用正向和反向遗传学方法鉴定与籽粒大小/粒重相关的基因具有重要的理论和实践意义。利用拟南芥和水稻等模式植物中已明确功能的调控籽粒大小/粒重的基因,基于序列相似和结构域相同的原则,在大豆全基因组内筛选到175个同源基因,通过基因表达谱分析发现有22个基因在大豆种子中特异性表达。利用56份大豆种质资源重测序数据查找这些基因内的SNP位点,共得到2769个SNP位点,从中筛选得到在野生大豆和栽培大豆中分化明显的SNP位点121个。通过扩增测序对其中的16个导致非同义变异的SNP位点进行验证,发现有5个SNP位点在野生大豆中为一种变异,而在栽培大豆中为另一种变异。利用2368份大豆种质资源的重测序数据获得了其中的4个SNP位点的变异数据,结合其中1695份材料的百粒重表型分析,发现每个SNP位点对应的野生和突变基因型材料的百粒重表型间都存在极显著差异,并且每个SNP位点中野生基因型材料的百粒重大部分≥12g,突变基因型材料的百粒重大部分＜12g,因此上述4个SNP位点所在的基因（Glyma.05G019800、Glyma.07G022800、Glyma.13G259700和Glyma.13G261700）可能与大豆籽粒大小/粒重的调控有关。获得了与大豆百粒重相关的4个候选基因,为大豆百粒重QTL的精细定位和功能标记的开发以及调控大豆籽粒大小/粒重的基因的功能研究提供了参考。 相似文献
20.
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