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Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol 2023; 40:msad247. [PMID: 37987553 PMCID: PMC10691879 DOI: 10.1093/molbev/msad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
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Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
| | - Frances Swift
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems 17493, Germany
| | | | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona 08003, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona 08010, Spain
| | - Kate M Detwiler
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
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Zhu M, Yang Y, Yang H, Zhao Z, Zhang H, Blair HT, Zheng W, Wang M, Fang C, Yu Q, Zhou H, Qi H. Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits. BMC Genomics 2023; 24:392. [PMID: 37434152 DOI: 10.1186/s12864-023-09479-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. RESULTS We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. CONCLUSIONS Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.
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Affiliation(s)
- Mengting Zhu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China.
| | - Zongsheng Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China.
| | - Hongmei Zhang
- First Affiliated Hospital, School of Medical College, Shihezi University, Shihezi, Xinjiang, China
| | - Hugh T Blair
- Institute Veterinary, Animal & Biomedical Sciences, Massey University, Auckland, Palmerston North, New Zealand
| | - Wei Zheng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Mingyuan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Chenhui Fang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Huaqian Zhou
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Hangdong Qi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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Barbas JP, Pimenta J, Baptista MC, Marques CC, Pereira RMLN, Carolino N, Simões J. Ram Semen Cryopreservation for Portuguese Native Breeds: Season and Breed Effects on Semen Quality Variation. Animals (Basel) 2023; 13:ani13040579. [PMID: 36830367 PMCID: PMC9951670 DOI: 10.3390/ani13040579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The semen quality is one of the determinant factors of ram semen cryopreservation. The present retrospective study aimed to characterize the seasonal ram pattern during the year for ten Portuguese local sheep breeds, hypothesizing that the breed and season had low effects on the main spermatozoa traits. A total of 1471 ejaculates were used and evaluated (fresh semen) from 85 rams between 2004 and 2020 and re-evaluated after thawing (thawed semen). The effect of breed, season, and sperm cryopreservation on nine semen traits were evaluated. The volume per ejaculate, spermatozoa (SPZ) concentration, and total number of SPZ per ejaculate, were affected by breed (p < 0.001) but not by season (p > 0.05). As expected, the semen processing was the most significant (p < 0.001) factor of variation on seminal parameters. Moreover, breed and interactions between breed × semen processing, modulated the response of alive SPZ, abnormal morphology, head, and intermediate piece defects. In fresh semen, season only affected the intermediate piece defects due to the highest percentage observed between February and April period in some breeds. Overall, and despite the mentioned particularities, there were similarities among the ten local breeds. We also concluded that the seasonal effect on ejaculate and SPZ traits is not significant in our region. These local ram breeds have low seasonality and can be employed in natural mating as well as semen donors for cryopreservation and assisted reproductive biotechnologies during the whole year at our latitude.
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Affiliation(s)
- João Pedro Barbas
- Department of Biotechnology and Genetic Resources of Instituto Nacional de Investigação Agrária e Veterinária, Quinta da Fonte Boa, 2005-048 Vale de Santarém, Portugal
- CIISA-AL4AnimalS-Faculty of Veterinary Medicina, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Jorge Pimenta
- Department of Biotechnology and Genetic Resources of Instituto Nacional de Investigação Agrária e Veterinária, Quinta da Fonte Boa, 2005-048 Vale de Santarém, Portugal
- CIISA-AL4AnimalS-Faculty of Veterinary Medicina, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Maria Conceição Baptista
- Department of Biotechnology and Genetic Resources of Instituto Nacional de Investigação Agrária e Veterinária, Quinta da Fonte Boa, 2005-048 Vale de Santarém, Portugal
| | - Carla Cruz Marques
- Department of Biotechnology and Genetic Resources of Instituto Nacional de Investigação Agrária e Veterinária, Quinta da Fonte Boa, 2005-048 Vale de Santarém, Portugal
| | - Rosa Maria Lino Neto Pereira
- Department of Biotechnology and Genetic Resources of Instituto Nacional de Investigação Agrária e Veterinária, Quinta da Fonte Boa, 2005-048 Vale de Santarém, Portugal
- CIISA-AL4AnimalS-Faculty of Veterinary Medicina, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Nuno Carolino
- Department of Biotechnology and Genetic Resources of Instituto Nacional de Investigação Agrária e Veterinária, Quinta da Fonte Boa, 2005-048 Vale de Santarém, Portugal
- CIISA-AL4AnimalS-Faculty of Veterinary Medicina, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - João Simões
- Department of Veterinary Sciences, Veterinary and Animal Research Centre (CECAV), AL4AnimalS, School of Agricultural and Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Correspondence: ; Tel.: +351-259-350-666
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Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Marin-Nahuelpi R, Gomez-Uchida D, Canales-Aguirre CB, Orozco-terWengel P, Yáñez JM. Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss). Genomics 2021; 113:3395-3404. [PMID: 34339816 DOI: 10.1016/j.ygeno.2021.07.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022]
Abstract
Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.
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Affiliation(s)
- María I Cádiz
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - María E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | | | - Giovanna Cáceres
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile
| | - Rodrigo Marin-Nahuelpi
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Daniel Gomez-Uchida
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Cristian B Canales-Aguirre
- Centro i~Mar, Universidad de Los Lagos, Camino Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | | | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile.
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Jiang J, Cao Y, Shan H, Wu J, Song X, Jiang Y. The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep. Front Genet 2021; 12:642552. [PMID: 34093644 PMCID: PMC8173124 DOI: 10.3389/fgene.2021.642552] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/20/2021] [Indexed: 12/03/2022] Open
Abstract
Body size is an important indicator of growth and health in sheep. In the present study, we performed Genome-Wide Association Studies (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) associated with Hu sheep's body size. After genotyping parental (G1) and offspring (G2) generation of the nucleus herd for meat production of Hu sheep and conducting GWAS on the body height, chest circumference, body length, tail length, and tail width of the two groups, 5 SNPs associated with body height and 4 SNPs correlated with chest circumference were identified at the chromosomal significance level. No SNPs were significantly correlated to body length, tail length, and width. Four out of the 9 SNPs were found to be located within the 4 genes. KITLG and CADM2 are considered as candidate functional genes related to body height; MCTP1 and COL4A6 are candidate functional genes related to chest circumference. The 9 SNPs found in GWAS were verified using the G3 generation of the nucleus herd for meat production. Nine products were amplified around the 9 sites, and 29 SNPs were found; 3 mutation sites, G > C mutation at 134 bp downstream of s554331, T > G mutation at 19 bp upstream of s26859.1, and A > G mutation at 81 bp downstream of s26859.1, were significantly correlated to the body height. Dual-luciferase reporter gene experiments showed that the 3 SNPs could significantly impact dual-luciferase and gene transcription activity.
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Affiliation(s)
- Junfang Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuhao Cao
- Zhejiang Key Laboratory of Pathophysiology, Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, China
| | - Huili Shan
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianliang Wu
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xuemei Song
- Zhejiang Key Laboratory of Pathophysiology, Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, China
| | - Yongqing Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Lakhssassi K, Lahoz B, Sarto P, Iguácel LP, Folch J, Alabart JL, Serrano M, Calvo JH. Genome-Wide Association Study Demonstrates the Role Played by the CD226 Gene in Rasa Aragonesa Sheep Reproductive Seasonality. Animals (Basel) 2021; 11:ani11041171. [PMID: 33921837 PMCID: PMC8074133 DOI: 10.3390/ani11041171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary To elucidate the genetic basis of reproductive seasonality in Rasa Aragonesa sheep breed, we performed a genome-wide association study (GWAS) in order to detect single nucleotide polymorphisms (SNPs) or regions associated with traits related to ovarian function and behavioural signs of estrous. The GWAS included 205 ewes with genotypes for 583882 SNPs. Only one SNP overcame the genome-wide significance level. Nine potential SNPs overcame the chromosome-wise significance level (FDR 10%). Gene annotation demonstrated that CD226molecule (CD226) and neuropeptide Y (NPY) genes that could be involved in reproductive seasonality were close to the significant SNPs. To validate the results, we sequenced the entire coding region of the NPY gene and four exons of the CD226 gene to search for polymorphisms that could be involved in the phenotypes studied. Two synonymous and two nonsynonymous SNPs in the NPY and CD226 genes, respectively, were genotyped in the whole population. We demonstrated that the AA genotype of the SNP rs404360094 located in exon 3 of the CD226 gene was associated with higher and lower total days of anoestrus and oestrous cycling months, respectively. Therefore, this SNP could be utilized as a genetic marker for assisted selection marker to reduce seasonality. Abstract A genome-wide association study (GWAS) was used to identify genomic regions influencing seasonality reproduction traits in Rasa Aragonesa sheep. Three traits associated with either ovarian function based on blood progesterone levels (total days of anoestrus and progesterone cycling months) or behavioral signs of oestrous (oestrous cycling months) were studied. The GWAS included 205 ewes genotyped using the 50k and 680k Illumina Ovine Beadchips. Only one SNP associated with the progesterone cycling months overcame the genome-wide significance level (rs404991855). Nine SNPs exhibited significant associations at the chromosome level, being the SNPs rs404991855 and rs418191944, that are located in the CD226 molecule (CD226) gene, associated with the three traits. This gene is related to reproductive diseases. Two other SNPs were located close to the neuropeptide Y (NPY) gene, which is involved in circadian rhythms. To validate the GWAS, partial characterization of both genes by Sanger sequencing, and genotyping of two synonymous and two nonsynonymous SNPs in the NPY and CD226 genes, respectively, were performed. SNP association analysis showed that only SNP rs404360094 in the exon 3 of the CD226 gene, which produces an amino acid substitution from asparagine (uncharged polar) to aspartic acid (acidic), was associated with the three seasonality traits. Our results suggest that the CD226 gene may be involved in the reproductive seasonality in Rasa Aragonesa.
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Affiliation(s)
- Kenza Lakhssassi
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
- INRA, Instituts Morocco, 6356 Rabat, Morocco
| | - Belén Lahoz
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Pilar Sarto
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Laura Pilar Iguácel
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - José Folch
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - José Luis Alabart
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Malena Serrano
- Departamento de Mejora Genética Animal INIA, 28040 Madrid, Spain;
| | - Jorge Hugo Calvo
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
- The Aragonese Foundation for Research and Development (ARAID), 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34976716471
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Tao L, He X, Jiang Y, Liu Y, Ouyang Y, Shen Y, Hong Q, Chu M. Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep. Genes (Basel) 2021; 12:480. [PMID: 33810234 PMCID: PMC8065816 DOI: 10.3390/genes12040480] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
The litter size of domestic goats and sheep is an economically important trait that shows variation within breeds. Strenuous efforts have been made to understand the genetic mechanisms underlying prolificacy in goats and sheep. However, there has been a paucity of research on the genetic convergence of prolificacy between goats and sheep, which likely arose because of similar natural and artificial selection forces. Here, we performed comparative genomic and transcriptomic analyses to identify the genetic convergence of prolificacy between goats and sheep. By combining genomic and transcriptomic data for the first time, we identified this genetic convergence in (1) positively selected genes (CHST11 and SDCCAG8), (2) differentially expressed genes (SERPINA14, RSAD2, and PPIG at follicular phase, and IGF1, GPRIN3, LIPG, SLC7A11, and CHST15 at luteal phase), and (3) biological pathways (genomic level: osteoclast differentiation, ErbB signaling pathway, and relaxin signaling pathway; transcriptomic level: the regulation of viral genome replication at follicular phase, and protein kinase B signaling and antigen processing and presentation at luteal phase). These results indicated the potential physiological convergence and enhanced our understanding of the overlapping genetic makeup underlying litter size in goats and sheep.
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Affiliation(s)
- Lin Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
- College of Life Science and Food Engineering, Hebei University of Engineering, Handan 056038, China
| | - Yina Ouyang
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Yezhen Shen
- Annoroad Gene Technology Co., Ltd., Beijing 100176, China;
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
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8
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Lakhssassi K, Serrano M, Lahoz B, Sarto MP, Iguácel LP, Folch J, Alabart JL, Calvo JH. The LEPR Gene Is Associated with Reproductive Seasonality Traits in Rasa Aragonesa Sheep. Animals (Basel) 2020; 10:ani10122448. [PMID: 33371230 PMCID: PMC7766475 DOI: 10.3390/ani10122448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 01/23/2023] Open
Abstract
The aim of this study was to characterize and identify causative polymorphisms in the leptin receptor (LEPR) gene responsible for the seasonal variation of reproductive traits in sheep. Three reproductive seasonality traits were studied: the total days of anoestrous (TDA), the progesterone cycling months (P4CM) and the oestrous cycling months (OCM). In total, 18 SNPs were detected in 33 ewes with extreme values for TDA and OCM. Six SNPs were non-synonymous substitutions and two of them were predicted in silico as deleterious: rs596133197 and rs403578195. These polymorphisms were then validated in 239 ewes. The SNP rs403578195, located in exon 8 and leading to a change of alanine to glycine (Ala284Gly) in the extracellular domain of the protein, was associated with the OCM trait, being the G allele associated with a decrease of 12 percent of the OCM trait. Haplotype analyses also suggested the involvement of other non-synonymous SNP located in exon 20 (rs405459906). This SNP also produces an amino acid change (Lys1069Glu) in the intracellular domain of the protein and segregates independently of rs403578195. These results confirm for the first time the role of the LEPR gene in sheep reproductive seasonality.
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Affiliation(s)
- Kenza Lakhssassi
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2), CITA–Zaragoza University, 50059 Zaragoza, Spain; (K.L.); (B.L.); (M.P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Malena Serrano
- Departamento de Mejora Genética Animal INIA, 28040 Madrid, Spain;
| | - Belén Lahoz
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2), CITA–Zaragoza University, 50059 Zaragoza, Spain; (K.L.); (B.L.); (M.P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - María Pilar Sarto
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2), CITA–Zaragoza University, 50059 Zaragoza, Spain; (K.L.); (B.L.); (M.P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Laura Pilar Iguácel
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2), CITA–Zaragoza University, 50059 Zaragoza, Spain; (K.L.); (B.L.); (M.P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - José Folch
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2), CITA–Zaragoza University, 50059 Zaragoza, Spain; (K.L.); (B.L.); (M.P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - José Luis Alabart
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2), CITA–Zaragoza University, 50059 Zaragoza, Spain; (K.L.); (B.L.); (M.P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Jorge Hugo Calvo
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2), CITA–Zaragoza University, 50059 Zaragoza, Spain; (K.L.); (B.L.); (M.P.S.); (L.P.I.); (J.F.); (J.L.A.)
- ARAID, 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34-976-716-471
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Hernández-Montiel W, Martínez-Núñez MA, Ramón-Ugalde JP, Román-Ponce SI, Calderón-Chagoya R, Zamora-Bustillos R. Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep. Animals (Basel) 2020; 10:ani10030434. [PMID: 32143402 PMCID: PMC7143297 DOI: 10.3390/ani10030434] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/22/2022] Open
Abstract
The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor β (TGF-β) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p < 3.0 × 10-3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy.
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Affiliation(s)
- Wilber Hernández-Montiel
- TecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal, Yucatán 97345, Mexico; (W.H.-M.); (J.P.R.-U.)
- Departamento de Ciencias Agropecuarias, Universidad del Papaloapan, Loma Bonita Oaxaca 68400, Mexico
| | - Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico;
| | - Julio Porfirio Ramón-Ugalde
- TecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal, Yucatán 97345, Mexico; (W.H.-M.); (J.P.R.-U.)
| | - Sergio Iván Román-Ponce
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán Colón, Querétaro 76280, Mexico;
- Correspondence: (S.I.R.-P.); (R.Z.-B.); Tel.: +52-5538718700 (ext. 80208) (S.I.R.-P.); +52-999-341-0860 (ext. 7631) (R.Z.-B.)
| | - Rene Calderón-Chagoya
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán Colón, Querétaro 76280, Mexico;
| | - Roberto Zamora-Bustillos
- TecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal, Yucatán 97345, Mexico; (W.H.-M.); (J.P.R.-U.)
- Correspondence: (S.I.R.-P.); (R.Z.-B.); Tel.: +52-5538718700 (ext. 80208) (S.I.R.-P.); +52-999-341-0860 (ext. 7631) (R.Z.-B.)
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Posbergh CJ, Thonney ML, Huson HJ. Genomic Approaches Identify Novel Gene Associations with Out of Season Lambing in Sheep. J Hered 2019; 110:577-586. [DOI: 10.1093/jhered/esz014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
Abstract
Sheep are seasonally polyestrous, traditionally breeding when the day length shortens in the autumn. The changing photoperiod stimulates reproductive hormones through a series of chemical pathways, ultimately leading to cyclicity. Some breeds of sheep, such as the Polypay and Dorset, have been selected for reduced seasonality and can lamb year-round. Despite this selection, there is still variation within these breeds in the ability to lamb out of season. The identification of out of season lambing quantitative trait loci has the potential to improve genetic progress using genomic selection schemes. Association studies, fixation index (FST), and runs of homozygosity (ROH) were evaluated to identify regions of the genome that influence the ability of ewes to lamb out of season. All analyses used genotypic data from the Illumina Ovine HD beadchip. Genome-wide associations were tested both across breeds in 257 ewes and within the Dorset and Polypay breeds. FST was measured across breeds and between UK and US Dorsets to assess population differences. ROH were estimated in ewes to identify homozygous regions contributing to out of season lambing. Significant associations after multiple testing correction were found through these approaches, leading to the identification of several candidate genes for further study. Genes involved with eye development, reproductive hormones, and neuronal changes were identified as the most promising for influencing the ewe’s ability to lamb year-round. These candidate genes could be advantageous for selection for improved year-round lamb production and provide better insight into the complex regulation of seasonal reproduction.
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Affiliation(s)
| | | | - Heather J Huson
- Department of Animal Science, Cornell University, Ithaca, NY
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Maiorano AM, Lourenco DL, Tsuruta S, Ospina AMT, Stafuzza NB, Masuda Y, Filho AEV, Cyrillo JNDSG, Curi RA, Silva JAIIDV. Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information. PLoS One 2018; 13:e0200694. [PMID: 30071036 PMCID: PMC6071998 DOI: 10.1371/journal.pone.0200694] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022] Open
Abstract
Gir is one of the main cattle breeds raised in tropical South American countries. Strong artificial selection through its domestication resulted in increased genetic differentiation among the countries in recent years. Over the years, genomic studies in Gir have become more common. However, studies of population structure and signatures of selection in divergent Gir populations are scarce and need more attention to better understand genetic differentiation, gene flow, and genetic distance. Genotypes of 173 animals selected for growth traits and 273 animals selected for milk production were used in this study. Clear genetic differentiation between beef and dairy populations was observed. Different criteria led to genetic divergence and genetic differences in allele frequencies between the two populations. Gene segregation in each population was forced by artificial selection, promoting isolation, and increasing genetic variation between them. Results showed evidence of selective forces in different regions of the genome. A total of 282 genes were detected under selection in the test population based on the fixation index (Fst), integrated haplotype score (iHS), and cross-population extend haplotype homozygosity (XP-EHH) approaches. The QTL mapping identified 35 genes associated with reproduction, milk composition, growth, meat and carcass, health, or body conformation traits. The investigation of genes and pathways showed that quantitative traits associated to fertility, milk production, beef quality, and growth were involved in the process of differentiation of these populations. These results would support further investigations of population structure and differentiation in the Gir breed.
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Affiliation(s)
- Amanda Marchi Maiorano
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
- * E-mail:
| | - Daniela Lino Lourenco
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Shogo Tsuruta
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Alejandra Maria Toro Ospina
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
| | - Nedenia Bonvino Stafuzza
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
| | - Yutaka Masuda
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | | | | | - Rogério Abdallah Curi
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, Sao Paulo, Brazil
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12
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Calvo J, Serrano M, Martinez-Royo A, Lahoz B, Sarto P, Ibañez-Deler A, Folch J, Alabart J. SNP rs403212791 in exon 2 of the MTNR1A gene is associated with reproductive seasonality in the Rasa aragonesa sheep breed. Theriogenology 2018; 113:63-72. [DOI: 10.1016/j.theriogenology.2018.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/06/2018] [Accepted: 02/10/2018] [Indexed: 11/27/2022]
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