The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

Amills, M.

doi:10.1155/2014/904281

Cited by 13 publications

(15 citation statements)

References 140 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Potentially high‐density SNP data or whole genome sequences would allow the detection of this economically important gene cluster. Among others, GHR (CHI20, 31.4 Mb), DGAT1 (CHI14, 11.3 Mb) and LIPE (CHI18, 49.6 Mb) are additional candidate genes related to milk yield and milk composition in goats (Amills ) which remained undetected in our study.…”

Section: Discussionmentioning

confidence: 65%

“…; Santana et al . ); GDF9 and PDGFD for reproduction traits (Amills ; Wei et al . ); IL2 for immune response (Pariset et al .…”

Section: Discussionmentioning

confidence: 99%

“…The broad effect of the casein alpha s1 gene ( CSNS1S ) on different dairy phenotypes is well described (Amills ). No selection signature was observed in this gene here.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

et al. 2016

View full text Add to dashboard Cite

We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (F ) with pedigree-based inbreeding coefficients (F ). The linear relationship between F and F was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). F appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.

show abstract

Section: Discussionmentioning

confidence: 65%

“…; Santana et al . ); GDF9 and PDGFD for reproduction traits (Amills ; Wei et al . ); IL2 for immune response (Pariset et al .…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Identification of genetic markers and candidate genes that affect economically important traits is therefore of high value from a biological point of view, as well as providing practical benefits to industry. Compared with that in cattle and sheep, the number of QTL studies in goats is limited; however, at present, goat QTL are not included in Animal QTLdb database (http:// www .animalgenome .org/ cgi -bin/ QTLdb/ index), which makes it difficult to judge the exact number of studies in this species (for review, see Amills, 2014).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

Mucha

Mrode

Coffey

et al. 2018

Journal of Dairy Science

View full text Add to dashboard Cite

Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.

show abstract

“…For a long time, research on genotype–phenotype relationships in goats has lagged behind similar studies in cattle and sheep (Amills ). As reported in the Online Mendelian Inheritance in Animals database (http://omia.angis.org.au/home), the number of Mendelian traits and causal mutations identified in goats (16 and 10 respectively) are much lower than those detected in cattle (238 and 140 respectively) and sheep (101 and 48 respectively).…”

Section: Genetic Constitution and Relevant Phenotypes Of Goat Breedsmentioning

confidence: 99%

Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces

2017

View full text Add to dashboard Cite

Domestic goats (Capra hircus) are spread across the five continents with a census of 1 billion individuals. The worldwide population of goats descends from a limited number of bezoars (Capra aegagrus) domesticated 10 000 YBP (years before the present) in the Fertile Crescent. The extraordinary adaptability and hardiness of goats favoured their rapid spread over the Old World, reaching the Iberian Peninsula and Southern Africa 7000 YBP and 2000 YBP respectively. Molecular studies have revealed one major mitochondrial haplogroup A and five less frequent haplogroups B, C, D, F and G. Moreover, the analysis of autosomal and Y-chromosome markers has evidenced an appreciable geographic differentiation. The implementation of new molecular technologies, such as whole-genome sequencing and genome-wide genotyping, allows for the exploration of caprine diversity at an unprecedented scale, thus providing new insights into the evolutionary history of goats. In spite of a number of pitfalls, the characterization of the functional elements of the goat genome is expected to play a key role in understanding the genetic determination of economically relevant traits. Genomic selection and genome editing also hold great potential, particularly for improving traits that cannot be modified easily by traditional selection.

show abstract

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

Cited by 13 publications

References 140 publications

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces

Contact Info

Product

Resources

About