Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses

Metzger, Julia; Karwath, Matthias; Tonda, Raúl; Beltrán, Sergi; Águeda, Lídia; Gut, Marta; Gut, Ivo; Distl, O.

doi:10.1186/s12864-015-1977-3

Cited by 115 publications

(122 citation statements)

References 80 publications

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“…In the equine industry, reproductive traits are greatly important due to the high economic impact they have on stud fees and foal crop (Binns et al, ; Metzger et al, ). However, our knowledge about genetic factors and their role in equine reproduction is limited.…”

Section: Discussionmentioning

confidence: 99%

Whole‐genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

Nanaei

Mehrgardi

Esmailizadeh

2020

Reprod Domestic Animals

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The primary objective of most horse breeding operations was to maximize reproductive efficiency and minimize the cost of producing live foals. Here, we compared individual horses from the Thoroughbred population (n = 17), known as a horse breed with poor reproductive performance, with other six horse populations (n = 28), to detect genomic signatures of positive selection underlying of reproductive traits. A number of protein‐coding genes with significant (p‐value <.01) higher FST values (616 genes) and a lower value for nucleotide diversity (π) (310 genes) were identified. The results of our study revealed some candidate genes such as IGFBP2, IGFBP5, GDF9, BRINP3 and GRID1 are possibly associated with functions influencing reproductive traits. These genes may have been under selection due to their essential roles in reproduction performance in horses. The candidate selected genes identified in this work should be of great interest for future research into genetic architecture of traits relevant to horse breeding programmes.

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Section: Discussionmentioning

confidence: 99%

Whole‐genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

Nanaei

Mehrgardi

Esmailizadeh

2020

Reprod Domestic Animals

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“…Another method for detecting signatures of positive selection based on intra-population analysis is the identification of high-homozygosity regions [6]. Since ROHs are normally abundant in regions under positive selection, their accumulation at specific loci, or islands, has been used to identify genomic regions that reflect directional selection in cattle [19], sheep [20], horse [21] and goat [22]. We therefore checked if such regions of high-homozygosity overlapped with putative selection signatures in the sheep breeds considered in this study.…”

Section: Discussionmentioning

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

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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...

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“…All those studies were related to human (Kirin et al, 2010;Nothnagel et al, 2010;Pemberton et al, 2012) and livestock populations (Ferencakovic et al, 2011;Bosse et al, 2012;Purfield et al, 2012;Ferenčaković et al, 2013a,b), since those are well known for systematic and informative pedigrees as well as in computer simulations (Howrigan et al, 2011). Currently, F ROH is considered as standard procedure for quantifying autozygosity and its popularity is exponentially increasing to a number of studies in human (Pippucci et al, 2014;Ben Halim et al, 2015), cattle (Mészáros et al, 2015;Zavarez et al, 2015;Zhang et al, 2015a), pig (Gomez-Raya et al, 2015;Saura et al, 2015;Silió et al, 2015), horse (Metzger et al, 2015), poultry (Orazietti, 2015), dog (Mortlock et al, 2016), and sheep and goat (Al-Mamun et al, 2015;Kim et al, 2016) populations as well as in wild (Iacolina et al, 2016), and captive populations (Nuijten et al 2016). Not only it is a measure of true or realized inbreeding that is sensitive to the selection, the concept of F ROH is easy to interpret and has several features that surpass F PED in estimating negative consequences of inbreeding.…”

Section: Runs Of Homozygosity: a New Dimension In Estimating Autozygomentioning

confidence: 99%

Genomic dissection of inbreeding depression: a gate to new opportunities

2017

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-Inbreeding depression, reduction in performance of quantitative traits, including reproduction and survival, caused by inbreeding, is a well-known phenomenon observed in almost all experimental, domesticated, and natural populations. In spite of its importance to the fate of a small population and numerous research performed in the last century, the genetic basis of inbreeding depression is still unclear. Recent fast development of molecular techniques has enabled estimation of a genomic inbreeding coefficient (F ROH ), which reflects realized autozygosity and can be further partitioned to chromosomes and chromosomal segments. In this review, we first describe classical approach used in the estimation of inbreeding in livestock populations, followed by early concepts of replacing pedigree inbreeding coefficient by individual heterozygosity. Then, we explain runs of homozygosity as key approach in estimating realized autozygosity. Furthermore, we present two different concepts of analysing regions that substantially contribute to the inbreeding depression. Thus, we describe how to identify or map mutations that result in the reduction of performance and, in terms of quantitative genetics, how to analyse the architecture of inbreeding depression. At the end, we discuss future perspectives in eliminating deleterious mutations from livestock populations.

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Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses

Cited by 115 publications

References 80 publications

Whole‐genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

Whole‐genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

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

Genomic dissection of inbreeding depression: a gate to new opportunities

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