scholarly journals Single nucleotide polymorphism (SNP) discovery and linkage mapping of bovine cytokine genes

1999 ◽  
Vol 10 (11) ◽  
pp. 1062-1069 ◽  
Author(s):  
William M. Grosse
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Linkage Mapping ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cytokine Genes

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

scholarly journals Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

2021 ◽  
Vol 12 ◽  
Author(s):  
Lingli Li ◽  
Yingjun Zhang ◽  
Yong Zhang ◽  
Ming Li ◽  
Dengan Xu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Linkage Mapping ◽  
Cost Effective ◽  
Wheat Breeding ◽  
Preharvest Sprouting ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Grain Color ◽  
Sprouting Resistance

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6–18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D, respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection.

scholarly journals Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

2009 ◽  
Vol 7 (4) ◽  
pp. 347-354 ◽  
Author(s):  
Peter C. Bundock ◽  
Frances G. Eliott ◽  
Gary Ablett ◽  
Adam D. Benson ◽  
Rosanne E. Casu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Plant Species ◽  
454 Sequencing ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Polyploid Plant

Single nucleotide polymorphism (SNP) discovery in porcine expressed genes

2002 ◽  
Vol 33 (3) ◽  
pp. 186-195 ◽  
Author(s):  
S. C. Fahrenkrug ◽  
B. A. Freking ◽  
T. P. L. Smith ◽  
G. A. Rohrer ◽  
J. W. Keele
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Effects of single nucleotide polymorphism ascertainment on population structure inferences

2021 ◽  
Author(s):  
Kotaro Dokan ◽  
Sayu Kawamura ◽  
Kosuke M Teshima
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Natural Populations ◽  
Snp Markers ◽  
Ascertainment Bias ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Frequency Spectra ◽  
Single Nucleotide ◽  
Selection Of

Abstract Single nucleotide polymorphism (SNP) data are widely used in research on natural populations. Although they are useful, SNP genotyping data are known to contain bias, normally referred to as ascertainment bias, because they are conditioned by already confirmed variants. This bias is introduced during the genotyping process, including the selection of populations for novel SNP discovery and the number of individuals involved in the discovery panel and selection of SNP markers. It is widely recognized that ascertainment bias can cause inaccurate inferences in population genetics and several methods to address these bias issues have been proposed. However, especially in natural populations, it is not always possible to apply an ideal ascertainment scheme because natural populations tend to have complex structures and histories. In addition, it was not fully assessed if ascertainment bias has the same effect on different types of population structure. Here we examine the effects of bias produced during the selection of population for SNP discovery and consequent SNP marker selection processes under three demographic models: the island, stepping-stone, and population split models. Results show that site frequency spectra and summary statistics contain biases that depend on the joint effect of population structure and ascertainment schemes. Additionally, population structure inferences are also affected by ascertainment bias. Based on these results, it is recommended to evaluate the validity of the ascertainment strategy prior to the actual typing process because the direction and extent of ascertainment bias vary depending on several factors.

Single Nucleotide Polymorphism (SNP) Discovery within the UGT1A Gene Complex: Allelic Frequencies and Ethnic Differences.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3780-3780
Author(s):  
Jeeranut Sawattep ◽  
Thad A. Howard ◽  
Noppawan P. Morales ◽  
Yupin Sanvarinda ◽  
Pranee Fucharoen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
African American ◽  
Phenotypic Variability ◽  
Gene Complex ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Exon 1 ◽  
Intron 2

Abstract The UDP-glycosyltransferase (UGT1A) gene complex plays an important role in the hepatic metabolism of many chemicals, toxins, and drugs including bilirubin and acetaminophen. In this large gene complex that spans over 200kb, there are at least 13 different coding regions that can serve as exon 1, followed by a common sequence that contains exons 2–5. These variable exon 1 sequences confer different chemical specificities for binding compounds, while exons 2–5 provide glycosyltransferase function (glucuronidation) that enhances water solubility and excretion. Mutations and polymorphisms within the UGT1A complex may help explain the phenotypic variability that is observed in drug metabolism for patients with hematological diseases. To date, several important polymorphisms have been identified in the coding regions of the UGT1A1 and UGT1A6 exon 1 sequences, but formal single nucleotide polymorphism (SNP) discovery has not been reported. Using genomic DNA obtained from a cohort of Thai patients with beta-thalassemia/HbE (n=37) and African-American patients with sickle cell anemia (n=12), flanking and coding sequences for UGT1A1 exon 1 (1.5kb), UGT1A6 exon 1 (1.5kb), and UGT1A common exons 2–5 (2.5kb) were fully sequenced in both directions. Polymorphisms that occurred more than once were compared to wildtype sequences obtained from NCBI, Accession Number AF297093. Single Nucleotide Polymorphisms in the UGT1A gene complex SNP NCBI nucleotide Location African-American Thai * indicates a SNP previously identified in NCBI g/c 109183 5′ 1A6 Exon 1 .875/.125 .676/.324 c/g 109301 5′ 1A6 Exon 1 .833/.167 1.000/.000 g/t 109628 1A6 Exon 1 .458/.542 .662/.338 c/t 109713 1A6 Exon 1 1.000/.000 .905/.095 a/g * 109924 1A6 Exon 1 .542/.458 .689/.311 a/g * 110150 1A6 Exon 1 .708/.292 .689/.311 a/c * 110161 1A6 Exon 1 .625/.375 .662/.338 t/g 110236 1A6 Exon 1 .750/.250 .973/.027 c/t 174679 5′ 1A1 Exon 1 .500/.500 .770/.230 g/c 174979 5′ 1A1 Exon 1 1.000/.000 .946/.054 g/a * 175253 1A1 Exon 1 1.000/.000 .932/.068 a/g 182226 Intron 2 .955/.045 .689/.311 t/c 182521 Intron 2 .850/.150 .905/.095 c/t 187524 3′ Exon 5 .417/.583 .865/.135 c/g * 187652 3′ Exon 5 .625/.375 .851/.149 c/g * 187753 3′ Exon 5 .587/.417 .838/.162 In addition to the well-described UGT1A1 (TA)n promoter polymorphism, a total of 16 SNPs were identified in these regions, including 10 that have not been previously reported. Four novel promoter SNPs were identified, along with three new UGT1A6 exon 1 coding SNPs and three non-coding SNPs within the common exon 2–5 region. The alellic frequencies for these SNPs can only be estimated from this small sample size, but indicate substantial differences between Thai and African-American patients. A larger sample size will be used to determine a more accurate allelic frequency for each SNP, and to identify haplotype associations. These novel SNPs within the UGT1A gene complex may have important effects on drug metabolism and may explain some of the phenotypic variability observed in these patient populations.

Sign in / Sign up

Export Citation Format

Share Document