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1.
水稻单核苷酸多态性及其应用现状 总被引:6,自引:0,他引:6
单核苷酸多态性(single nucleotide polymorphisms, SNPs)在水稻中数量多,分布密度高,遗传稳定性高。水稻SNPs的发现方法主要有对样本DNA的PCR产物直接测序、从SSR区段检测SNPs和从基因组序列直接搜索等。目前已有多种基因分型技术运用到了水稻SNPs检测,SNPs检测的高度自动化使水稻SNPs基因分型非常方便。单核苷酸多态性在水稻遗传图谱的构建、基因克隆和功能基因组学研究、标记辅助选择育种、遗传资源分类及物种进化等方面的应用具有巨大潜力。 相似文献
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Litchi is an important fruit tree in tropical and subtropical areas of the world. However, there is widespread confusion regarding litchi cultivar nomenclature and detailed information of genetic relationships among litchi germplasm is unclear. In the present study, the potential of single nucleotide polymorphism (SNP) for the identification of 96 representative litchi accessions and their genetic relationships in China was evaluated using 155 SNPs that were evenly spaced across litchi genome. Ninety SNPs with minor allele frequencies above 0.05 and a good genotyping success rate were used for further analysis. A relatively high level of genetic variation was observed among litchi accessions, as quantified by the expected heterozygosity (He = 0.305). The SNP based multilocus matching identified two synonymous groups, ‘Heiye’ and ‘Wuye’, and ‘Chengtuo’ and ‘Baitangli 1’. A subset of 14 SNPs was sufficient to distinguish all the non-redundant litchi genotypes, and these SNPs were proven to be highly stable by repeated analyses of a selected group of cultivars. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis divided the litchi accessions analyzed into four main groups, which corresponded to the traits of extremely early-maturing, early-maturing, middle-maturing, and late-maturing, indicating that the fruit maturation period should be considered as the primary criterion for litchi taxonomy. Two subpopulations were detected among litchi accessions by STRUCTURE analysis, and accessions with extremely early- and late-maturing traits showed membership coefficients above 0.99 for Cluster 1 and Cluster 2, respectively. Accessions with early- and middle-maturing traits were identified as admixture forms with varying levels of membership shared between the two clusters, indicating their hybrid origin during litchi domestication. The results of this study will benefit litchi germplasm conservation programs and facilitate maximum genetic gains in litchi breeding programs. 相似文献
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Background
Genome-wide association studies (GWAS) identify disease-associations for single-nucleotide-polymorphisms (SNPs) from scattered genomic-locations. However, SNPs frequently reside on several different SNP-haplotypes, only some of which may be disease-associated. This circumstance lowers the observed odds-ratio for disease-association.Methodology/Principal Findings
Here we develop a method to identify the two SNP-haplotypes, which combine to produce each person’s SNP-genotype over specified chromosomal segments. Two multiple sclerosis (MS)-associated genetic regions were modeled; DRB1 (a Class II molecule of the major histocompatibility complex) and MMEL1 (an endopeptidase that degrades both neuropeptides and β-amyloid). For each locus, we considered sets of eleven adjacent SNPs, surrounding the putative disease-associated gene and spanning ∼200 kb of DNA. The SNP-information was converted into an ordered-set of eleven-numbers (subject-vectors) based on whether a person had zero, one, or two copies of particular SNP-variant at each sequential SNP-location. SNP-strings were defined as those ordered-combinations of eleven-numbers (0 or 1), representing a haplotype, two of which combined to form the observed subject-vector. Subject-vectors were resolved using probabilistic methods. In both regions, only a small number of SNP-strings were present. We compared our method to the SHAPEIT-2 phasing-algorithm. When the SNP-information spanning 200 kb was used, SHAPEIT-2 was inaccurate. When the SHAPEIT-2 window was increased to 2,000 kb, the concordance between the two methods, in both of these eleven-SNP regions, was over 99%, suggesting that, in these regions, both methods were quite accurate. Nevertheless, correspondence was not uniformly high over the entire DNA-span but, rather, was characterized by alternating peaks and valleys of concordance. Moreover, in the valleys of poor-correspondence, SHAPEIT-2 was also inconsistent with itself, suggesting that the SNP-string method is more accurate across the entire region.Conclusions/Significance
Accurate haplotype identification will enhance the detection of genetic-associations. The SNP-string method provides a simple means to accomplish this and can be extended to cover larger genomic regions, thereby improving a GWAS’s power, even for those published previously. 相似文献5.
Aliza A. Lindo Dwight E. Robinson Paula F. Tennant Lyndel W. Meinhardt Dapeng Zhang 《Tropical plant biology》2018,11(3-4):93-106
Cacao is an economically important commodity in Jamaica. Knowledge of the genetic diversity of Jamaican cacao germplasm is essential for their conservation and management. In spite of cacao’s economic importance in Jamaica, the crop is under studied, therefore limiting sound decisions toward improving productivity. Assessment of germplasm and on-farm genetic diversity is required to assist selecting superior genotypes to propagate and distribute across the island, as well as to use them as parental clones in breeding programs. Using 94 single nucleotide polymorphism (SNP) markers, 140 Jamaican cacao samples from two germplasm collections and a farmer’s estate along with 150 reference samples were analyzed. The principal coordinate analysis demonstrated that the majority of the Jamaican cacao selections were hybrids derived from five original germplasm groups, including Criollo, Amelonado and three Upper Amazon Forastero groups. Among the Upper Amazon groups, the Bayesian clustering analysis revealed that the Parinari (PA) ancestral lineage contributed the most (29.9%) to the Jamaican cacao germplasm. The germplasm collections showed greater diversity in terms of ancestral contributions compared to the farmer’s estate. However, the genetic differentiation between the three collecting sites was small (Fst?=?0.036), indicating that samples collected from the three sites were derived from a common pool of germplasm. The current study supports the historical records and clarified the ancestry of Jamaican cacao. Although the majority of the cacao genetic groups were observed in the Jamaican cacao collections, several diversity gaps were found in both germplasm collections and in the farmer’s estate, especially germplasm with disease resistance to cacao frosty pod rot that was recently found in Jamaica. 相似文献
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Massively parallel sequencing (MPS), since its debut in 2005, has transformed the field of genomic studies. These new sequencing technologies have resulted in the successful identification of causal variants for several rare Mendelian disorders. They have also begun to deliver on their promise to explain some of the missing heritability from genome-wide association studies (GWAS) of complex traits. We anticipate a rapidly growing number of MPS-based studies for a diverse range of applications in the near future. One crucial and nearly inevitable step is to detect SNPs and call genotypes at the detected polymorphic sites from the sequencing data. Here, we review statistical methods that have been proposed in the past five years for this purpose. In addition, we discuss emerging issues and future directions related to SNP detection and genotype calling from MPS data. 相似文献
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Matsumoto T Okumura N Uenishi H Hayashi T Hamasima N Awata T 《Biochemical genetics》2012,50(5-6):428-439
In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3'-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3'-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples. 相似文献
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Akiko Shiotani Takahisa Murao Yoshihiko Fujita Yoshinori Fujimura Takashi Sakakibara Kazuto Nishio Ken Haruma 《PloS one》2013,8(12)
Background
Aspirin-induced enteropathy is now increasingly being recognized although the pathogenesis of small intestinal damage induced by aspirin is not well understood and related risk factors have not been established.Aim
To investigate pharmacogenomic profile of low dose aspirin (LDA)-induced small bowel bleeding.Methods
Genome-wide analysis of single nucleotide polymorphisms (SNPs) was performed using the Affymetrix DMET™ Plus Premier Pack. Genotypes of candidate genes associated with small bowel bleeding were determined using TaqMan SNP Genotyping Assay kits and direct sequencing.Results
In the validation study in overall 37 patients with small bowel bleeding and 400 controls, 4 of 27 identified SNPs: CYP4F11 (rs1060463) GG (p=0.003), CYP2D6 (rs28360521) GG (p=0.02), CYP24A1 (rs4809957) T allele (p=0.04), and GSTP1 (rs1695) G allele (p=0.04) were significantly more frequent in the small bowel bleeding group compared to the controls. After adjustment for significant factors, CYP2D6 (rs28360521) GG (OR 4.11, 95% CI. 1.62 -10.4) was associated with small bowel bleeding.Conclusions
CYP4F11 and CYP2D6 SNPs may identify patients at increased risk for aspirin-induced small bowel bleeding. 相似文献9.
大豆抗胞囊线虫病种质rhg1和Rhg4位点的单核苷酸多态性(SNPs) 总被引:8,自引:0,他引:8
本研究以57份中美大豆抗胞囊线虫病种质资源为实验材料,利用基于检测微珠的单碱基延伸方法,对与大豆胞囊线虫病(SCN)抗性基因rhg1和Rhg4紧密连锁的SNPs进行分析,目的是阐明我国大豆抗性种质在这两个位点的SNPs等位变异分布频率,为中国大豆种质抗SCN资源的利用奠定基础。分析结果表明,SNPs的抗性等位基因与中国大豆种质综合抗性的关系比不同生理小种的抗性关系更为密切。在rhg1和Rhg4位点,美国的9份抗性种质中,有7份抗性种质的SNPs均为纯合抗病基因型,而中国48份抗性种质中有32份。分别占鏊定总数的77.8%和66.7%,推测大豆抗SCN种质中,以rhg1和Rhg4这两个基因协同作用表现出的抗性可能占多数.但还存在其他的抗性机制。 相似文献
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Qionglin Huang Zhonggang Duan Jinfen Yang Xinye Ma Ruoting Zhan Hui Xu Weiwen Chen 《PloS one》2014,9(12)
Amomum villosum Lour., produced from Yangchun, Guangdong Province, China, is a Daodi medicinal material of Amomi Fructus in traditional Chinese medicine. This herb germplasm should be accurately identified and collected to ensure its quality and safety in medication. In the present study, single nucleotide polymorphism typing method was evaluated on the basis of DNA barcoding markers to identify the germplasm of Amomi Fructus. Genomic DNA was extracted from the leaves of 29 landraces representing three Amomum species (A. villosum Lour., A. xanthioides Wall. ex Baker and A. longiligulare T. L. Wu) by using the CTAB method. Six barcoding markers (ITS, ITS2, LSU D1–D3, matK, rbcL and trnH-psbA) were PCR amplified and sequenced; SNP typing and phylogenetic analysis were performed to differentiate the landraces. Results showed that high-quality bidirectional sequences were acquired for five candidate regions (ITS, ITS2, LSU D1–D3, matK, and rbcL) except trnH-psbA. Three ribosomal regions, namely, ITS, ITS2, and LSU D1–D3, contained more SNP genotypes (STs) than the plastid genes rbcL and matK. In the 29 specimens, 19 STs were detected from the combination of four regions (ITS, LSU D1–D3, rbcL, and matK). Phylogenetic analysis results further revealed two clades. Minimum-spanning tree demonstrated the existence of two main groups: group I was consisting of 9 STs (ST1–8 and ST11) of A. villosum Lour., and group II was composed of 3 STs (ST16–18) of A. longiligulare T.L. Wu. Our results suggested that ITS and LSU D1–D3 should be incorporated with the core barcodes rbcL and matK. The four combined regions could be used as a multiregional DNA barcode to precisely differentiate the Amomi Fructus landraces in different producing areas. 相似文献
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Kenta Shirasawa Hiroyuki Fukuoka Hiroshi Matsunaga Yuhko Kobayashi Issei Kobayashi Hideki Hirakawa Sachiko Isobe Satoshi Tabata 《DNA research》2013,20(6):593-603
With the aim of understanding relationship between genetic and phenotypic variations in cultivated tomato, single nucleotide polymorphism (SNP) markers covering the whole genome of cultivated tomato were developed and genome-wide association studies (GWAS) were performed. The whole genomes of six tomato lines were sequenced with the ABI-5500xl SOLiD sequencer. Sequence reads covering ∼13.7× of the genome for each line were obtained, and mapped onto tomato reference genomes (SL2.40) to detect ∼1.5 million SNP candidates. Of the identified SNPs, 1.5% were considered to confer gene functions. In the subsequent Illumina GoldenGate assay for 1536 SNPs, 1293 SNPs were successfully genotyped, and 1248 showed polymorphisms among 663 tomato accessions. The whole-genome linkage disequilibrium (LD) analysis detected highly biased LD decays between euchromatic (58 kb) and heterochromatic regions (13.8 Mb). Subsequent GWAS identified SNPs that were significantly associated with agronomical traits, with SNP loci located near genes that were previously reported as candidates for these traits. This study demonstrates that attractive loci can be identified by performing GWAS with a large number of SNPs obtained from re-sequencing analysis. 相似文献
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单核苷酸多态性(single nucleotide polymorphism, SNP)是基因组中最常见的遗传多态性,在遗传学研究的许多方面具有重要的作用。综述了单核苷酸多态性的发现、特点及其应用等方面对植物SNP的研究进展,并展望其在作物遗传育种中的应用前景。 相似文献
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Randy Lambreghts Mi Shi William J. Belden David deCaprio Danny Park Matthew R. Henn James E. Galagan Meray Batürkmen Bruce W. Birren Matthew S. Sachs Jay C. Dunlap Jennifer J. Loros 《Genetics》2009,181(2):767-781
We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of sufficient density to allow fine mapping of most loci. Sequencing of Mauriceville cDNAs and alignment to the completed genomic sequence of the Oak Ridge strain identified 19,087 putative SNPs. Of these, a subset was validated by cleaved amplified polymorphic sequence (CAPS), a simple and robust PCR-based assay that reliably distinguishes between SNP alleles. Experimental confirmation resulted in the development of 250 CAPS markers distributed evenly over the genome. To demonstrate the applicability of this map, we used bulked segregant analysis followed by interval mapping to locate the csp-1 mutation to a narrow region on LGI. Subsequently, we refined mapping resolution to 74 kbp by developing additional markers, resequenced the candidate gene, NCU02713.3, in the mutant background, and phenocopied the mutation by gene replacement in the WT strain. Together, these techniques demonstrate a generally applicable and straightforward approach for the isolation of novel genes from existing mutants. Data on both putative and validated SNPs are deposited in a customized public database at the Broad Institute, which encourages augmentation by community users. 相似文献
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Ioannis Ganopoulos Aphrodite Tsaballa Aliki Xanthopoulou Panagiotis Madesis Athanasios Tsaftaris 《Plant Molecular Biology Reporter》2013,31(3):763-768
Single nucleotide polymorphisms (SNPs) provide an important tool for cultivar identification in studies of genetic diversity, but until now, the time-consuming and costly nature of DNA sequencing has limited the identification of new markers. Herein, we describe the application of high-resolution melting (HRM), a recent enhancement to traditional DNA melting analysis, for the characterization of polymerase chain reaction products and the identification of nine gene-based SNPs for distinguishing the main Greek sweet cherry cultivars. The expected heterozygosity value of nine SNPs averaged at 0.518. The combined power of discrimination for the SNP markers was 0.999969. The ability of HRM to accurately discern nucleotide changes in a DNA sequence makes it a cost- and time-effective alternative to traditional sequencing for the detection of gene-based SNPs. 相似文献
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The development of next generation sequencing (NGS) and high throughput genotyping are important techniques for the QTL mapping and genetic analysis of different crops. High-resolution melting (HRM) is an emerging technology used for detecting single-nucleotide polymorphisms (SNPs) in various species. However, its use is still limited in maize. The HRM analysis was integrated with SNPs to identify three types of populations (NIL population, RIL population and natural population), and the useful tags were screened. The patterns of temperature-shifted melting curves were investigated from the HRM analysis, and compared these with the kit. Among all 48 pairs of primers, 10 pairs of them were selected: six pairs of primers for the NIL population, three pairs of primers for the RIL population, and one pair of primer for the natural population. The marker for the natural population was developed with a matching rate of 80% for the plant height trait, based on the data of the phenotypic characteristics measured in the field. This study provides an effective method for maize genotyping in the classification of maize germplasm resources, which can be applied to other plants for high-throughput SNP genotyping or further mapping. 相似文献
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Amplified Fragment Length Polymorphism (AFLP) Provides Molecular Markers for the Identification of Caladium bicolor Cultivars 总被引:4,自引:0,他引:4
LOH JIN PHANG; KIEW RUTH; KEE ANDREA; GAN LEONG HUAT; GAN YIK-YUEN 《Annals of botany》1999,84(2):155-161
Caladiums are popular ornamental plants that have not been wellstudied at the molecular level. Identification of species withinthe genus Caladium (Araceae) has been based primarily on morphology.However, the lack of comprehensive references makes identificationof Caladium cultivars extremely difficult. Amplified fragmentlength polymorphism (AFLP) analysis using 17 primer combinationswas carried out on two species of Caladium (C. bicolor and C.schomburgkii), including six cultivars of C. bicolor. Resultsshowed that AFLP can be used to distinguish these two speciesby their unique and different banding patterns. Unweighted PairGroup Method using Arithmetic Averages (UPGMA) permitted clusteranalysis of data from 17 selected primer combinations on sixcultivars of C. bicolor and one cultivar ofC. schomburgkii .It showed that closely related species can clearly be differentiatedand that genetic difference between cultivars can also be established.Unique AFLP molecular markers were detected for all the C. bicolorcultivars used. The use of AFLP has potential for preciselycharacterizing and identifying particular caladium cultivarsas well as for the registration of new cultivars. It will alsobe useful in future breeding programmes and systematics studies.Copyright 1999 Annals of Botany Company Araceae, Caladium species and cultivars, AFLP DNA fingerprinting, diversity, AFLP markers. 相似文献