Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

Kijas, James W.; Lenstra, Johannes A.; Hayes, Ben J.; Boitard, Simon; Porto-Neto, Laércio R.; Cristobal, Magali San; Servin, Bertrand; McCulloch, Russell; Whan, Vicki; Gietzen, Kimberly; Paiva, Samuel Rezende; Barendse, W.; Ciani, Elena; Raadsma, Herman W.; McEwan, John C.; Dalrymple, Brian P.

doi:10.1371/journal.pbio.1001258

Cited by 701 publications

(1,151 citation statements)

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“…For low heritability traits, a very large number of records will be required in the TS to subsequently achieve high accuracies of GEBV in unphenotyped animals. If we consider our SBF population, where the effective population size (Ne) is~500 (Kijas et al, 2012), then according to the formula suggested by Daetwyler et al (2010b) to achieve an accuracy of 0.6, we would need 30 000 individuals for a trait with very low heritability (e.g. Nematodirus FEC at 16 weeks), and~5000 for a trait with moderate heritability (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…It has been suggested that the number of SNPs needed to predict unrelated individuals is equal to 10 NeL, where L is the length of the genome in Morgans (Meuwissen, 2009). In the SBF population, with Ne of~500 (Kijas et al, 2012) and L of approximately 27 Morgans, predictions for unrelated individuals would require at least 135 000 SNPs. This marker density may be achievable with the forthcoming high-density sheep SNP chip.…”

Section: Discussionmentioning

confidence: 99%

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Accuracy of genomic prediction within and across populations for nematode resistance and body weight traits in sheep

Riggio

Abdel-Aziz

Matika

et al. 2014

Animal

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Genomic prediction utilizes single nucleotide polymorphism (SNP) chip data to predict animal genetic merit. It has the advantage of potentially capturing the effects of the majority of loci that contribute to genetic variation in a trait, even when the effects of the individual loci are very small. To implement genomic prediction, marker effects are estimated with a training set, including individuals with marker genotypes and trait phenotypes; subsequently, genomic estimated breeding values (GEBV) for any genotyped individual in the population can be calculated using the estimated marker effects. In this study, we aimed to: (i) evaluate the potential of genomic prediction to predict GEBV for nematode resistance traits and BW in sheep, within and across populations; (ii) evaluate the accuracy of these predictions through within-population cross-validation; and (iii) explore the impact of population structure on the accuracy of prediction. Four data sets comprising 752 lambs from a Scottish Blackface population, 2371 from a Sarda × Lacaune backcross population, 1000 from a Martinik Black-Belly × Romane backcross population and 64 from a British Texel population were used in this study. Traits available for the analysis were faecal egg count for Nematodirus and Strongyles and BW at different ages or as average effect, depending on the population. Moreover, immunoglobulin A was also available for the Scottish Blackface population. Results show that GEBV had moderate to good within-population predictive accuracy, whereas across-population predictions had accuracies close to zero. This can be explained by our finding that in most cases the accuracy estimates were mostly because of additive genetic relatedness between animals, rather than linkage disequilibrium between SNP and quantitative trait loci. Therefore, our results suggest that genomic prediction for nematode resistance and BW may be of value in closely related animals, but that with the current SNP chip genomic predictions are unlikely to work across breeds.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Accuracy of genomic prediction within and across populations for nematode resistance and body weight traits in sheep

Riggio

Abdel-Aziz

Matika

et al. 2014

Animal

View full text Add to dashboard Cite

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“…We assumed that 100 Mb ¼ 1 Morgan (as for example in Kijas et al, 2012). We estimated average values of r 2 in 20 distance classes between 2.5 kb and 1 Mb (corresponding to 0.0025-1 cM).…”

Section: Estimation Of Past Demographic Changes In European Wolf Popumentioning

confidence: 99%

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

et al. 2013

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Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.

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“…A genome-wide association study (GWAS) of most of the world's sheep breeds revealed that the KIT, ASIP, and MITF genes that determine the sheep coat color have been under strong selection (Kijas et al, 2012). However, ASIP, which controls a series of alleles of black and white coat color, was not detected in a new GWAS of sheep selection (Zhang et al, 2013), although they used a different sheep breed.…”

Section: Discussionmentioning

confidence: 99%

Analysis of agouti signaling protein (ASIP) gene polymorphisms and association with coat color in Tibetan sheep (Ovis aries)

et al. 2015

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ABSTRACT. Tibetan sheep, an indigenous breed, have a wide variety of phenotypes and a colorful coat, which make this breed an interesting model for evaluating the effects of coat-color gene mutations on this phenotypic trait. The agouti signaling protein (ASIP) gene is a positional candidate gene, as was inferred based on previous study. In our research, ASIP gene copy numbers in genomic DNA were detected using a novel approach, and the exon 2 g.100-104 mutation and copy number variation (CNV) of ASIP were associated with coat color in 256 sheep collected from eight populations with different coat colors by highresolution melting curve assay. We found that the relative copy numbers of ASIP ranged from one to eight in Tibetan sheep. All of the g.100-104 genotypes in the populations were in Hardy-Weinberg equilibrium, and there was no relationship between the g.100-104 genotype and coat color (P > 0.05). The single ASIP CNV allele was found to be almost entirely associated with solid-black coat color; however, not all solidblack sheep displayed the putative single ASIP CNV genotype. From our Coat color in Tibetan sheep study, we speculate that the ASIP CNV is under great selective pressure and the single ASIP CNV allows selection for black coat color in Tibetan sheep, but this does not explain all black phenotypes in Tibetan sheep.

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Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

Abstract: Genomic structure in a global collection of domesticated sheep reveals a history of artificial selection for horn loss and traits relating to pigmentation, reproduction, and body size.

Cited by 701 publications

References 54 publications

Accuracy of genomic prediction within and across populations for nematode resistance and body weight traits in sheep

Accuracy of genomic prediction within and across populations for nematode resistance and body weight traits in sheep

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

Analysis of agouti signaling protein (ASIP) gene polymorphisms and association with coat color in Tibetan sheep (Ovis aries)

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