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Liu K, Liu Y, Chu M. Detection of polymorphisms in six genes and their association analysis with litter size in sheep. Anim Biotechnol 2024; 35:2309954. [PMID: 38294691 DOI: 10.1080/10495398.2024.2309954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Litter size in sheep is a complex trait controlled by micro-effective polygenes. APAF1, CLSTN2, CTH, PLCB1, PLCB4, and CHST11 are all involved in mammalian reproduction. However, the effects of these genes on litter size in sheep are still unclear. Therefore, in this study, we used Sequenom MassARRAY® SNP assay technology to type the single nucleotide polymorphisms (SNPs) loci of six genes in five sheep breeds. The results showed that most sheep breeds contain three genotypes at each locus. Then, we conducted population genetic analysis on the SNPs of six genes and found that the polymorphic information content in all sheep breeds ranged from 0 to 0.37, and most sheep breeds were in Hardy-Weinberg equilibrium (p > 0.05). In addition, association analysis in Small Tail Han sheep indicated that the rs399534524 locus in CLSTN2 was highly associated with first parity litter size, and litter size in ewes with CT genotype was higher than that in ewes with CC genotype or TT genotype. Furthermore, the rs407142552 locus in CTH was highly associated with second parity litter size in Small Tail Han sheep, and litter size in ewes with CT genotype was higher than that in ewes with TT genotype. Finally, we predicted the CTH and CLSTN2 protein interaction network and found that HTR1E, NOM1, CCDC174 and ALPK3 interact with CLSTN2 and have been reported as candidate genes related to litter size in sheep. These results suggest that they may be useful genetic markers for increasing litter size in sheep.
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Affiliation(s)
- Kai Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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2
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Zhao L, Yuan L, Li F, Zhang X, Tian H, Ma Z, Zhang D, Zhang Y, Zhao Y, Huang K, Li X, Cheng J, Xu D, Yang X, Han K, Weng X, Wang W. Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits. J Genet Genomics 2024; 51:866-876. [PMID: 38582298 DOI: 10.1016/j.jgg.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human civilization. Hu sheep are a local sheep breed unique to China with high reproductive rates and rapid growth. Genomic selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in livestock. Here, we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep (Asiatic mouflon) to investigate the genetic characteristics and selection signatures of Hu sheep. Based on six signatures of selection approaches, we detect genomic regions containing genes related to reproduction (BMPR1B, BMP2, PGFS, CYP19, CAMK4, GGT5, and GNAQ), vision (ALDH1A2, SAG, and PDE6B), nervous system (NAV1), and immune response (GPR35, SH2B2, PIK3R3, and HRAS). Association analysis with a population of 1299 Hu sheep reveals that those missense mutations in the GPR35 (GPR35 g.952651 A>G; GPR35 g.952496 C>T) and NAV1 (NAV1 g.84216190 C>T; NAV1 g.84227412 G>A) genes are significantly associated (P < 0.05) with immune and growth traits in Hu sheep, respectively. This research offers unique insights into the selection characteristics of Hu sheep and facilitates further genetic improvement and molecular investigations.
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Affiliation(s)
- Liming Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Lvfeng Yuan
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Huibin Tian
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Yukun Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Yuan Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Kai Huang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaolong Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Jiangbo Cheng
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Dan Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaobin Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Kunchao Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiuxiu Weng
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Weimin Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China.
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Zhao X, Fan C, Qie T, Fu X, Chen X, Wang Y, Wu Y, Fu X, Shi K, Yan W, Yu H. Diaph1 knockout inhibits mouse primordial germ cell proliferation and affects gonadal development. Reprod Biol Endocrinol 2024; 22:82. [PMID: 39010074 PMCID: PMC11247884 DOI: 10.1186/s12958-024-01257-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Exploring the molecular mechanisms of primordial germ cell (PGC) migration and the involvement of gonadal somatic cells in gonad development is valuable for comprehending the origins and potential treatments of reproductive-related diseases. METHODS Diaphanous related formin 1 (Diaph1, also known as mDia1) was screened by analyzing publicly available datasets (ATAC-seq, DNase-seq, and RNA-seq). Subsequently, the CRISPR-Cas9 technology was used to construct Diaph1 knockout mice to investigate the role of Diaph1 in gonad development. RESULTS Based on data from public databases, a differentially expressed gene Diaph1, was identified in the migration of mouse PGC. Additionally, the number of PGCs was significantly reduced in Diaph1 knockout mice compared to wild type mice, and the expression levels of genes related to proliferation (Dicer1, Mcm9), adhesion (E-cadherin, Cdh1), and migration (Cxcr4, Hmgcr, Dazl) were significantly decreased. Diaph1 knockout also inhibited Leydig cell proliferation and induced apoptosis in the testis, as well as granulosa cell apoptosis in the ovary. Moreover, the sperm count in the epididymal region and the count of ovarian follicles were significantly reduced in Diaph1 knockout mice, resulting in decreased fertility, concomitant with lowered levels of serum testosterone and estradiol. Further research found that in Diaph1 knockout mice, the key enzymes involved in testosterone synthesis (CYP11A1, 3β-HSD) were decreased in Leydig cells, and the estradiol-associated factor (FSH receptor, AMH) in granulosa cells were also downregulated. CONCLUSIONS Overall, our findings indicate that the knockout of Diaph1 can disrupt the expression of factors that regulate sex hormone production, leading to impaired secretion of sex hormones, ultimately resulting in damage to reproductive function. These results provide a new perspective on the molecular mechanisms underlying PGC migration and gonadal development, and offer valuable insights for further research on the causes, diagnosis, and treatment of related diseases.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Chunbiao Fan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Tongtong Qie
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Xinrui Fu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Xiaoshuang Chen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Yujia Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Yuan Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Xinyao Fu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Kesong Shi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Wenlong Yan
- School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong Province, China.
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China.
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Fountas S, Petinaki E, Bolaris S, Kargakou M, Dafopoulos S, Zikopoulos A, Moustakli E, Sotiriou S, Dafopoulos K. The Roles of GDF-9, BMP-15, BMP-4 and EMMPRIN in Folliculogenesis and In Vitro Fertilization. J Clin Med 2024; 13:3775. [PMID: 38999341 PMCID: PMC11242125 DOI: 10.3390/jcm13133775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/09/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
Growth differentiation factor 9 (GDF-9) contributes to early ovarian development and oocyte survival. Higher concentrations of GDF-9 in follicular fluid (FF) are associated with oocyte nuclear maturation and optimal embryo development. In in vitro fertilization (IVF), GDF-9 affects the ability of the oocyte to fertilize and subsequent embryonic development. Bone morphogenetic protein 15 (BMP-15) is involved in the regulation of ovarian function and affects oocyte development. During IVF, BMP-15 contributes to the formation of competent blastocysts. BMP-15 may play a role in embryo implantation by affecting endometrial receptivity. Bone morphogenetic protein 4 (BMP-4) is involved in the regulation of follicle growth and development and affects granulosa cell (GC) differentiation. In relation to IVF, BMP-4 is important for embryonic development, influences cell fate and differentiation, and plays a role in facilitating embryo-endometrial interactions during the implantation process. Extracellular matrix metalloproteinase inducer (EMMPRIN) is associated with ovulation and follicle rupture, promotes the release of mature eggs, and affects the modification of the extracellular matrix of the follicular environment. In IVF, EMMPRIN is involved in embryo implantation by modulating the adhesive properties of endometrial cells and promotes trophoblastic invasion, which is essential for pregnancy to occur. The purpose of the current article is to review the studies and recent findings of GDF-9, BMP-15, BMP-4 and EMMPRIN as fundamental factors in normal follicular development and in vitro fertilization.
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Affiliation(s)
- Serafeim Fountas
- Fertility and Sterility Unit, Elena Venizelou General-Maternity District Hospital, 11521 Athens, Greece
| | - Efthymia Petinaki
- Department of Microbiology, University Hospital of Larissa, 41110 Larissa, Greece
| | - Stamatis Bolaris
- Fertility and Sterility Unit, Elena Venizelou General-Maternity District Hospital, 11521 Athens, Greece
| | - Magdalini Kargakou
- Fertility and Sterility Unit, Elena Venizelou General-Maternity District Hospital, 11521 Athens, Greece
| | - Stefanos Dafopoulos
- Department of Health Sciences, European University Cyprus, 2404 Nicosia, Cyprus
| | | | - Efthalia Moustakli
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Sotirios Sotiriou
- Department of Embryology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
| | - Konstantinos Dafopoulos
- ART Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
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Zhuang Z, Li K, Yang K, Gao G, Li Z, Zhu X, Zhao Y. Genome-Wide Association Study Reveals Novel Candidate Genes Influencing Semen Traits in Landrace Pigs. Animals (Basel) 2024; 14:1839. [PMID: 38997951 PMCID: PMC11240458 DOI: 10.3390/ani14131839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Artificial insemination plays a crucial role in pig production, particularly in enhancing the genetic potential of elite boars. To accelerate genetic progress for semen traits in pigs, it is vital to understand and identify the underlying genetic markers associated with desirable traits. Herein, we genotyped 1238 Landrace boars with GeneSeek Porcine SNP50 K Bead chip and conducted genome-wide association studies to identify genetic regions and candidate genes associated with 12 semen traits. Our study identified 38 SNPs associated with the analyzed 12 semen traits. Furthermore, we identified several promising candidate genes, including HIBADH, DLG1, MED1, APAF1, MGST3, MTG2, and ZP4. These candidate genes have the potential function to facilitate the breeding of boars with improved semen traits. By further investigating and understanding the roles of these genes, we can develop more effective breeding strategies that contribute to the overall enhancement of pig production. The results of our study provide valuable insights for the pig-breeding industry and support ongoing research efforts to optimize genetic selection for superior semen traits.
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Affiliation(s)
- Zhanwei Zhuang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Kebiao Li
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Kai Yang
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Guangxiong Gao
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Zhili Li
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Xiaoping Zhu
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Yunxiang Zhao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- Guangxi Yangxiang Co., Ltd., Guigang 537100, China
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6
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Smitchger JA, Taylor JB, Mousel MR, Schaub D, Thorne JW, Becker GM, Murdoch BM. Genome-wide associations with longevity and reproductive traits in U.S. rangeland ewes. Front Genet 2024; 15:1398123. [PMID: 38859938 PMCID: PMC11163081 DOI: 10.3389/fgene.2024.1398123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/18/2024] [Indexed: 06/12/2024] Open
Abstract
Introduction: Improving ewe longevity is an important breeding and management goal, as death loss and early culling of mature ewes are economic burdens in the sheep industry. Ewe longevity can be improved by selecting for positive reproductive outcomes. However, the breeding approaches for accomplishing this come with the challenge of recording a lifetime trait. Characterizing genetic factors underpinning ewe longevity and related traits could result in the development of genomic selection strategies to improve the stayability of sheep through early, informed selection of replacement ewes. Methods: Towards this aim, a genome-wide association study (GWAS) was performed to identify genetic markers associated with ewe longevity, reproductive, and production traits. Traits evaluated included longevity (i.e., length of time in the flock), parity and the lifetime number of lambs born, lambs born alive, lambs weaned, and weight of lambs weaned. Ewe records from previous studies were used. Specifically, Rambouillet (n = 480), Polypay (n = 404), Suffolk (n = 182), and Columbia (n = 64) breed ewes (N = 1,130) were analyzed against 503,617 SNPs in across-breed and within-breed GWAS conducted with the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model in R. Results: The across-breed GWAS identified 25 significant SNPs and the within-breed GWAS for Rambouillet, Polypay, and Suffolk ewes identified an additional 19 significant SNPs. The most significant markers were rs411309094 (13:22,467,143) associated with longevity in across-breed GWAS (p-value = 8.3E-13) and rs429525276 (2:148,398,336) associated with both longevity (p-value = 6.4E-15) and parity (p-value = 4.8E-15) in Rambouillet GWAS. Significant SNPs were identified within or in proximity (±50 kb) of genes with known or proposed roles in reproduction, dentition, and the immune system. These genes include ALPL, ANOS1, ARHGEF26, ASIC2, ASTN2, ATP8A2, CAMK2D, CEP89, DISC1, ITGB6, KCNH8, MBNL3, MINDY4, MTSS1, PLEKHA7, PRIM2, RNF43, ROBO2, SLCO1A2, TMEM266, TNFRSF21, and ZNF804B. Discussion: This study proposes multiple SNPs as candidates for use in selection indices and suggests genes for further research towards improving understanding of the genetic factors contributing to longevity, reproductive, and production traits of ewes.
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Affiliation(s)
- Jamin A. Smitchger
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - J. Bret Taylor
- USDA, Agriculture Research Service, Range Sheep Production Efficiency Research Unit, U.S. Sheep Experiment Station, Dubois, ID, United States
| | - Michelle R. Mousel
- Animal Diseases Research Unit, Agricultural Research Service, US Department of Agriculture, Pullman, WA, United States
| | - Daniel Schaub
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Jacob W. Thorne
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
- Texas A&M AgriLife Research and Extension, San Angelo, TX, United States
| | - Gabrielle M. Becker
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Brenda M. Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
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Gudra D, Valdovska A, Jonkus D, Kairisa D, Galina D, Ustinova M, Viksne K, Fridmanis D, Kalnina I. Genetic characterization of the Latvian local goat breed and genetic traits associated with somatic cell count. Animal 2024; 18:101154. [PMID: 38703755 DOI: 10.1016/j.animal.2024.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 05/06/2024] Open
Abstract
The Latvian local goat (LVK) breed represents the only native domestic goat breed in Latvia, but its limited population places it within the endangered category. However, the LVK breed has not yet undergone a comprehensive genetic characterization. Therefore, we completed whole genome sequencing to reveal the genetic foundation of the LVK breed while identifying genetic traits linked to the somatic cell count (SCC) levels. The study included 40 genomes of LVK goats sequenced to acquire at least 35x or 10x coverage. A Principal component analysis, a genetic distance tree, and an admixture analysis showed LVK's similarity to some European breeds, such as Finnish Landrace, Alpine, and Saanen, which aligns with the breed's history. An analysis of genome-wide heterozygosity, nucleotide diversity, and LD analysis indicated that the LVK population exhibits substantial levels of genetic diversity. LVK genome was dominated by short runs of homozygosity (ROHs, ≤ 500 kb) with a median length of 25 kb. With FROH 2.49%, average inbreeding levels were low; however, FROH ranged broadly from 0.13 to 12.2%. With the exception of one pure-blood breeding buck exhibiting FROH of 9.3% and FSNP of 8.5%, animals with at least 66% LVK ancestry showed moderate or no inbreeding. Overall, this study demonstrated that the LVK goats can be differentiated from imported breeds, although the population has a complex genetic structure. We were able to identify potential genetic traits associated with SCC levels, although the kinship of the animals and the heterogenic substructure of the population might have largely influenced the association analysis. We identified 26 genetic variants associated with SCC levels, which included the potentially relevant SNP rs662053371 in the OSBPL8 gene, indicating a potential signal linked to lipid metabolism in goats. To conclude, these findings present valuable insight into the genetic structure of the LVK breed for the conservation of local genetic resources.
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Affiliation(s)
- D Gudra
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - A Valdovska
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia.
| | - D Jonkus
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Kairisa
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Galina
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - M Ustinova
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - K Viksne
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - D Fridmanis
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - I Kalnina
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
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8
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Beer MA, Proft KM, Veillet A, Kozakiewicz CP, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Burridge CP, Margres MJ, Jones ME, Storfer A. Disease-driven top predator decline affects mesopredator population genomic structure. Nat Ecol Evol 2024; 8:293-303. [PMID: 38191839 DOI: 10.1038/s41559-023-02265-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024]
Abstract
Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Anne Veillet
- Hilo Core Genomics Facility, University of Hawaii at Hilo, Hilo, HI, USA
| | - Christopher P Kozakiewicz
- Department of Integrative Biology, Michigan State University, W.K. Kellogg Biological Station, Hickory Corners, MI, USA
| | - David G Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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Wijayanti D, Bai Y, Hanif Q, Chen H, Zhu H, Qu L, Guo Z, Lan X. Goat CLSTN2 gene: tissue expression profile, genetic variation, and its associations with litter size. Anim Biotechnol 2023; 34:2674-2683. [PMID: 35980330 DOI: 10.1080/10495398.2022.2111311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Calsyntenin-2 (CLSTN2) is involved in cell proliferation, differentiation, cell death, tumorigenesis, and follicular expression. Although CLSTN2 has been identified as a potential candidate gene for sheep prolificacy, no studies have been done on its effect on goat prolificacy. The purpose of this study was to identify mRNA expression and genetic variation within goat CLSTN2, and its association with prolificacy. Herein, we uncovered significant differences in mRNA levels of the CLSTN2 gene in different tissues in female goats (p < 0.01), including ovary tissue. Nine putative indels were designed to investigate their correlation to litter size, but only one 16-bp deletion was discovered in female Shaanbei white cashmere goats (n = 902). We discovered that a 16-bp deletion within the CLSTN2 gene was significantly correlated with first-born litter size (p = 0.0001). As shown by the chi-squared test, the genotypic II of single-lambs and multi-lambs was dramatically higher than with genotype ID (p = 0.005). Our findings suggest that indel within the CLSTN2 gene is a candidate gene affecting prolificacy in goats and may be used for Marker Assisted Selection (MAS) in goats.
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Affiliation(s)
- Dwi Wijayanti
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, Indonesia
| | - Yangyang Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, PR China and Life Science Research Center, Yulin University, Yulin, Shaanxi, PR China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, PR China and Life Science Research Center, Yulin University, Yulin, Shaanxi, PR China
| | - Zhengang Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Institute of Animal Husbandry and Veterinary Science of Bijie City, Guizhou, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Ahmad SF, Chandrababu Shailaja C, Vaishnav S, Kumar A, Gaur GK, Janga SC, Ahmad SM, Malla WA, Dutt T. Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds. BMC Genomics 2023; 24:616. [PMID: 37845620 PMCID: PMC10580622 DOI: 10.1186/s12864-023-09720-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated. RESULTS Overall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds. CONCLUSION The present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale.
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Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
| | - Celus Chandrababu Shailaja
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Sakshi Vaishnav
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Amit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Gyanendra Kumar Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing & Engineering, Indiana University Indianapolis (IUI), Indianapolis, 46202, USA
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and AH, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu & Kashmir, 190006, India.
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Triveni Dutt
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
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11
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Hervás-Rivero C, Srihi H, López-Carbonell D, Casellas J, Ibáñez-Escriche N, Negro S, Varona L. Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs. Genes (Basel) 2023; 14:1941. [PMID: 37895290 PMCID: PMC10606707 DOI: 10.3390/genes14101941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120.
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Affiliation(s)
- Carlos Hervás-Rivero
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.H.-R.); (D.L.-C.)
| | - Houssemeddine Srihi
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.H.-R.); (D.L.-C.)
| | - David López-Carbonell
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.H.-R.); (D.L.-C.)
| | - Joaquim Casellas
- Department Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Noelia Ibáñez-Escriche
- Instituto Universitario de Ciencia y Tecnología Animal, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Sara Negro
- Programa de Mejora Genética “Castua”, INGA FOOD S. A. (Nutreco), 06200 Almendralejo, Spain
| | - Luis Varona
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.H.-R.); (D.L.-C.)
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12
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Revelo HA, López-Alvarez D, Palacios YA, Vergara OD, Yánez MB, Ariza MF, Molina SLC, Sanchez YO, Alvarez LÁ. Genome-wide association study reveals candidate genes for traits related to meat quality in Colombian Creole hair sheep. Trop Anim Health Prod 2023; 55:357. [PMID: 37823994 PMCID: PMC10570192 DOI: 10.1007/s11250-023-03688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 07/06/2023] [Indexed: 10/13/2023]
Abstract
Genome-wide association studies (GWAS) allow identifying genomic regions related to traits of economic importance in animals of zootechnical interest. The objective of this research was to conduct a genome-wide association study on meat quality traits using the Illumina OvineSNPs50 BeadChip array. The animals were sampled in the departments of Córdoba, Cesar, and Valle del Cauca. The genotypes obtained with the Illumina OvineSNP50 BeadChip microarray were analyzed SNP (single-nucleotide polymorphism) data to conduct a GWAS for pH and water-holding capacity (WHC) traits measured after 7 days of maturation, in the Longissimus dorsi (LD) muscle, in 167 Creole hair sheep of 12 months old belonging to Pelibuey (CHSP, n = 60), Ethiopian (CHSE, n = 44), and Sudan (CHSS, n = 63) breeds. The GWAS was done using a mixed linear model (MLMA) and based on the Ovis aries v3.1 genome. The CHSE showed the lowest meat juice release and, consequently, the highest water-holding capacity (WHC = 30.6 ± 0.1), suggesting that this breed has better performance in the meat industry compared with CHSS (WHC = 41.7 ± 0.1) and CHSP (WHC = 36.8 ± 0.1), since there is a relationship between WHC and juiciness. For the character pH, it was not possible to annotate genes related to meat quality, while, for the WHC, they have obtained 11 candidate genes associated (ELOVL2, ARAP2, LOC101102527, SHOC2, AIPL1, CSRNP3, IFRD, KDM8, NANS, DAPK1, IBN2, TPM2). Particularly, ELOVL2, ARAP2, IBN2, and TPM2 genes are involved in muscle contraction and fatty acid composition in sheep. In this study, we generated a baseline for GWAS related to meat quality traits in Colombian Creole hair sheep that can be used for future genomic selection plans.
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Affiliation(s)
- Herman Alberto Revelo
- Grupo de Investigación de Recursos Zoogenéticos, Departamento de Ciencia Animal, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, 763533 Palmira, Colombia
- Present Address: Facultad de Medicina Veterinaria y Zootecnia, Universidad San Martin Cali Colombia, Carrera 122 #23-395 del, Vía Cali-Puerto Tejada, 760022 Cali, Colombia
| | - Diana López-Alvarez
- Grupo de Investigación de Recursos Zoogenéticos, Departamento de Ciencia Animal, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, 763533 Palmira, Colombia
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, 763533 Palmira, Colombia
| | - Yineth Alexandra Palacios
- Grupo de Investigación de Recursos Zoogenéticos, Departamento de Ciencia Animal, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, 763533 Palmira, Colombia
| | - Oscar David Vergara
- Grupo de Investigación en Producción Animal Tropical, Universidad de Córdoba, 14014 Córdoba, Colombia
| | - Moris Bustamante Yánez
- Grupo de Investigación en Producción Animal Tropical, Universidad de Córdoba, 14014 Córdoba, Colombia
| | - Manuel Fernando Ariza
- Department of Animal Production, Universidad Nacional de Colombia, 111321 Bogotá D.C, Colombia
| | | | - Yurany Ortiz Sanchez
- Department of Animal Production, Universidad Nacional de Colombia, 111321 Bogotá D.C, Colombia
| | - Luz Ángela Alvarez
- Grupo de Investigación de Recursos Zoogenéticos, Departamento de Ciencia Animal, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, 763533 Palmira, Colombia
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13
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Pallotti S, Picciolini M, Antonini M, Renieri C, Napolioni V. Genome-wide scan for runs of homozygosity in South American Camelids. BMC Genomics 2023; 24:470. [PMID: 37605116 PMCID: PMC10440933 DOI: 10.1186/s12864-023-09547-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. RESULTS A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. CONCLUSIONS The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.
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Affiliation(s)
- Stefano Pallotti
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.
| | | | - Marco Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Roma, Italy
| | - Carlo Renieri
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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14
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Liu Z, Fu S, He X, Liu X, Shi C, Dai L, Wang B, Chai Y, Liu Y, Zhang W. Estimates of Genomic Heritability and the Marker-Derived Gene for Re(Production) Traits in Xinggao Sheep. Genes (Basel) 2023; 14:genes14030579. [PMID: 36980850 PMCID: PMC10048694 DOI: 10.3390/genes14030579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Xinggao sheep are a breed of Chinese domestic sheep that are adapted to the extremely cold climatic features of the Hinggan League in China. The economically vital reproductive trait of ewes (litter size, LS) and productive traits of lambs (birth weight, BWT; weaning weight, WWT; and average daily gain, ADG) are expressed in females and later in life after most of the selection decisions have been made. This study estimated the genetic parameters for four traits to explore the genetic mechanisms underlying the variation, and we performed genome-wide association study (GWAS) tests on a small sample size to identify novel marker trait associations (MTAs) associated with prolificacy and growth. We detected two suggestive significant single-nucleotide polymorphisms (SNPs) associated with LS and eight significant SNPs for BWT, WWT, and ADG. These candidate loci and genes also provide valuable information for further fine-mapping of QTLs and improvement of reproductive and productive traits in sheep.
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Affiliation(s)
- Zaixia Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Shaoyin Fu
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xiaolong He
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xuewen Liu
- College of Agronomy, Animal Husbandry and Bioengineering, Xing’an Vocational and Technical College, Ulanhot 137400, China
| | - Caixia Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lingli Dai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- Veterinary Research Institute, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Biao Wang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Yuan Chai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yongbin Liu
- School of Life Science, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (Y.L.); (W.Z.)
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- Correspondence: (Y.L.); (W.Z.)
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15
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Castillo-Salas CA, Luna-Nevárez G, Reyna-Granados JR, Luna-Ramirez RI, Limesand SW, Luna-Nevárez P. Molecular markers for thermo-tolerance are associated with reproductive and physiological traits in Pelibuey ewes raised in a semiarid environment. J Therm Biol 2023; 112:103475. [PMID: 36796920 DOI: 10.1016/j.jtherbio.2023.103475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
Pelibuey sheep exhibit reproductive activity through the year, but warm weather lowers their fertility and demonstrates physiological limitations of environmental heat stress. Single nucleotide polymorphisms (SNPs) associated with heat stress tolerance in sheep have been reported previously. The objective was to validate the association of seven thermo-tolerance SNP markers with reproductive and physiological traits in Pelibuey ewes raised in a semiarid region. Pelibuey ewes were assigned to a cool (January 1st.- March 31st.; n = 101) or warm (April 1st.- August 31st.; n = 104) experimental group. All ewes were exposed to fertile rams and assessed for pregnancy diagnosis 90 days later; lambing day was reported at birth. These data served to calculate the reproductive traits of services per conception, prolificacy, days to estrus, days to conception, conception rate and lambing rate. Rectal temperature, rump/leg skin temperature and respiratory rate were measured and reported as physiological traits. Blood samples were collected and processed to extract DNA, which was genotyped using the TaqMan allelic discrimination method and qPCR. A mixed effects statistical model was used to validate associations between SNP genotypes and phenotypic traits. The SNPs rs421873172, rs417581105 and rs407804467 were confirmed as markers associated with reproductive and physiological traits (P < 0.05), and these SNPs were in the genes PAM, STAT1 and FBXO11, respectively. Interestingly, these SNP markers resulted as predictors for the evaluated traits but only in ewes from the warm group, which indicated their association with heat-stress tolerance. An additive SNP effect was confirmed with the highest contribution (P < 0.01) of the SNP rs417581105 for the evaluated traits. Reproductive performance improved (P < 0.05) and physiological parameters decreased in ewes carrying favorable SNP genotypes. In conclusion, three thermo-tolerance SNP markers were associated with improved reproductive and physiological traits in a prospective population of heat-stressed ewes raised in a semiarid environment.
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Affiliation(s)
- Candelario A Castillo-Salas
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Javier R Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Rosa I Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Sean W Limesand
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México.
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16
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Cai D, Wang Z, Zhou Z, Lin D, Ju X, Nie Q. Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens. Poult Sci 2023; 102:102504. [PMID: 36739803 PMCID: PMC9932115 DOI: 10.1016/j.psj.2023.102504] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Egg production performance plays an important role in the poultry industry across the world. Previous studies have shown a great difference in egg production performance between pendulous-comb (PC) and upright-comb (UC) chickens. However, there are no reports to identify potential candidate genes for egg production in PC and UC chickens. In the present study, 1,606 laying chickens were raised, and the egg laid by individual chicken was collected for 100 d. Moreover, the expression level of estrogen and progesterone hormones was measured at the start-laying and peak-laying periods of hens. Besides, 4 PC and 4 UC chickens were selected at 217 d of age to perform transcriptome sequencing (RNA-seq) and whole genome resequencing (WGS) to screen the potential candidate genes of egg production. The results showed that PC chicken demonstrated better egg production performance (P < 0.05) and higher estrogen and progesterone hormone expression levels than UC chicken (P < 0.05). RNA-seq analysis showed that 341 upregulated and 1,036 downregulated differentially expressed genes (DEGs) were identified in the ovary tissues of PC and UC chickens. These DEGs were mainly enriched in protein-related, lipid-related, and nucleic acids-related biological processes including ribosome, peptide biosynthetic process, lipid transport terms, and catalytic activity acting on RNA which can significantly affect egg production in chicken. The enrichment results of WGS analysis were consistent with RNA-seq. Further, joint analysis of WGS and RNA-seq data was utilized to screen 30 genes and CAMK1D, CLSTN2, MAST2, PIK3C2G, TBC1D1, STK3, ADGRB3, and PPARGC1A were identified as potential candidate genes for egg production in PC and UC chickens. In summary, our study provides a wealth of information for a better understanding of the genetic and molecular mechanism for the future breeding of PC and UC chickens for egg production.
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Affiliation(s)
- Danfeng Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Zhijun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China,College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Lin'an 311300, China
| | - Zhen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Duo Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Xing Ju
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Qinghua Nie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China.
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Jiang H, Chai ZX, Cao HW, Zhang CF, Zhu Y, Zhang Q, Xin JW. Genome-wide identification of SNPs associated with body weight in yak. BMC Genomics 2022; 23:833. [PMID: 36522700 PMCID: PMC9756674 DOI: 10.1186/s12864-022-09077-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The yak is the most important livestock in the Qinghai-Tibet Plateau, and body weight directly affects the economic values of yak. Up to date, the genome-wide profiling of single-nucleotide polymorphisms (SNPs) associating with body weight has not been reported in yak. In the present study, the SNPs in 480 yaks from three breeds were analyzed using the commercial high-density (600 K) yak SNP chips. RESULTS The results identified 12 and 4 SNPs potentially associated with body weight in male and female yaks, respectively. Among them, 9 and 2 SNPs showed significant difference in yak body weight between different genotypes at each locus in male and female yaks, respectively. Further exploration found 33 coding genes within the 100 kbp upstream or downstream to the SNP loci, which might be potentially affected by the variation of SNPs. Among them, G protein-coupled receptor kinase 4 (GRK4) might be potentially affected by the SNP AX-174555047, which has been reported to affect the functioning of two body-weight associated hormones (parathyroid hormone, PTH, and adrenomedullin, ADM). Determination of PTH and ADM levels in yak revealed positive relationship between PTH level and body weight, negative relationship between ADM level and body weight along with the variation of AX-174555047 mutation. CONCLUSIONS These results suggested that the SNP AX-174555047 might potentially affect body weight through mediating GRK4 expression and then PTH and ADM functioning. Thus, the SNP AX-174555047 might be used as a biomarker for molecular breeding of yak. More investigations are required to validate this point.
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Affiliation(s)
- Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Zhi-Xin Chai
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041 Sichuan China
| | - Han-Wen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Cheng-Fu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Jin-Wei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
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18
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Ajafar MH, Kadhim AH, Al-Thuwaini TM, Al-Shuhaib MBS, Hussein TH. Dr Association of bone morphogenetic protein 15 and growth differentiation factor 9 with litter size in livestock: a review study. ACTA SCIENTIARUM: ANIMAL SCIENCES 2022. [DOI: 10.4025/actascianimsci.v45i1.57927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
. Litter size is one of the crucial factors in livestock production and is of high economic value, which is affected by ovulation rate, hormones, and growth factors. Growth factors play a multifaceted role in reproductive physiology. This review aims to investigate the association of bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) with litter size in livestock. The transforming growth factor β (TGF- β) superfamily includes more than 34 members; GDF9 and BMP15 are among the most significant factors for regulating fertility and litter size in most livestock species. Ovarian follicles release BMP15 and GDF9 that are involved in the maturation of primary follicles into the basal form, proliferation of granulosa and theca cells, steroidogenesis, ovulation, and formation of the corpus luteum. Besides, these factors are highly expressed in oocytes and are necessary for female fertility and multiple ovulation in several livestock species. Animals with two inactive copies of these factors are sterile, while those with one inactive copy are fertile. Thus, the present review provides valuable information on the association of BMP15 and GDF9 with litter size in livestock that can be used as biological markers of multiple ovulation or for improving fertility in livestock.
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Mahmoudi P, Rashidi A, Nazari-Ghadikolaei A, Rostamzadeh J, Razmkabir M, Huson HJ. Genome-wide association study reveals novel candidate genes for litter size in Markhoz goats. Front Vet Sci 2022; 9:1045589. [PMID: 36504837 PMCID: PMC9727218 DOI: 10.3389/fvets.2022.1045589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction The Markhoz goat is the only breed that can produce high-quality fiber called mohair in Iran; however, the size of its population has faced a dramatic decline during the last decades, mainly due to the reluctance of farmers to rear Markhoz goats caused by a reduction in goat production income. Litter size at birth (LSB) and weaning (LSW) are two economically important reproductive traits for local goat breeders and have the potential of increasing the population growth rate. The present study was aimed to identify possible genomic regions that are associated with LSB and LSW in Markhoz goats using a genome-wide association study (GWAS). Methods To this end, 136 Markhoz goats with record(s) of kidding were selected for GWAS using the Illumina Caprine 50K bead chip. The individual breeding values (BV) of available LSB and LSW records estimated under an animal mixed model were used as the dependent variable in the GWAS, thereby incorporating repeated categorical variables of litter size. Results Four SNPs on chromosomes 2, 20 and 21 were identified to be significantly associated (FDR p < 0.05) with LSB after multiple testing correction under a Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model. Least-square analysis was performed to investigate the effects of detected genotypes on LSB. Ultimately, the GWAS results introduced six candidate genes, including GABRA5, AKAP13, SV2B, PPP1R1C, SSFA2 and TRNAS-GCU in a 100 kb adjacent region of the identified SNPs. Previous studies proposed functional roles of GABRA5 and AKAP13 genes in reproductive processes; however, the role of other candidate genes in reproduction is not clear. Conclusion These findings warrant further investigation for use in marker-assisted selection programs in Markhoz goats.
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Affiliation(s)
- Peyman Mahmoudi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Amir Rashidi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran,*Correspondence: Amir Rashidi
| | - Anahit Nazari-Ghadikolaei
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jalal Rostamzadeh
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran,Jalal Rostamzadeh
| | - Mohammad Razmkabir
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran,Mohammad Razmkabir
| | - Heather Jay Huson
- Department of Animal Science, Cornell University, Ithaca, NY, United States
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20
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A Genome-Wide Search for Candidate Genes of Meat Production in Jalgin Merino Considering Known Productivity Genes. Genes (Basel) 2022; 13:genes13081337. [PMID: 35893074 PMCID: PMC9331477 DOI: 10.3390/genes13081337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
In a group of Jalgin merino rams with no significant influence on the dispersion of the phenotypes of known productivity genes (MSTN, MEF2B, FABP4, etc.), a genome-wide search for associations of individual polymorphisms with intravital indicators of meat productivity was performed. Using the Ovine Infinium HD BeadChip 600K, 606,000 genome loci were evaluated. Twenty-three substitutions were found to be significantly associated with external measurements of the body and ultrasonic parameters. This made it possible to describe 14 candidate genes, the structural features of which can cause changes in animal phenotypes. No closely spaced genes were found for two substitutions. The identified polymorphisms were found in the exons, introns, and adjacent regions of the following genes and transcripts: CDCA2, ENSOARG00000014477, C4BPA, RIPOR2, ENSOARG00000007198, ENSOARG00000026965 (LincRNA), ENSOARG00000026436 (LincRNA), ENSOARG00000026782 (LincRNA), TENM3, RTL8A, MOSPD1, RTL8С, RIMS2, and P4HA3. The detected genes affect the metabolic pathways of cell differentiation and proliferation and are associated with the regulation of the immune system. This confirms their possible participation in the formation of the phenotypes of productivity parameters in animals and indicates the need for further study of the structure of candidate genes in order to identify their internal polymorphisms.
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21
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Wang X, Ran X, Niu X, Huang S, Li S, Wang J. Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs. Sci Rep 2022; 12:11823. [PMID: 35821031 PMCID: PMC9276726 DOI: 10.1038/s41598-022-14686-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.
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Affiliation(s)
- Xiying Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.,Tongren University, Tongren, 554300, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
| | - Xi Niu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Shihui Huang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Sheng Li
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jiafu Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
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22
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Khalkhali-Evrigh R, Hedayat N, Ming L, Jirimutu. Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data. Sci Rep 2022; 12:9653. [PMID: 35688969 PMCID: PMC9187634 DOI: 10.1038/s41598-022-14376-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
The Old World camels play an important role as one of the main food sources in large parts of Asia and Africa. Natural selection combined with artificial selection by human has affected parts of the domestic animal genome for adapting them to their habitats and meeting human needs. Here, we used whole genome sequencing data of 34 camels (including 14 dromedaries and 20 Bactrian camels) to identify the genomic signature of selection in the Iranian dromedary (ID) and Bactrian camels (IB). To detect the mentioned regions, we used two methods including population differentiation index (Fst) and cross-population extended haplotype homozygosity (XP-EHH) with 50 kb sliding window and 25 kb step size. Based on gene ontology analysis on the candidate genes identified for IB camels, we found GO terms associated with lung development, nervous system development, immune system and behavior. Also, we identified several genes related to body thermoregulation (ZNF516), meat quality (ANK1 and HSPA13), and high-altitude adaptation (OPA1) for IB camels. In the list of detected candidate genes under selection in ID camels, the genes related to energy metabolism (BDH1), reproduction (DLG1, IMMP2L and FRASI), long-term memory (GRIA1), kidney (SLC12A1), lung development (EMILIN2 and FBN1) and immunity (SOCS2, JAK1, NRROS and SENP1) were found. Our findings, along with further studies in this field, will strengthen our knowledge about the effect of selection on the camelid genome under different geographical, climatic and even cultural conditions.
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Affiliation(s)
- Reza Khalkhali-Evrigh
- Department of Animal Science, Faculty of Agriculture and Natural Recourses, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Nemat Hedayat
- Department of Animal Science, Faculty of Agriculture and Natural Recourses, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Liang Ming
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Jirimutu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
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23
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Yan X, Zhang T, Liu L, Yu Y, Yang G, Han Y, Gong G, Wang F, Zhang L, Liu H, Li W, Yan X, Mao H, Li Y, Du C, Li J, Zhang Y, Wang R, Lv Q, Wang Z, Zhang J, Liu Z, Wang Z, Su R. Accuracy of Genomic Selection for Important Economic Traits of Cashmere and Meat Goats Assessed by Simulation Study. Front Vet Sci 2022; 9:770539. [PMID: 35372544 PMCID: PMC8966406 DOI: 10.3389/fvets.2022.770539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic selection in plants and animals has become a standard tool for breeding because of the advantages of high accuracy and short generation intervals. Implementation of this technology is hindered by the high cost of genotyping and other factors. The aim of this study was to determine an optional marker density panel and reference population size for using genomic selection of goats, with speculation on the number of QTLs that affect the important economic traits of goats. In addition, the effect of buck population size in the reference population on the accuracy of genomic estimated breeding value (GEBV) was discussed. Based on the previous genetic evaluation results of Inner Mongolia White Cashmere Goats, live body weight (LBW, h2 = 0.11) and fiber diameter (FD, h2 = 0.34) were chosen to perform genomic selection in this study. Reasonable genome parameters and generation transmission processes were set, and phenotypic and genotype data of the two traits were simulated. Then, different sizes of the reference population and validation population were selected from progeny. The GEBVs were obtained by six methods, including GBLUP (Genomic Best Linear Unbiased Prediction), ssGBLUP (Single Step Genomic Best Linear Unbiased Prediction), BayesA, BayesB, Bayesian ridge regression, and Bayesian LASSO. The correlation coefficient between the predicted and realized phenotypes from simulation was calculated and used as a measure of the accuracy of GEBV in each trait. The results showed that the medium marker density Panel (45 K) could be used for genomic selection in goats, which can ensure the accuracy of the GEBV. The reference population size of 1,500 can achieve greater genetic progress in genomic selection for fiber diameter and live body weight in goats by comparing with the population size below this level. The accuracy of the GEBV for live body weight and fiber diameter was better when the number of QTLs was 100 and 50, respectively. Additionally, the accuracy of GEBV was discovered to be good when the buck population size was up to 200. Meanwhile, the accuracy of the GEBV for medium heritability traits (FDs) was found to be higher than the accuracy of the GEBV for low heritability traits (LBWs). These findings will provide theoretical guidance for genomic selection in goats by using real data.
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Affiliation(s)
- Xiaochun Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Tao Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Bigvet Co., Ltd., Hohhot, China
| | - Lichun Liu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongsheng Yu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Guang Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yaqian Han
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Gao Gong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Fenghong Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Lei Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongfu Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenze Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaomin Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Haoyu Mao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yaming Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Chen Du
- Department of Obstetrics and Gynaecology, Inner Mongolia Medical University, Hohhot, China
| | - Jinquan Li
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, China
- Engineering Research Centre for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jiaxin Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- *Correspondence: Zhiying Wang
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Rui Su
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Anderson SJ, Côté SD, Richard JH, Shafer ABA. Genomic architecture of phenotypic extremes in a wild cervid. BMC Genomics 2022; 23:126. [PMID: 35151275 PMCID: PMC8841092 DOI: 10.1186/s12864-022-08333-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 12/30/2022] Open
Abstract
Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.
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Gholizadeh M, Esmaeili-Fard SM. Meta-analysis of genome-wide association studies for litter size in sheep. Theriogenology 2021; 180:103-112. [PMID: 34968818 DOI: 10.1016/j.theriogenology.2021.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/19/2021] [Accepted: 12/19/2021] [Indexed: 01/01/2023]
Abstract
Litter size and ovulation rate are important reproduction traits in sheep and have important impacts on the profitability of farm animals. To investigate the genetic architecture of litter size, we report the first meta-analysis of genome-wide association studies (GWAS) using 522 ewes and 564,377 SNPs from six sheep breeds. We identified 29 significant associations for litter size which 27 of which have not been reported in individual GWAS for each population. However, we could confirm the role of BMPR1B in prolificacy. Our gene set analysis discovered biological pathways related to cell signaling, communication, and adhesion. Functional clustering and enrichment using protein databases identified epidermal growth factor-like domain affecting litter size. Through analyzing protein-protein interaction data, we could identify hub genes like CASK, PLCB4, RPTOR, GRIA2, and PLCB1 that were enriched in most of the significant pathways. These genes have a role in cell proliferation, cell adhesion, cell growth and survival, and autophagy. Notably, identified SNPs were scattered on several different chromosomes implying different genetic mechanisms underlying variation of prolificacy in each breed. Given the different layers that make up the follicles and the need for communication and transfer of hormones and nutrients through these layers to the oocyte, the significance of pathways related to cell signaling and communication seems logical. Our results provide genetic insights into the litter size variation in different sheep breeds.
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Affiliation(s)
- Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
| | - Seyed Mehdi Esmaeili-Fard
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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27
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Wang FH, Zhang L, Gong G, Yan XC, Zhang LT, Zhang FT, Liu HF, Lv Q, Wang ZY, Wang RJ, Zhang YJ, Wang ZX, Liu ZH, He LB, Su R, Zhao YH, Li JQ. Genome-wide association study of fleece traits in Inner Mongolia Cashmere goats. Anim Genet 2021; 52:375-379. [PMID: 33778967 PMCID: PMC8251931 DOI: 10.1111/age.13053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 12/14/2022]
Abstract
Inner Mongolia Cashmere goat is a well-known local cashmere goat breed in China. It is famous for excellent fleece quality and a significant advantage in cashmere yield compared to other cashmere goat breeds. In this study, a genome-wide association study was used to investigate fiber length, fiber diameter, and cashmere yield of 192 Inner Mongolia Cashmere goats using the Illumina GoatSNP52K Beadchip panel. We discovered that four single nucleotide polymorphisms (SNPs) reached genome-wide significance levels. These SNPs were located in some genes, e.g. FGF12, SEMA3D, EVPL, and SOX5, possibly related to fleece traits in Inner Mongolia Cashmere goat. Gene ontology enrichment analysis revealed that these genes were enriched in several biological pathways that were involved in hair follicle development in cashmere goats. In summary, the identified significant SNPs and genes provide useful information to explore genetic mechanisms underlying the variation in fleece traits and genomic selection of Chinese cashmere goat.
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Affiliation(s)
- F. H. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - L. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - G. Gong
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - X. C. Yan
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - L. T. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - F. T. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - H. F. Liu
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Q. Lv
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Z. Y. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - R. J. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Y. J. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Z. X. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
- Key Laboratory of Animal Genetics, Breeding and ReproductionHohhotInner Mongolia Autonomous Region010018China
| | - Z. H. Liu
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
- Key Laboratory of Mutton Sheep Genetics and BreedingMinistry of Agriculture and Rural AffairsHohhot010018China
| | - L. B. He
- Key Laboratory of Mutton Sheep Genetics and BreedingMinistry of Agriculture and Rural AffairsHohhot010018China
| | - R. Su
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Y. H. Zhao
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - J. Q. Li
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
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28
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Tao L, He XY, Wang FY, Pan LX, Wang XY, Gan SQ, Di R, Chu MX. Identification of genes associated with litter size combining genomic approaches in Luzhong mutton sheep. Anim Genet 2021; 52:545-549. [PMID: 34002409 DOI: 10.1111/age.13078] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
Litter size is one of the most important reproductive traits of sheep, which has pronounced effects on the profit of husbandry enterprises and enthusiasm of breeders. Despite the importance of litter size, the underlying genetic mechanisms have not been entirely elucidated. Therefore, based on a high-density SNP chip, genome-wide comparative analysis was performed between two groups with different fecundity to reveal candidate genes linked to litter size via detection of homozygosity and selection signatures in Luzhong mutton sheep. Consequently, nine promising genes were identified from six runs of homozygosity islands, and functionally linked to reproduction (ACTL7A, ACTL7B, and ELP1), embryonic development (KLF5 and PIBF1), and cell cycle (DACH1, BORA, DIS3, and MZT1). A total of 128 genes were observed under selection, of which HECW1 and HTR1E were related to total lambs born, GABRG3, LRP1B, and MACROD2 to teat number, and AGBL1 to reproductive seasonality. Additionally, the presence of inbreeding depression implies the urgency of reasonable mating system to increase litter size in the present herd. These findings provide a comprehensive insight to the genetic makeup of litter size, and also contribute to implementation of marker-assisted selection in sheep.
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Affiliation(s)
- L 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
| | - X Y 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
| | - F Y Wang
- 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 X Pan
- Ji'nan Laiwu Yingtai Agriculture and Animal Husbandry Technology Co., Ltd, Ji'nan, Shandong, 271114, China
| | - X Y Wang
- 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
| | - S Q Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang, 832000, China
| | - R Di
- 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
| | - M X 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
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Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages. Sci Rep 2021; 11:5865. [PMID: 33712687 PMCID: PMC7971002 DOI: 10.1038/s41598-021-85245-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/22/2021] [Indexed: 12/23/2022] Open
Abstract
Ovary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.
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Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model. Int J Mol Sci 2021; 22:ijms22052679. [PMID: 33800945 PMCID: PMC7961483 DOI: 10.3390/ijms22052679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022] Open
Abstract
A combined Genotyping By Sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) protocol was used to identify—in parallel—genetic variation (Genomic-Wide Association Studies (GWAS) and epigenetic differences of Differentially Methylated Regions (DMR) in the genome of spermatozoa from the porcine animal model. Breeding boars with good semen quality (n = 11) and specific and well-documented differences in fertility (farrowing rate, FR) and prolificacy (litter size, LS) (n = 7) in artificial insemination programs, using combined FR and LS, were categorized as High Fertile (HF, n = 4) or Low Fertile (LF, n = 3), and boars with Unknown Fertility (UF, n = 4) were tested for eventual epigenetical similarity with those fertility-proven. We identified 165,944 Single Nucleotide Polymorphisms (SNPs) that explained 14–15% of variance among selection lines. Between HF and LF individuals (n = 7, 4 HF and 3 LF), we identified 169 SNPs with p ≤ 0.00015, which explained 58% of the variance. For the epigenetic analyses, we considered fertility and period of ejaculate collection (late-summer and mid-autumn). Approximately three times more DMRs were observed in HF than in LF boars across these periods. Interestingly, UF boars were clearly clustered with one of the other HF or LF groups. The highest differences in DMRs between HF and LF experimental groups across the pig genome were located in the chr 3, 9, 13, and 16, with most DMRs being hypermethylated in LF boars. In both HF and LF boars, DMRs were mostly hypermethylated in late-summer compared to mid-autumn. Three overlaps were detected between SNPs (p ≤ 0.0005, n = 1318) and CpG sites within DMRs. In conclusion, fertility levels in breeding males including FR and LS can be discerned using methylome analyses. The findings in this biomedical animal model ought to be applied besides sire selection for andrological diagnosis of idiopathic sub/infertility.
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Blay C, Haffray P, Bugeon J, D’Ambrosio J, Dechamp N, Collewet G, Enez F, Petit V, Cousin X, Corraze G, Phocas F, Dupont-Nivet M. Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss. Front Genet 2021; 12:639223. [PMID: 33692832 PMCID: PMC7937956 DOI: 10.3389/fgene.2021.639223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1-4% of the genetic variance. Within these regions, we identified several genes (htr1, gnpat, ephx1, bcmo1, and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits.
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Affiliation(s)
- Carole Blay
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | - Jonathan D’Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- SYSAAF, Station LPGP-INRAE, Rennes, France
| | - Nicolas Dechamp
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | | | - Xavier Cousin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
| | - Geneviève Corraze
- INRAE, University of Pau & Pays Adour, E2S UPPA, UMR 1419 NuMéA, Saint-Pée-sur-Nivelle, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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32
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Esmaeili-Fard SM, Gholizadeh M, Hafezian SH, Abdollahi-Arpanahi R. Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep. PLoS One 2021; 16:e0244408. [PMID: 33481819 PMCID: PMC7822323 DOI: 10.1371/journal.pone.0244408] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Litter size is one of the most important economic traits in sheep. Identification of gene variants that are associated with the prolificacy rate is an important step in breeding program success and profitability of the farm. So, to identify genetic mechanisms underlying the variation in litter size in Iranian Baluchi sheep, a two-step genome-wide association study (GWAS) was performed. GWAS was conducted using genotype data from 91 Baluchi sheep. Estimated breeding values (EBVs) for litter size calculated for 3848 ewes and then used as the response variable. Besides, a pathway analysis using GO and KEGG databases were applied as a complementary approach. A total of three single nucleotide polymorphisms (SNPs) associated with litter size were identified, one each on OAR2, OAR10, and OAR25. The SNP on OAR2 is located within a novel putative candidate gene, Neurotrophic receptor tyrosine kinase 2. This gene product works as a receptor which is essential for follicular assembly, early follicular growth, and oocyte survival. The SNP on OAR25 is located within RAB4A which is involved in blood vessel formation and proliferation through angiogenesis. The SNP on OAR10 was not associated with any gene in the 1Mb span. Moreover, gene-set analysis using the KEGG database identified several pathways, such as Ovarian steroidogenesis, Steroid hormone biosynthesis, Calcium signaling pathway, and Chemokine signaling. Also, pathway analysis using the GO database revealed several functional terms, such as cellular carbohydrate metabolic, biological adhesion, cell adhesion, cell junction, and cell-cell adherens junction, among others. This is the first study that reports the NTRK2 gene affecting litter size in sheep and our study of this gene functions showed that this gene could be a good candidate for further analysis.
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Affiliation(s)
- Seyed Mehdi Esmaeili-Fard
- Department of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
- * E-mail:
| | - Mohsen Gholizadeh
- Department of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | - Seyed Hasan Hafezian
- Department of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
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Luna-Nevarez G, Kelly AC, Camacho LE, Limesand SW, Reyna-Granados JR, Luna-Nevarez P. Discovery and validation of candidate SNP markers associated to heat stress response in pregnant ewes managed inside a climate-controlled chamber. Trop Anim Health Prod 2020; 52:3457-3466. [PMID: 32939704 DOI: 10.1007/s11250-020-02379-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/10/2020] [Indexed: 11/28/2022]
Abstract
Sheep production in desert environments during summer is challenging due to heat stress which reduces feed intake, growth, and fertility. Despite warm conditions, some ewes are able to maintain a normal performance suggesting the existence of genetic bases underlying heat tolerance. Our objective was to discover and validate genetic markers associated with thermo-tolerance in pregnant ewes exposed to warm environmental conditions. Using a well-defined model laboratory of heat stress in sheep, pregnant Columbia-Rambouillet crossbred ewes (n = 100) were examined. Following acclimation to the laboratory at thermo-neutral conditions, heat stress was induced in ewes by increasing the temperature-humidity index in a control environmental chamber during mid-gestation. Feed intake, water consumption, and rectal temperature were recorded daily and used to establish the heat stress tolerance index (HSTI) for each ewe. Rectal temperature was a predictor (P < 0.05) of feed intake, and the regression coefficient was used to classify the HSTI. In a subset of 24 ewes, a genome-wide association study (GWAS) was performed using the Illumina OvineSNP50 BeadChip. Single-marker analysis detected 3 intragenic SNPs associated with HSTI (P value = 10-5). Bayesian multi-marker approach discovered 26 chromosomal regions across the genome which accounted for 9.8% of the variation associated with HSTI. In an independent sheep population (n = 42), the three discovered SNPs were validated as molecular markers associated with thermo-tolerance phenotypic traits. These SNPs were located within the genes F13A1, PAM, and PRELID2. In conclusion, three SNPs appear to be novel molecular markers associated with heat stress tolerance in pregnant ewes providing new knowledge about genetic foundations of thermo-tolerance.
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Affiliation(s)
- Guillermo Luna-Nevarez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México
| | - Amy C Kelly
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Leticia E Camacho
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Sean W Limesand
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Javier R Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México
| | - Pablo Luna-Nevarez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México.
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