scholarly journals 164 Single nucleotide variants and indels identified from whole-genome resequencing of Gyr, Girolando, and Holstein cattle breeds

2017 ◽  
Vol 95 (suppl_4) ◽  
pp. 80-81
Author(s):  
N. B. Stafuzza ◽  
A. Zerlotini ◽  
F. P. Lobo ◽  
M. E. B. Yamagishi ◽  
T. C. S. Chud ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Whole Genome Resequencing

scholarly journals Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0173954 ◽  
Author(s):  
Nedenia Bonvino Stafuzza ◽  
Adhemar Zerlotini ◽  
Francisco Pereira Lobo ◽  
Michel Eduardo Beleza Yamagishi ◽  
Tatiane Cristina Seleguim Chud ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Cattle Breeds

scholarly journals Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Somatic Mutations ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Diversity Pattern ◽  
Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

scholarly journals Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Paul Stothard ◽  
Jung-Woo Choi ◽  
Urmila Basu ◽  
Jennifer M Sumner-Thomson ◽  
Yan Meng ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Development a Set of 46 SNP Markers for the Yellow Catfish (Tachysurus Fulvidraco)

2021 ◽  
Author(s):  
Huaxing Zhou ◽  
Tingshuang Pan ◽  
Huan Wang ◽  
He Jiang ◽  
Jun Ling ◽  
...  
Keyword(s):  
Snp Markers ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Yellow Catfish ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Whole Genome Resequencing ◽  
Tachysurus Fulvidraco

Abstract The whole genome resequencing was used to develop single nucleotide polymorphisms (SNP) markers for the yellow catfish (Tachysurus fulvidraco). A total of 46 SNP markers were selected from 5550676 genotyping markers which distributed on 26 chromosomes. Of the 46 SNPs analyzed, 35 SNPs conformed to Hardy-Weinberg equilibrium. The observed and expected heterozygosity of these markers ranged from 0.2519 to 0.771 and from 0.265 to 0.5018, respectively. This set of markers will be of great useful for population genetics of the yellow catfish.

scholarly journals Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

2020 ◽  
Author(s):  
Alia Parveen ◽  
Christa D. Jackson ◽  
Shatovisha Dey ◽  
Katy Tarrant ◽  
Nicholas B Anthony ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Chicken Chromosome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Whole Genome Resequencing ◽  
Ascites Syndrome

Abstract Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

scholarly journals Genome-wide identifying of G-quadruplex structures directly by whole-genome resequencing

2021 ◽  
Author(s):  
Jing Tu ◽  
Mengqin Duan ◽  
Wenli Liu ◽  
Na Lu ◽  
Xiao Sun ◽  
...  
Keyword(s):  
Individual Differences ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Genome Wide ◽  
G Quadruplex ◽  
Sequencing Quality ◽  
Single Nucleotide Variations ◽  
Whole Genome Resequencing ◽  
The Given

Abstract We present a convenient genome-wide DNA G-quadruplex (G4) profiling method that identifies G4 structures from ordinary whole-genome resequencing data by seizing the slight fluctuation of sequencing quality. We identified 736,689 G4 structures within human genome, in which 44.9% of all predicted canonical G4-froming sequences were contained. We observed that some of the single nucleotide variations (SNVs) influenced the formation of G4 structures, including homozygous SNVs and heterozygous SNVs. Due to SNVs contain individual differences, the given approach is available to identify and characterize G4s genome-wide for specific individuals.

scholarly journals Construction of A High-Density Genetic Map and Mapping of Fruit Traits in Watermelon (Citrullus Lanatus L.) Based on Whole-Genome Resequencing

2018 ◽  
Vol 19 (10) ◽  
pp. 3268 ◽  
Author(s):  
Bingbing Li ◽  
Xuqiang Lu ◽  
Junling Dou ◽  
Ali Aslam ◽  
Lei Gao ◽  
...  
Keyword(s):  
Genetic Map ◽  
Citrullus Lanatus ◽  
Snp Markers ◽  
High Density ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Parental Lines ◽  
Whole Genome Resequencing

Watermelon (Citrullus lanatus L.) is an important horticultural crop that is grown worldwide and has a high economic value. To dissect the loci associated with important horticultural traits and to analyze the genetic and genomic information of this species, a high-density genetic map was constructed based on whole-genome resequencing (WGR), a powerful high-resolution method for single-nucleotide polymorphism (SNP) marker development, genetic map construction, and gene mapping. Resequencing of both parental lines and 126 recombinant inbred lines (RIL) resulted in the detection of 178,762 single-nucleotide polymorphism (SNP) markers in the parental lines at a sequencing depth greater than four-fold. Additionally, 2132 recombination bin markers comprising 103,029 SNP markers were mapped onto 11 linkage groups (LGs). Substantially more SNP markers were mapped to the genetic map compared with other recent studies. The total length of the linkage map was 1508.94 cM, with an average distance of 0.74 cM between adjacent bin markers. Based on this genetic map, one locus for fruit bitterness, one locus for rind color, and one locus for seed coat color with high LOD scores (58.361, 18.353, 26.852) were identified on chromosome 1, chromosome 8, and chromosome 3, respectively. These prominent loci were identified in a region of 6.16 Mb, 2.07 Mb, and 0.37 Mb, respectively. On the basis of current research, the high-density map and mapping results will provide a valuable tool for identifying candidate genes, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in watermelon breeding.

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