Genetic Diversity Analyses Reveal First Insights Into Breed‐Specific
Total Page：16
File Type：pdf, Size：1020Kb
doi: 10.1111/age.12476 Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds † ‡ ‡ A. Burren*1, M. Neuditschko 1, H. Signer-Hasler*, M. Frischknecht*, I. Reber , F. Menzi , ‡ C. Drogem€ uller€ and C. Flury* *School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Langgasse€ 85, 3052 Zollikofen, Switzerland. † ‡ Swiss National Stud Farm, Agroscope Research Station, Les Longs-Pres, 1580 Avenches, Switzerland. Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001 Bern, Switzerland. Summary 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 (FROH) with pedigree-based inbreeding coefficients (FPED). The linear relationship between FROH and FPED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROH 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. Keywords inbreeding coefficient, pedigree, runs of homozygosity, selection signals, SNP dairy goats. However, so far, only attempts in France (Carillier Introduction et al. 2013, 2014) and the UK (Mucha et al. 2015) are being In 2011,the International Goat Genome Consortiumreported undertaken to implement genomic selection in dairy goat genome-wide SNPdata at ~50 000 markers in 281 goatsfrom breeding programs, as the global breeding industry is not as 10 geographically and biologically diverse breeds (Tosser- well established when compared with that for dairy cattle. Klopp et al. 2014). Through these activities, the caprine 50k Furthermore, Kijas et al. (2013) have demonstrated that SNP Illumina BeadChip became available for commercial use. This array technology offers great potential to enhance the BeadChip was used in different studies after its release, understanding ofdomestication andgeneticdiversityin goats. including in the investigations ofgenes forcoat color variation Based on genome-wide SNP information, three Australian (Beckeret al.2014),wattles (Reber et al.2015)andpolledness goat breeds clustered separately, although model-based clus- (Kijas et al. 2013). In addition, this caprine 50k Illumina tering suggested that admixture has occurred and that BeadChip was used to evaluate genomic selection programs in (historical) genetic links exist between the breeds (Kijas et al. 2013).Nicolosoet al.(2015)investigatedthegeneticdiversity Address for correspondence of 14 Italian goat breeds based on 50k genotypes and reported a north–south geographic pattern in present-day genetic A. Burren, School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, La¨ nggasse 85, 3052 Zollikofen. diversity. Both SNP-based goat diversity studies highlighted E-mail: [email protected] the high levels of polymorphisms and concluded that goats containmorepolymorphicsitesthandootherlivestockspecies 1These authors contributed equally to this work. (Kijas et al. 2013; Nicoloso et al. 2015). Accepted for publication 16 June 2016 © 2016 Stichting International Foundation for Animal Genetics, 47, 727–739 727 728 Burren et al. Switzerland has 10 local goat breeds: Appenzell (APP), per breed is given in Table 1. Pedigree information was Booted (SGB), Chamois colored (CHA), Grisons striped (GST), obtained for 249 animals from the corresponding herd Nera Verzasca goat (NVE), Peacock (PEA), Saanen (SAA), books (Table 1). We incorporated closely related individuals Tessin grey (TGR), Toggenburg (TOG) and Valais (VAG). into the analysis for the derivation of ROH. This involved There are two different coat color strains in the Valais goat the additional inclusion of 189 genotypes from highly breed: one with a black neck (‘black-neck’; Glowatzki-Mullis related animals (Data2), all with known pedigree informa- et al. 2008) and a rare one with a TYRP1-associated brown tion (Table 1). For each breed, phenotypic characteristics neck (‘copper-neck’; Becker et al. 2014). To date, 43 related to coat color, hair length, polledness, body size, microsatellite markers have been used to determine genetic performance and its classification as a main or rare breed diversity measures for these breeds (Glowatzki-Mullis et al. are summarized in Table S1. 2008). At this stage, it has not been possible to separate three breeds from each other, namely, PEA, NVE and TGR Data editing (Glowatzki-Mullis et al. 2008), and samples of the copper- neck strain of VAG were not available. PLINK ped and map files (v1.7/v1.9; Purcell et al. 2007; With the availability of genome-wide SNP data, there is Chang et al. 2015) were prepared based on the TOP format an increased interest in estimating genomic inbreeding from the available Illumina raw data files. The map file was through genome-wide runs of homozygosity (ROH) (Curik created by downloading SNP positions on the Chinese goat et al. 2014). So far, the suitability of ROH for the estimation assembly CHI_1.0 (Dong et al. 2013) from the SNPchiMp of inbreeding coefficients has been demonstrated for cattle database (Nicolazzi et al. 2014). A total of 3406 sex- (Ferencakovic et al. 2011, 2013a,b; Purfield et al. 2012) chromosomal and non-annotated SNPs were removed. and pigs (Herrero-Medrano et al. 2013; Silio et al. 2013). Data1 contained 48 019 SNPs after filtering for minor Kim et al. (2015) found a higher proportion of individuals allele frequency (>0.01), for missing genotypes at individual lacking long stretches in the Barki goat breed – an and marker levels (<0.1) as well as for SNPs deviating from indigenous goat breed from a hot arid environment – when Hardy-Weinberg equilibrium (P > 0.0001). Across all auto- compared with the Boer goat breed and other exotic breeds. somal caprine chromosomes (CHI) and informative mark- Furthermore, the same authors derived selection signatures ers, a mean gap of 49.996 kb (minimum, 0.029 kb; for the Barki goat and the Barki sheep and concluded that maximum, 475.015 kb) was observed between adjacent these signatures identified genes underlying local adapta- SNPs, with a mean r2 value of 0.089 (Table S2). The tion. Benjelloun et al. (2015) used whole genome sequenc- 48 019 SNPs in Data1 were also considered to be informa- ing data from 44 individuals from three phenotypically tive for Data2. Data2 is available as part of a Dryad data distinct goat populations in Morocco and presented several package (doi: 10.5061/dryad.q1cv6). genomic regions that are influenced by positive selection. In the current study, we used 50k Illumina BeadChip Population structure genotypes from the aforementioned Swiss goat breeds for the re-assessment of population structure. Furthermore, we Various parameters related to genetic diversity and popu- derived ROH and compared marker-based measures of lation structure were assessed based on Data1. Expected inbreeding with pedigree-based inbreeding coefficients. Finally, selection signatures were calculated and potential Table 1 Overview of sampled individuals per breed in Data1 (genetic loci leading to population differentiation are presented. The diversity and selection signature analyses) and Data2 (ROH analysis). results are put forward as a contemporary background for the The number of animals with pedigree information are indicated in the management of genetic diversity in local Swiss goat breeds. second column for Data1 and in the fourth column for Data2. Data1 Data2 Materials and methods Total With Total With Breed animals pedigree animals pedigree Sample collection and genotypes Appenzell goat, APP 21 18 29 26 In the context of this and other projects (Becker et al. 2014; Grisons striped goat, GST 26 24 49 47 Reber et al. 2015), 473 animals from the 10 Swiss goat Tessin grey goat, TGR 27 19 37 29 Chamois colored, CHA 61 61 124 124 breeds were genotyped for the caprine 50k Illumina Valais goat, VAG 24 15 43 34 BeadChip. PLINK v1.07 (Purcell et al. 2007) was used Nera Verzasca goat, NVE 29 19 42 32 for the derivation of genomic relationships by using the Peacock goat, PEA 22 22 31 31 --genome function, as described in Burren et al. (2014). Saanen goat, SAA 34 34 64 64 After exclusion of closely related individuals (genomic Booted goat, SGB 16 13 23 20 > Toggenburg goat, TOG 24 24 31 31 relationship 0.30), the final data set (Data1) included Total 284 249 473 438 284 individuals from 10 breeds. The number of genotypes