Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Summary 18The availability of dense single-nucleotide polymorphism (SNP) assays allows for the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 F o r P e e r R e v i e wThe abundance of single-nucleotide polymorphisms (SNPs) throughout the genome and the 44 availability of dense SNP assays, makes these markers particularly suitable for the detection of 45 genomic regions where a reduction in heterozygosity occurred (Kim et al. 2013). Runs of 46 homozygosity (ROH) are contiguous segments of homozygous genotypes that are present in an 47 individual due to parents transmitting identical haplotypes to their offspring (Gibson et al. 2006). 48In animal genetics, ROH are used as predictors of whole genome inbreeding levels (Purfield et 49 al. 2012; Marras et al. 2015; Mastrangelo et al. 2016), to characterize the genomic distribution of 50 inbreeding depression on a phenotype (Biscarini et al. 2014; Pryce et al. 2014), and to identify 51 genes associated with traits of economic interest present in these regions (Zhang et al. 2015; 52 Szmatola et al. 2016; Purfield et al. 2017). Selection pressure and mating schemes can be 53 disentangled by ROH; therefore, ROH detection can also be used to minimize inbreeding and to 54 improve mating systems (Bosse et al. 2012; Zhang et al. 2015 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 Runs of homozygosity definition 106Runs of homozygosity were estimated for each animal using PLINK (Purcell et al. 2007). No where L ROH is the total length of all ROH in the genome of an individual, and L aut the specified 118 length of the autosomal genome covered by SNPs on the chip (2 452.06 Mb). 119Each ROH was categorized based on its physical length into 1 to <5 Mb, 5 to <10 Mb, 10 to <15 and averaging this per breed. 123The genomic inbreeding coefficient based on the difference between observed vs. expected 124 number of homozygous genotypes (F HOM ) was also estimated using PLINK (Purcell et al. 2007). 125Pearson's correlation between the two measures of inbreeding was calculated. 127Detection of common runs of homozygosity 128To identify the genomic regions most commonly associated with ROH for the meta-population, 129and for groups on the basis of production purposes (milk, meat, wool and "milk and meat"), the 136Genomic coordinates for all the identified ROH islands were used for the annotation of genes 137 that were fully or partially contained within each selected region using the UCSC Genome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59...

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“…; Mastrangelo et al . ). After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively.…”

Section: Resultsmentioning

confidence: 97%

“…In particular, the first dimension (C1) distinguished Barbaresca from other breeds, as also reported in a previous study (Mastrangelo et al . ).…”

Section: Resultsmentioning

confidence: 97%

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Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

et al. 2018

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“…Studies of ROA in the genomes of ancient hominins [29][30][31] and early Europeans [32] have provided unique insights into the mating patterns and effective population sizes of our early forbearers. In non-humans, ROA patterns have provided insights into the differential histories of woolly mammoth [33], great ape [34,35], cat [36], canid [37][38][39][40][41][42], and bird [43] populations, while in livestock breeds they have provided insights into their origins, relationships, and recent management [42,[44][45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60][61] and the lasting effects of artificial section [58,[61][62][63][64][65][66][67][68][69][70][71][72]…”

Section: Introductionmentioning

confidence: 99%

Weighted likelihood inference of genomic autozygosity patterns in dense genotype data

Blant

Kwong

Szpiech

et al. 2017

Preprint

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Background: Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to infer ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns. Methods: We report a weighted likelihood approach for inferring ROA in dense genotype data that accounts for autocorrelation among genotyped positions and the possibilities of unobserved mutation and recombination events, and variability in the confidence of individual genotype calls in whole genome sequence (WGS) data. Results: Forward-time genetic simulations under two demographic scenarios that reflect situations where inbreeding and its effect on fitness are of interest suggest this approach is better powered than existing state-of-the-art methods to infer ROA at marker densities consistent with WGS and popular microarray genotyping platforms used in human and non-human studies. Moreover, we present evidence that suggests this approach is able to distinguish ROA arising via consanguinity from ROA arising via endogamy. Using subsets of The 1000 Genomes Project Phase 3 data we show that, relative to WGS, intermediate and long ROA are captured robustly with popular microarray platforms, while detection of short ROA is more variable and improves with marker density. Worldwide ROA patterns inferred from WGS data are found to accord well with those previously reported on the basis of microarray genotype data. Finally, we highlight the potential of this approach to detect genomic regions enriched for autozygosity signals in one group relative to another based upon comparisons of per-individual autozygosity likelihoods instead of inferred ROA frequencies. Conclusions: This weighted likelihood ROA inference approach can assist population-and disease-geneticists working with a wide variety of data types and species to explore ROA patterns and to identify genomic regions with differential ROA signals among groups, thereby advancing our understanding of evolutionary history and the role of recessive variation in phenotypic variation and disease.

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“…The combination of biodiversity and quality of products is, therefore, a current issue (Martini et al 2010). Therefore, the conservation and monitoring of the genetic diversity of these local breeds are fundamental to meet future breeding needs, especially in the context of a global climate change (Mastrangelo et al 2017a). An interesting situation is represented by an ancient and rare local breed reared in Sicily, the Girgentana goat breed.…”

Section: Introductionmentioning

confidence: 99%

The Girgentana Goat Breed: A Zootechnical Overview on Genetics, Nutrition and Dairy Production Aspects

Mastrangelo

Bonanno

2017

Sustainable Goat Production in Adverse Environments: Volume II

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In recent years, there has been a great interest in recovering and preserving local livestock breeds. An interesting situation is represented by the Girgentana goat, an ancient local breed reared in Sicily. Over recent years, this breed has become almost extinct, in part as a consequence of the marked decrease in fresh goat milk consumption. On the basis of these considerations, several studies on its genetic structure and management aspects have been conducted in order to protect the Girgentana goat from the risk of extinction and recover its genetic and economic value. In this context, information on genetics, nutrition and dairy production aspects may have a crucial role in the improvement and management of the breed. Thus, this chapter describes some points of these applications through recent investigations on this goat breed.

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Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Cited by 48 publications

References 44 publications

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

Weighted likelihood inference of genomic autozygosity patterns in dense genotype data

The Girgentana Goat Breed: A Zootechnical Overview on Genetics, Nutrition and Dairy Production Aspects

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