A whole genome sequence association study for puberty in a large Duroc × Erhualian F2 population

2017 ◽  
Vol 49 (1) ◽  
pp. 29-35 ◽  
Author(s):  
W. S. Xin ◽  
F. Zhang ◽  
G. R. Yan ◽  
W. W. Xu ◽  
S. J. Xiao ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
F2 Population

scholarly journals Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Guorong Yan ◽  
Ruimin Qiao ◽  
Feng Zhang ◽  
Wenshui Xin ◽  
Shijun Xiao ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome

scholarly journals A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population

2020 ◽  
Vol 33 (5) ◽  
pp. 704-711
Author(s):  
Tianfu Guo ◽  
Jun Gao ◽  
Bin Yang ◽  
Guorong Yan ◽  
Shijun Xiao ◽  
...  
Keyword(s):  
Association Study ◽  
Muscle Fibre ◽  
Muscle Fiber ◽  
Whole Genome Sequence ◽  
Meat Production ◽  
Whole Genome ◽  
F2 Population ◽  
Fiber Number ◽  
Fiber Traits ◽  
Fibre Traits

Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc× Erhualian F2 population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study.Methods: A whole-genome sequences association study was performed in the F2 population. Genotyping was performed for 1,020 individuals (19 F0, 68 F1, and 933 F2). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits.Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified.Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.

scholarly journals Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1163
Author(s):  
Manuel J. Wolf ◽  
Tong Yin ◽  
Guilherme B. Neumann ◽  
Paula Korkuć ◽  
Gudrun A. Brockmann ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Sequence ◽  
Genome Wide Association Study ◽  
Fasciola Hepatica ◽  
Genome Wide Association ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Potential Candidate ◽  
Genome Wide

This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.

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