Genome-wide association study for wattles trait in the dairy goat breed

Xu, Xiaolong; Guo, Yingwei; Li, Miaoyu; Duan, Qiangde; Li, Fu; Wang, Jintao; Liu, Nan; Huzheng, Jiamei; Wang, Xihong; An, Xiaopeng

doi:10.1080/10495398.2022.2149545

Cited by 4 publications

(2 citation statements)

References 23 publications

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“…Interestingly, our analyses identified both the NEDD4 gene (included in ROH of animals with wattles) and its binding protein N4BP1 (through F ST ), further supporting their potential roles in the development of wattles in goats. Another study, instead, suggested possible association between the same phenotype and CSMD1 [43], which emerged from our analyses as well. Additionally, two other genes might be relevant: KIF7, whose mutation causes acrocallosal syndrome in humans, often presenting preauricular skin tags [44], and ADAMTSL3, known to influence the shape of the comb in chickens [45].…”

Section: Selection Signaturessupporting

confidence: 49%

Phenotypic and Genomic Characterization of the Comune di Sicilia Goat: Towards the Conservation of an Endangered Local Breed

Bionda,

Lopreiato,

Amato

et al. 2023

Animals

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The Comune di Sicilia, a local goat breed from Sicily (Italy), is currently undergoing recognition as a distinct breed. This study aims to characterize the population both phenotypically and genomically to advance its recognition process. A total of 78 subjects from two locations were enrolled, and their phenotypic data, including qualitative traits and morphometric measurements of adult animals, were recorded and statistically analyzed. The goats were genotyped using the Illumina 50 k Goat SNPchip, comparing them with 473 goats from 15 Italian breeds. Population structure, phylogenetic relationships, admixture, and genomic inbreeding were analyzed. Additionally, subjects with different morphological traits were compared using FST and runs of homozygosity, leading to the identification of potential candidate genes associated with anotia and wattle presence in goats. The Comune di Sicilia breed exhibited distinctive genomic and phenotypic features, setting it apart from other breeds in the same region. However, moderate variability, possibly influenced by selection practices, was also observed. To ensure the breed’s preservation and prevent excessive inbreeding, a comprehensive approach considering both morphology and genomic background is recommended. This study contributes valuable insights into the genetic peculiarities of the Comune di Sicilia goat, supporting its recognition as a unique and valuable breed.

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Section: Selection Signaturessupporting

confidence: 49%

Phenotypic and Genomic Characterization of the Comune di Sicilia Goat: Towards the Conservation of an Endangered Local Breed

Bionda,

Lopreiato,

Amato

et al. 2023

Animals

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show abstract

“…Indeed, a private population's genetic background can severely influence the identification of target-trait-associated markers when a single breed represents the target trait in a GWAS. Accordingly, different associated candidate genomic regions of goat wattle traits were identified from previous reports with various breeds [48,49]. Furthermore, several GWASs on sheep ear size have shown an inconsistently associated candidate genomic region because of the genetic composition of the testing animals [50,51].…”

Section: Resultsmentioning

confidence: 99%

Novel Heredity Basis of the Four-Horn Phenotype in Sheep Using Genome-Wide Sequence Data

Zhang,

Yang,

Liu

et al. 2023

Animals

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Horns are an important breeding trait for sheep. However, no widely recognized viewpoint on the regulatory genes and mechanisms of horns is available, and the genetic basis of the four-horn phenotype (FHP) is unclear. This work conducted a genome-wide association study with 100 sheep genomes from multiple breeds to investigate the genetic basis of the FHP. The results revealed three significant associations (corrected as p < 1.64 × 10−8) of the InDels (CHR2: g.133,742,709delA, g.133,743,215insC, and g.133,743,940delT) for FHP in the intergenic sequence (IGS) between the MTX2 and the LOC105609047 of CHR2. Moreover, 14 significant associations (corrected as p < 1.42 × 10−9) of SNPs with the FHP phenotype were identified in CHR2 and CHR16, including five (e.g., CHR16: g.40,351,378G > A and g.40,352,577G > A) located in the intron of the ADAMTS12 gene, eight (e.g., CHR2: g.133,727,513C > T and g.133,732,145T > G) in the IGS between MTX2 and LOC105609047, and only one (CHR2: g.133,930,761A > G) in the IGS between HOXD1 and MTX2. Obvious divergence was also observed in genotype patterns between the FHP and others (two horns and hornless) in the HOXD1 and ADAMTS12 gene regions. An extremely significant linkage also occurred between Loci I and Loci II within 100 individuals (LD = −156.02186, p < 0.00001). In summary, our study indicated that the genomic sequences from CHR2 and CHR16 contributed to the FHP in sheep, specifically the key candidate genes HOXD1 and ADAMTS12. These results improved our understanding of the Mendelian genetic basis of the FHP in sheep.

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Genomic regions underlying variation in wattles, horns, and supernumerary teats phenotypes in Egyptian goats

Sallam

2024

Can. J. Anim. Sci.

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Goats play a crucial role in providing humans with various types of valuable products including milk and meat. The underlying genetic mechanisms of important morphological aspects remain largely unknown in goats, highlighting the need for further investigation. A genome-wide association analysis (GWAS) was conducted for three morphological phenotypes in Egyptian goats. All animals were genotyped using the Illumina 65K SNP BeadChips. Results of GWAS for wattles identified two significant (P ≤ 1.4x10-6, FDR ≤ 0.05) single nucleotide polymorphisms (SNPs) on chromosome 10 within a region (72-74 Mb) containing FMN1 and GREM1 genes that are important for limb development and growth. For horns, three significant SNPs were identified on chromosome 1 (119-131 Mb) harboring candidate genes for embryonic development and tissue differentiation, such as CEP70, DZIP1L, CLDN18, SOX14 and SLC35G2. For supernumerary teats, four significant SNPs located on chromosomes 25 (8.7 Mb), 9 (47.8 Mb), 17 (45.1 Mb) and 28 (6.7 Mb) were identified, harboring candidate genes involved in morphogenesis and reproductive traits such as EMP2, MDN1, PCDH10 and GHITM. This study identified novel candidate genes alongside previously reported ones in other goat breeds, suggesting their potential as candidate genes for the studied traits in Egyptian goats.

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Genome-wide association study for wattles trait in the dairy goat breed

Cited by 4 publications

References 23 publications

Phenotypic and Genomic Characterization of the Comune di Sicilia Goat: Towards the Conservation of an Endangered Local Breed

Phenotypic and Genomic Characterization of the Comune di Sicilia Goat: Towards the Conservation of an Endangered Local Breed

Novel Heredity Basis of the Four-Horn Phenotype in Sheep Using Genome-Wide Sequence Data

Genomic regions underlying variation in wattles, horns, and supernumerary teats phenotypes in Egyptian goats

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