Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed

Öner, Yasemin; Serrano, M.; Sarto, P.; Iguácel, Laura Pilar; Piquer-Sabanza, María; Estrada, Olaia; Juan, Teresa; Calvo, J.H.

doi:10.3390/ani11061531

Cited by 6 publications

(3 citation statements)

References 46 publications

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“…For example, significant associations with body weight, growth-related and body conformation traits were identified by GWAS in 150 Dazu Black goats [ 18 ], in 95 Sudanese goats [ 28 ], in 69 Egyptian Barki sheep [ 33 ], and in 96 Baluchi sheep [ 34 ]. Genome-wide associations with other economic important traits were found in sample sizes of 192 animals [ 35 , 36 ]. In this regard, we believe that it possible to use a sample of 269 animals for our research.…”

Section: Discussionmentioning

confidence: 99%

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

Easa

Selionova

Aibazov

et al. 2022

Genes

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The objective of this study was to identify the SNPs and candidate genes related to body weight and seven body conformation traits at the age of 8 months in the Russian aboriginal Karachai goats (n = 269) by conducting genome-wide association studies (GWAS), using genotypes generated by Goat SNP BeadChip (Illumina Inc., San Diego, CA, USA). We identified 241 SNPs, which were significantly associated with the studied traits, including 47 genome-wide SNPs (p < 10−5) and 194 suggestive SNPs (p < 10−4), distributed among all goat autosomes except for autosome 23. Fifty-six SNPs were common for two and more traits (1 SNP for six traits, 2 SNPs for five traits, 12 SNPs for four traits, 20 SNPs for three traits, and 21 SNPs for two traits), while 185 SNPs were associated with single traits. Structural annotation within a window of 0.4 Mb (±0.2 Mb from causal SNPs) revealed 238 candidate genes. The largest number of candidate genes was identified at Chr13 (33 candidate genes for the five traits). The genes identified in our study were previously reported to be associated with growth-related traits in different livestock species. The most significant genes for body weight were CRADD, HMGA2, MSRB3, MAX, HACL1 and RAB15, which regulate growth processes, body sizes, fat deposition, and average daily gains. Among them, the HMGA2 gene is a well-known candidate for prenatal and early postnatal development, and the MSRB3 gene is proposed as a candidate gene affecting the growth performance. APOB, PTPRK, BCAR1, AOAH and ASAH1 genes associated with withers height, rump height and body length, are involved in various metabolic processes, including fatty acid metabolism and lipopolysaccharide catabolism. In addition, WDR70, ZBTB24, ADIPOQ, and SORCS3 genes were linked to chest width. KCNG4 was associated with rump height, body length and chest perimeter. The identified candidate genes can be proposed as molecular markers for growth trait selection for genetic improvement in Karachai goats.

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Section: Discussionmentioning

confidence: 99%

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

Easa

Selionova

Aibazov

et al. 2022

Genes

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“…Öner et al [48] reported the development of GWASs in Assaf sheep using animals with extreme values (the highest 10% and the lowest 14% values) of somatic cell count, and the validation of the results using all the analyzed animals. Li et al [49] reported the development of GWASs in beef cattle using all the animals and GWASs using animals with extreme values (different combinations of high and low percentiles) of yearling weight.…”

Section: Methods 1 Linear Modelmentioning

confidence: 99%

Genome-Wide Association Study of Fiber Diameter in Alpacas

More,

Veli,

Cruz

et al. 2023

Animals

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The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (−log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.

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“…Mastitis is the most common inflammatory condition that develops as a result of infection with pathogenic microorganisms or physical trauma. The expense of lost milk, as well as diminished milk output and quality, are all related to significant economic losses for the dairy sheep industry [2]. Somatic cell count (SCC) or log transformed SCC (somatic cell score, SCS) has relatively higher heritability compared to mastitis (from 0.14 to 0.19 for SCS and from 0.02 to 0.05 for mastitis) and are used as the first trait to improve mastitis resistance [3].…”

Section: Introductionmentioning

confidence: 99%

Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Score in Valle del Belice Dairy Sheep

Mohammadi

Farahani

Moradi

et al. 2022

Animals

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The objective of this study was to uncover genomic regions explaining a substantial proportion of the genetic variance in milk production traits and somatic cell score in a Valle del Belice dairy sheep. Weighted single-step genome-wide association studies (WssGWAS) were conducted for milk yield (MY), fat yield (FY), fat percentage (FAT%), protein yield (PY), protein percentage (PROT%), and somatic cell score (SCS). In addition, our aim was also to identify candidate genes within genomic regions that explained the highest proportions of genetic variance. Overall, the full pedigree consists of 5534 animals, of which 1813 ewes had milk data (15,008 records), and 481 ewes were genotyped with a 50 K single nucleotide polymorphism (SNP) array. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. We considered the top 10 genomic regions in terms of their explained genomic variants as candidate window regions for each trait. The results showed that top ranked genomic windows (1 Mb windows) explained 3.49, 4.04, 5.37, 4.09, 3.80, and 5.24% of the genetic variances for MY, FY, FAT%, PY, PROT%, and total SCS, respectively. Among the candidate genes found, some known associations were confirmed, while several novel candidate genes were also revealed, including PPARGC1A, LYPLA1, LEP, and MYH9 for MY; CACNA1C, PTPN1, ROBO2, CHRM3, and ERCC6 for FY and FAT%; PCSK5 and ANGPT1 for PY and PROT%; and IL26, IFNG, PEX26, NEGR1, LAP3, and MED28 for SCS. These findings increase our understanding of the genetic architecture of six examined traits and provide guidance for subsequent genetic improvement through genome selection.

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Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed

Cited by 6 publications

References 46 publications

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

Genome-Wide Association Study of Fiber Diameter in Alpacas

Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Score in Valle del Belice Dairy Sheep

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