Whole-Genome Selective Scans Detect Genes Associated With Important Phenotypic Traits in Sheep (Ovis aries)

Xu, Song-Song; Gao, Lei; Shen, Min; Lyu, Fenghua

doi:10.3389/fgene.2021.738879

Cited by 20 publications

(13 citation statements)

References 45 publications

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“…SNPs identified in this region include FAM110B, UBXN2B, LOC101116841, SDCBP, and NSMAF. It has been reported that these SNPs are associated with meat and carcass traits such as adiposity, sensory and anatomical characteristics (Lee et al 2013;Li & Kim 2015;Li et al 2017;Hay & Roberts 2018;de las Heras-Saldana et al 2020;Naserkheil et al 2020;Srikanth et al 2020;Srivastava et al 2020;Takeda et al 2020;Naserkheil et al 2021;Xu et al 2021;Fonseca et al 2022); health traits such as resistance to temperature stress, mastitis, and diseases (Kommadath et al 2014;Chen et al 2015;Minuti et al 2015;Smith et al 2019;Deng et al 2020;Li et al 2020;Naserkheil et al 2020;Brunes et al 2021;Londoño-Gil et al 2021;Ruan et al 2021;Haire et al 2022); production traits such as growth, feed intake, and feed conversion (Weng et al 2016;Seabury et al 2017); reproductive traits such as female fertility and age at calving (Fortes et al 2012;Gaddis et al 2017;Mota et al 2017;Silva et al 2020;Oliveira et al 2021;Fonseca et al 2022) and appearance traits such as coat color (Senczuk et al 2020;Chhotaray et al 2021). Genomic regions and genes identified as under selection using iHS and ROH approaches have been associated with various ecological and economic traits in studies conducted on livestock.…”

Section: Discussionmentioning

confidence: 99%

Identification of Selection Signatures and Genetic Diversity in the Sheep

KARABAŞ,

YILMAZ

2024

Preprint

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The study utilized genome-wide data from the Illumina OvineSNP50K platform and specifically targeted the Eşme sheep population. The integrated haplotype score (iHS) and runs of homozygosity (ROH) statistical approaches were used to identify selection signatures. Using the iHS analysis, it was discovered that there are 10 genomic regions and 51 genes on chromosomes 1, 9, 11, and 12 that are under selection. Three genomic regions and 97 genes on chromosomes 6 and 11 were found to be under selection using the ROH analysis. Candidate genes associated with economic and ecological traits were detected using both approaches. Among the genetic diversity parameters considered in the study, the minor allele frequency (MAF), genetic distance between individuals (D), observed heterozygosity (Ho), and expected heterozygosity (He) values were found to be 0.300, 0.309, 0.388, and 0.390, respectively. The ratio of polymorphic SNPs (PN) was 0.947, and the average values of FROH and FHOM were 0.030 and 0.029, respectively. The study demonstrates that selection signature approaches can define the economic and ecological characteristics of farm animals using phenotypic information. The information obtained through these approaches can be utilized in breeding and conservation programs for the genetic resources of farm animals.

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Section: Discussionmentioning

confidence: 99%

Identification of Selection Signatures and Genetic Diversity in the Sheep

KARABAŞ,

YILMAZ

2024

Preprint

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“…From these findings and discussions, it can be concluded that RGS20, TCEA1, LYPLA1, MRPL15 , and EIF5 genes are strongly associated with carcass weight in Hawai’i beef cattle. Additionally, MYCT1 and CERS6 are possibly candidate genes for carcass weight in cattle, as their roles have been identified in pigs and sheep ( Wu et al, 2020 ; Xu et al, 2021 ). Further studies are required to ascertain the association of MYCT1 and CERS6 genes with carcass weight and to better understand their biological roles in cattle.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study for carcass weight in pasture-finished beef cattle in Hawai’i

et al. 2023

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Introduction: Genome-wide association studies (GWAS) have identified genetic markers for cattle production and reproduction traits. Several publications have reported Single Nucleotide Polymorphisms (SNPs) for carcass-related traits in cattle, but these studies were rarely conducted in pasture-finished beef cattle. Hawai’i, however, has a diverse climate, and 100% of its beef cattle are pasture-fed.Methods: Blood samples were collected from 400 cattle raised in Hawai’i islands at the commercial harvest facility. Genomic DNA was isolated, and 352 high-quality samples were genotyped using the Neogen GGP Bovine 100 K BeadChip. SNPs that did not meet the quality control standards were removed using PLINK 1.9, and 85 k high-quality SNPs from 351 cattle were used for association mapping with carcass weight using GAPIT (Version 3.0) in R 4.2. Four models were used for the GWAS analysis: General Linear Model (GLM), the Mixed Linear Model (MLM), the Fixed and Random Model Circulating Probability Unification (FarmCPU), the Bayesian-Information and Linkage-Disequilibrium Iteratively Nested Keyway (BLINK).Results and Discussion: Our results indicated that the two multi-locus models, FarmCPU and BLINK, outperformed single-locus models, GLM and MLM, in beef herds in this study. Specifically, five significant SNPs were identified using FarmCPU, while BLINK and GLM each identified the other three. Also, three of these eleven SNPs (“BTA-40510-no-rs”, “BovineHD1400006853”, and “BovineHD2100020346”) were shared by multiple models. The significant SNPs were mapped to genes such as EIF5, RGS20, TCEA1, LYPLA1, and MRPL15, which were previously reported to be associated with carcass-related traits, growth, and feed intake in several tropical cattle breeds. This confirms that the genes identified in this study could be candidate genes for carcass weight in pasture-fed beef cattle and can be selected for further breeding programs to improve the carcass yield and productivity of pasture-finished beef cattle in Hawai’i and beyond.

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“…KEGG analysis further validated SCD5 ’s role in fatty acid metabolism and the biosynthesis of unsaturated fatty acids but added the AMPK signaling pathway. A recent study implemented whole-genome tests for various economically important traits in sheep and suggested SCD5 as a strong candidate for body size [ 54 ]. Given that SCD5 was previously proposed to partake in the body size development of grass-fed Brangus steers [ 55 ], there is support for this gene as a strong candidate involved in sheep growth.…”

Section: Discussionmentioning

confidence: 99%

Genetic Parameters and Genomic Regions Underlying Growth and Linear Type Traits in Akkaraman Sheep

Kızılaslan

Arzık

White

et al. 2022

Genes

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In the current study, the genetic architecture of growth and linear type traits were investigated in Akkaraman sheep. Estimations of genomic heritability, genetic correlations, and phenotypic correlations were implemented for 17 growth and linear type traits of 473 Akkaraman lambs by the univariate and multivariate analysis of animal mixed models. Correspondingly, moderate heritability estimates, as well as high and positive genetic/phenotypic correlations were found between growth and type traits. On the other hand, 2 genome-wide and 19 chromosome-wide significant single nucleotide polymorphisms were found to be associated with the traits as a result of animal mixed model-based genome-wide association analyses. Accordingly, we propose several genes located on different chromosomes (e.g., PRDM2, PTGDR, PTPRG, KCND2, ZNF260, CPE, GRID2, SCD5, SPIDR, ZNF407, HCN3, TMEM50A, FKBP1A, TLE4, SP1, SLC44A1, and MYOM3) as putative quantitative trait loci for the 22 growth and linear type traits studied. In our study, specific genes (e.g., TLE4, PTGDR, and SCD5) were found common between the traits studied, suggesting an interplay between the genetic backgrounds of these traits. The fact that four of the proposed genes (TLE4, MYOM3, SLC44A1, and TMEM50A) are located on sheep chromosome 2 confirms the importance of these genomic regions for growth and morphological structure in sheep. The results of our study are therefore of great importance for the development of efficient selection indices and marker-assisted selection programs, as well as for the understanding of the genetic architecture of growth and linear traits in sheep.

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Whole-Genome Selective Scans Detect Genes Associated With Important Phenotypic Traits in Sheep (Ovis aries)

Cited by 20 publications

References 45 publications

Identification of Selection Signatures and Genetic Diversity in the Sheep

Identification of Selection Signatures and Genetic Diversity in the Sheep

Genome-wide association study for carcass weight in pasture-finished beef cattle in Hawai’i

Genetic Parameters and Genomic Regions Underlying Growth and Linear Type Traits in Akkaraman Sheep

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