A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds
Genetic selection for higher productivity increased dairy sheep susceptibility to diseases and environmental stressors, challenging their health and welfare status and production efficiency. Improving resilience to such stressors can enhance their ability to face these challenges without compromisin...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-11-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1294573/full |
| _version_ | 1797490873464782848 |
|---|---|
| author | Angeliki Argyriadou Sofia Michailidou Sofia Michailidou Sotiria Vouraki Valentina Tsartsianidou Valentina Tsartsianidou Alexandros Triantafyllidis Alexandros Triantafyllidis Athanasios Gelasakis Georgios Banos Georgios Arsenos |
| author_facet | Angeliki Argyriadou Sofia Michailidou Sofia Michailidou Sotiria Vouraki Valentina Tsartsianidou Valentina Tsartsianidou Alexandros Triantafyllidis Alexandros Triantafyllidis Athanasios Gelasakis Georgios Banos Georgios Arsenos |
| author_sort | Angeliki Argyriadou |
| collection | DOAJ |
| description | Genetic selection for higher productivity increased dairy sheep susceptibility to diseases and environmental stressors, challenging their health and welfare status and production efficiency. Improving resilience to such stressors can enhance their ability to face these challenges without compromising productivity. Our objective was to estimate genomic heritability and perform genome-wide association studies (GWAS) to detect SNPs and candidate genes associated with three proxy traits for resilience (milk somatic cell count—SCC, lactation persistency—LP, body condition score—BCS) of Chios and Frizarta dairy ewes. We used genome-wide genotypes of 317 Chios and 346 Frizarta ewes. Individual records of milk yield and BCS, and milk samples were collected monthly for two consecutive milking periods; samples were analyzed to determine SCC. The LP was calculated as the regression coefficient of daily milk yield on days from lambing. Within breed, variance components analyses and GWAS were performed using genomic relatedness matrices in single-trait animal linear mixed models. Genomic-based heritability estimates were relatively high (BCS: h2 = 0.54 and 0.55, SCC: h2 = 0.25 and 0.38, LP: h2 = 0.43 and 0.45, for Chios and Frizarta ewes, respectively), compared to previous pedigree-based studies. The GWAS revealed 7 novel SNPs associated with the studied traits; one genome-wide and two suggestive significant SNPs for SCC (Frizarta: rs403061409, rs424064526 and rs428540973, on chromosomes 9, 1 and 12, respectively), one suggestive significant SNP for BCS (Chios: rs424834097 on chromosome 4) and three suggestive significant SNPs for LP (Frizarta: rs193632931 and rs412648955 on chromosomes 1 and 6, Chios: rs428128299 on chromosome 3). Nineteen candidate genes were detected: two for BCS (Chios: POT1, TMEM229A), thirteen for SCC (Frizarta: NTAQ1, ZHX1, ZHX2, LOC101109545, HAS2, DERL1, FAM83A, ATAD2, RBP7, FSTL1, CD80, HCLS1, GSK3B) and four for LP (Frizarta: GRID2, FAIM, CEP70—Chios: GRIP1). Present results show that resilience in the studied dairy sheep breeds is heritable and advance existing knowledge on the genomic background of SCC, LP, and BCS. Future research will quantify effects of different alleles of significant SNPs on the studied traits and search for possible correlations among traits to facilitate their effective incorporation in breeding programs aiming to improve resilience. |
| first_indexed | 2024-03-10T00:39:18Z |
| format | Article |
| id | doaj.art-71bde92b3b4a4e9aaff2147e9c4ba00a |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-10T00:39:18Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-71bde92b3b4a4e9aaff2147e9c4ba00a2023-11-23T15:10:09ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-11-011410.3389/fgene.2023.12945731294573A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breedsAngeliki Argyriadou0Sofia Michailidou1Sofia Michailidou2Sotiria Vouraki3Valentina Tsartsianidou4Valentina Tsartsianidou5Alexandros Triantafyllidis6Alexandros Triantafyllidis7Athanasios Gelasakis8Georgios Banos9Georgios Arsenos10Laboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, GreeceLaboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, GreeceCentre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, GreeceLaboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, GreeceDepartment of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, GreeceGenomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, GreeceDepartment of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, GreeceGenomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, GreeceLaboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, GreeceScotland’s Rural College, Easter Bush, Midlothian, United KingdomLaboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, GreeceGenetic selection for higher productivity increased dairy sheep susceptibility to diseases and environmental stressors, challenging their health and welfare status and production efficiency. Improving resilience to such stressors can enhance their ability to face these challenges without compromising productivity. Our objective was to estimate genomic heritability and perform genome-wide association studies (GWAS) to detect SNPs and candidate genes associated with three proxy traits for resilience (milk somatic cell count—SCC, lactation persistency—LP, body condition score—BCS) of Chios and Frizarta dairy ewes. We used genome-wide genotypes of 317 Chios and 346 Frizarta ewes. Individual records of milk yield and BCS, and milk samples were collected monthly for two consecutive milking periods; samples were analyzed to determine SCC. The LP was calculated as the regression coefficient of daily milk yield on days from lambing. Within breed, variance components analyses and GWAS were performed using genomic relatedness matrices in single-trait animal linear mixed models. Genomic-based heritability estimates were relatively high (BCS: h2 = 0.54 and 0.55, SCC: h2 = 0.25 and 0.38, LP: h2 = 0.43 and 0.45, for Chios and Frizarta ewes, respectively), compared to previous pedigree-based studies. The GWAS revealed 7 novel SNPs associated with the studied traits; one genome-wide and two suggestive significant SNPs for SCC (Frizarta: rs403061409, rs424064526 and rs428540973, on chromosomes 9, 1 and 12, respectively), one suggestive significant SNP for BCS (Chios: rs424834097 on chromosome 4) and three suggestive significant SNPs for LP (Frizarta: rs193632931 and rs412648955 on chromosomes 1 and 6, Chios: rs428128299 on chromosome 3). Nineteen candidate genes were detected: two for BCS (Chios: POT1, TMEM229A), thirteen for SCC (Frizarta: NTAQ1, ZHX1, ZHX2, LOC101109545, HAS2, DERL1, FAM83A, ATAD2, RBP7, FSTL1, CD80, HCLS1, GSK3B) and four for LP (Frizarta: GRID2, FAIM, CEP70—Chios: GRIP1). Present results show that resilience in the studied dairy sheep breeds is heritable and advance existing knowledge on the genomic background of SCC, LP, and BCS. Future research will quantify effects of different alleles of significant SNPs on the studied traits and search for possible correlations among traits to facilitate their effective incorporation in breeding programs aiming to improve resilience.https://www.frontiersin.org/articles/10.3389/fgene.2023.1294573/fulldairy sheepChios breedFrizarta breedgenome-wide associationresiliencemilk somatic cell count |
| spellingShingle | Angeliki Argyriadou Sofia Michailidou Sofia Michailidou Sotiria Vouraki Valentina Tsartsianidou Valentina Tsartsianidou Alexandros Triantafyllidis Alexandros Triantafyllidis Athanasios Gelasakis Georgios Banos Georgios Arsenos A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds Frontiers in Genetics dairy sheep Chios breed Frizarta breed genome-wide association resilience milk somatic cell count |
| title | A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds |
| title_full | A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds |
| title_fullStr | A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds |
| title_full_unstemmed | A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds |
| title_short | A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds |
| title_sort | genome wide association study reveals novel snp markers associated with resilience traits in two mediterranean dairy sheep breeds |
| topic | dairy sheep Chios breed Frizarta breed genome-wide association resilience milk somatic cell count |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1294573/full |
| work_keys_str_mv | AT angelikiargyriadou agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT sofiamichailidou agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT sofiamichailidou agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT sotiriavouraki agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT valentinatsartsianidou agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT valentinatsartsianidou agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT alexandrostriantafyllidis agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT alexandrostriantafyllidis agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT athanasiosgelasakis agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT georgiosbanos agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT georgiosarsenos agenomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT angelikiargyriadou genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT sofiamichailidou genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT sofiamichailidou genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT sotiriavouraki genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT valentinatsartsianidou genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT valentinatsartsianidou genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT alexandrostriantafyllidis genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT alexandrostriantafyllidis genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT athanasiosgelasakis genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT georgiosbanos genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds AT georgiosarsenos genomewideassociationstudyrevealsnovelsnpmarkersassociatedwithresiliencetraitsintwomediterraneandairysheepbreeds |