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Genomic Selection Signatures in Sheep from the Western Pyrenees Otsanda Ruiz-Larrañaga, Jorge Langa, Fernando Rendo, Carmen Manzano, Mikel Iriondo, Andone Estonba

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Genomic Selection Signatures in Sheep from the Western Pyrenees Otsanda Ruiz-Larrañaga, Jorge Langa, Fernando Rendo, Carmen Manzano, Mikel Iriondo, Andone Estonba Genomic selection signatures in sheep from the Western Pyrenees Otsanda Ruiz-Larrañaga, Jorge Langa, Fernando Rendo, Carmen Manzano, Mikel Iriondo, Andone Estonba To cite this version: Otsanda Ruiz-Larrañaga, Jorge Langa, Fernando Rendo, Carmen Manzano, Mikel Iriondo, et al.. Genomic selection signatures in sheep from the Western Pyrenees. Genetics Selection Evolution, BioMed Central, 2018, 50 (1), pp.9. 10.1186/s12711-018-0378-x. hal-02405217 HAL Id: hal-02405217 https://hal.archives-ouvertes.fr/hal-02405217 Submitted on 11 Dec 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Ruiz-Larrañaga et al. Genet Sel Evol (2018) 50:9 https://doi.org/10.1186/s12711-018-0378-x Genetics Selection Evolution RESEARCH ARTICLE Open Access Genomic selection signatures in sheep from the Western Pyrenees Otsanda Ruiz‑Larrañaga1* , Jorge Langa1, Fernando Rendo2, Carmen Manzano1, Mikel Iriondo1 and Andone Estonba1 Abstract Background: The current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for diferent production traits such as wool, milk and meat, and its natural adaptation to new environments. In this study, we scanned the genome of 25 Sasi Ardi and 75 Latxa sheep from the Western Pyrenees for three types of regions under selection: (1) regions underlying local adaptation of Sasi Ardi semi-feral sheep, (2) regions related to a long traditional dairy selection pressure in Latxa sheep, and (3) regions experiencing the specifc efect of the modern genetic improvement program established for the Latxa breed during the last three decades. Results: Thirty-two selected candidate regions including 147 annotated genes were detected by using three statisti‑ cal parameters: pooled heterozygosity H, Tajima’s D, and Wright’s fxation index F­ st. For Sasi Ardi sheep, chromosomes Ovis aries (OAR)4, 6, and 22 showed the strongest signals and harbored several candidate genes related to energy metabolism and morphology (BBS9, ELOVL3 and LDB1), immunity (NFKB2), and reproduction (H2AFZ). The major genomic diference between Sasi Ardi and Latxa sheep was on OAR6, which is known to afect milk production, with highly selected regions around the ABCG2, SPP1, LAP3, NCAPG, LCORL, and MEPE genes in Latxa sheep. The efect of the modern genetic improvement program on Latxa sheep was also evident on OAR15, on which several olfactory genes are located. We also detected several genes involved in reproduction such as ESR1 and ZNF366 that were afected by this selection program. Conclusions: Natural and artifcial selection have shaped the genome of both Sasi Ardi and Latxa sheep. Our results suggest that Sasi Ardi traits related to energy metabolism, morphological, reproductive, and immunological features have been under positive selection to adapt this semi-feral sheep to its particular environment. The highly selected Latxa sheep for dairy production showed clear signatures of selection in genomic regions related to milk production. Furthermore, our data indicate that the selection criteria applied in the modern genetic improvement program afect immunity and reproduction traits. Background [2]. From the beginning, humans selected sheep for desir- Sheep is one of the frst species that was domesticated able production traits such as wool, milk and meat [3]. approximately 11,000 years ago in the Fertile Crescent Tis selection process, combined with natural adaptation [1] due in part to its small size, docile behavior and to new environments, has led to a large spectrum of phe- high adaptability to very diferent environments. Dur- notypic diversity with more than one thousand diferent ing the following 3000 to 4000 years, sheep spread across sheep breeds currently described [4]. Europe, Africa and Asia together with the expansion of In the Western Pyrenees, two sheep breeds are the Neolithic culture and the development of agriculture described: Latxa sheep, also known as Manexa or Manech, and Sasi Ardi. Although these breeds show mor- phological and genetic similarities [5], there are marked *Correspondence: [email protected] 1 Genetics, Physical Anthropology and Animal Physiology Department, diferences in their habitat and breeding systems that University of the Basque Country (UPV/EHU), Leioa, Spain make them good candidates for the study of the genetic Full list of author information is available at the end of the article response to artifcial selection and local adaptation. © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Ruiz-Larrañaga et al. Genet Sel Evol (2018) 50:9 Page 2 of 12 Most of the Western Pyrenees sheep belong to the Methods Latxa breed, which has good dairy aptitude and is well Whole‑genome resequencing adapted to the prevailing climatological and orographic Seventy-fve female DNA samples from three popula- conditions in its area of production. Two main varieties tions were sequenced following the Pool-Seq approach of Latxa sheep are distinguished according to facial and [9]: 25 Sasi Ardi (SAS), 25 Latxa individuals included in extremity pigmentation [6]: Latxa Blonde Face and Latxa the genetic improvement program (LAS), and 25 Latxa Black Face. Latxa sheep have been traditionally selected individuals not included in the genetic improvement pro- for increased milk production; with the introduction of gram (LAN). All analyzed Latxa individuals belonged to modern quantitative genetics methodologies, a genetic the Latxa Blonde Face ecotype. DNA was extracted with improvement program for this breed was established the NucleoSpin® 96 Blood Core Kit (Macherey–Nagel) in 1981. Initially, the selection goal was to increase milk commercial kit and pooled in equimolar quantities (4 µl production in order to improve the proftability of the at 20 ng/µl). Tree DNA libraries were generated, one for focks. Later, milk composition and udder morphology each pooled population, using the TruSeq DNA PCR- traits were also included among the major selection crite- Free Sample Preparation Kit of Illumina (fragment size ria of the program, together with resistance to transmis- average 350 bp) and sequenced on a HiSeq 2000 instru- sible spongiform encephalopathies. ment (paired-end, 2 × 100 nt) according to the manufac- In contrast to Latxa sheep, Sasi Ardi is a scarcely known turer’s instructions. semi-feral breed, which is highly adapted to wooded mountainous areas that are poorly accessible to humans Data processing or to other sheep breeds [7]. Because of this specifcity, Illumina adaptors and low-quality bases were Sasi Ardi sheep represent an environmentally and socially removed by applying the Trimmomatic v0.32 pro- important breed by contributing largely to the clear- gram [10] with the following parameters: AVGQUAL:3 ing and cleaning of the understory, thus preserving the ILLUMINACLIP:TruSeq 3-PE-2.fa:2:30:10 MINLEN:31 environment from fres and maintaining the landscape. LEADING:19 TRAILING:19 MINLEN:31. High-quality Sasi Ardi sheep have a smaller body size than Latxa, with sequences were mapped against the domestic sheep ref- slightly elongated extremities, a uniform blonde or red- erence assembly Ovis aries (OAR) v3.1 [11] with Bowtie2 dish color, and a straight wool-less neck. Although there v2.2.3 [12], using the –no-unal option. SAMtools v0.1.19 is no specifc breeding scheme for production traits in [13] and Picard-tools v1.124 (http://broadinstitute. Sasi Ardi sheep, currently it is mainly bred for meat pro- github.io/picard/) were used to convert between SAM duction. Tese sheep are raised in an extensive produc- and BAM formats (samtools view), remove duplicate tion system with grazing as the only food source [7], and reads (picard-tools MarkDuplicates), sort the BAM fle thus, natural selection is the main evolutionary factor (picard-tools SortSam), remove reads with low-quality that has driven the genetic pool of the breed. Since 1997, mapping (MAPQ quality score < 20 and retain only pairs Sasi Ardi is considered as an autochthonous breed under that are properly mapped: samtools view − q 20 − f 2 − F special protection, and since 2007 as a breed in danger of 4 − F 8), and to perform proper variant calling (samtools extinction (Ofcial Catalog of Spanish Livestock Breeds; mpileup -B -Q 0). Finally, indels were also removed using http://www.mapama.gob.es/es/ganaderia/temas/zoot- the flter-pileup-by-gtf.pl Perl script from the PoPoola- ecnia/) [8]. Tis situation has slightly improved during tion package [14].
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