Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

Brito, Luiz F.; Kijas, James W.; Ventura, Ricardo Vieira; Sargolzaei, Mehdi; Porto-Neto, Laércio R.; Cánovas, Ángela; Feng, Zeny; Jafarikia, Mohsen; Schenkel, F.S.

doi:10.1186/s12864-017-3610-0

Cited by 140 publications

(158 citation statements)

References 86 publications

Supporting

Mentioning

129

Contrasting

Unclassified

Order By: Relevance

“…The practical aspect of these population genomics studies lies on the possibility of detecting selected genes associated with traits of economic interest and acts as complement to gene mapping approaches (e.g., genomewide association studies [GWAS]) that may help to further genetically improve these traits on domestic species (Qanbari & Simianer, ). Furthermore, this knowledge is important from an evolutionary perspective by highlighting traits that have been exposed to natural and artificial selection as well as using this information to design and/or update breeding programs for conservation purposes worldwide (Brito et al., ; Cesconeto et al., ; Zhao, McParland, Kearney, Lixin, & Berry, ).…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, this knowledge is important from an evolutionary perspective by highlighting traits that have been exposed to natural and artificial selection as well as using this information to design and/ or update breeding programs for conservation purposes worldwide (Brito et al, 2017;Cesconeto et al, 2017;Zhao, McParland, Kearney, Lixin, & Berry, 2015).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

López

Benestan

Moore

et al. 2018

Evolutionary Applications

View full text Add to dashboard Cite

Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population‐specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

López

Benestan

Moore

et al. 2018

Evolutionary Applications

View full text Add to dashboard Cite

show abstract

“…Only one genomic region located on chromosome BTA11 was overlapped on the ROH islands and shared by the two populations, probably because of the recent divergence between the two lineages (dairy and beef), with ancestral segments of the breed remaining on chromosome 11. This may indicate a strong selection for different traits such as beef and milk production (Brito et al, ). Maiorano et al () studied the same populations (Bp and Dp) and demonstrated proximity between these populations indicated by the low fixation index (Fst = 0.003), as they belong to the same breed and originated from the same ancestral population.…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Ospina

Faria

Filho

et al. 2020

Reprod Domestic Animals

View full text Add to dashboard Cite

Runs of homozygosity (ROH) are contiguous homozygous regions of the genome. These regions can be used to identify genes associated with traits of economic interest, as well as inbreeding levels. The aim of the present study was to analyse the length and distribution of ROH islands in Gyr cattle and to identify genes within these regions. A population of 173 animals selected for beef production and a population of 291 animals selected for dairy production were used. Differences in the number of short ROH (ROH1‐2 Mb) were observed between the two populations, while the number of long ROH (ROH>16 Mb) was similar. ROH islands with the highest incidences (>0.50) overlapped in several segments of the genome in the two populations. The genes identified were associated with milk production, growth, reproduction, immune response and resistance traits. Our results contribute to the understanding of how selection can shape the distribution of ROH and ROH islands within the same breed when animals are selected for different purposes such as dairy or beef production.

show abstract

“…Natural selection plays an important role in determining the individuals that are best adapted to novel and existing environmental conditions. Besides natural selection, artificial selection has been widely applied to livestock species to achieve more desirable/profitable phenotypes [1]. For instance, sheep (Ovis aries) have been selected since domestication, approximately 9,000 years ago [2].…”

Section: Introductionmentioning

confidence: 99%

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

Mastrangelo¹,

Bahbahani²,

Moioli³

et al. 2018

Preprint

View full text Add to dashboard Cite

34Genomic regions subjected to selection frequently show signatures such as within-35 population reduced nucleotide diversity and outlier values of differentiation among differentially 36 selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging 37 to 23 sheep breeds of different geographic origins using the Rsb and F ST statistical approaches, to 38 identify loci associated with the fat-tail phenotype. We also checked if these putative selection 39 signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel 40 signals and confirmed the presence of selection signature in genomic regions that harbor candidate 41 genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH 42 were also identified within each breed, but only two ROH islands overlapped with the putative 43 selection signatures. The results reported herein provide the most complete genome-wide study of 44 selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights 45 into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the 46 mechanisms that underlie quantitative traits, such as the fat-tail. 47 48 3 51been widely applied to livestock species to achieve more desirable/profitable phenotypes [1]. For 52 instance, sheep (Ovis aries) have been selected since domestication, approximately 9,000 years ago 53 [2]. This process of selection resulted in divergent sheep breeds, reared in different geographic 54 regions due to their different adaptability. Among these, fat-tail are an important class of sheep 55 breeds and represent about 25% of the world's sheep population [3] mainly distributed in the 56 Middle East, North and East Africa and Central Asia. According to Xu et al. [4] fat tails represent 57 the energy reserve necessary to survive critical conditions such as drought seasons and food 58 shortage. This statement being emphasized by Mwacharo et al. [5] who confirmed that the fat-tails 59 are the predominant sheep across the deserts of northern Africa, and in the highlands, semi-arid and 60 arid environments of eastern and southern Africa while the thin-tails occur in Sudan and in the sub-61 humid and humid regions of West Africa. 62The unique genetic patterns inscribed in the genome of individuals by natural and/or 63 artificial selection are defined as signatures of selection, which are usually regions of the genome 64 that harbor functionally important sequence variants [6]. Although human consumption of animal 65 fat has dramatically reduced in preference of leaner meat, the investigation of the potential 66 candidate genes involved in the fat-tail might contribute to exploring the genetics of fat deposition, 67 energy storage and adaptation to climate changes [7][8][9]. With the aim to identify candidate genes 68 with a potential role in these traits, several authors performed studies targeting the fat-tail 69 phenotype contrasted with the thi...

show abstract

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

Cited by 140 publications

References 86 publications

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

Contact Info

Product

Resources

About