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Montgomery GW. Genetic regulation of ovulation rate and multiple births. Reprod Fertil Dev 2024; 36:RD24083. [PMID: 39222471 DOI: 10.1071/rd24083] [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: 06/10/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
Ovulation rate in many mammalian species is controlled to regulate the numbers of offspring and maximise reproductive success. Pathways that regulate ovulation rate still respond to genetic and environmental factors and show considerable variation within and between species. Genetic segregation, positional cloning, and association studies have discovered numerous mutations and genetic risk factors that contribute to this variation. Notable among the discoveries has been the role of mutations in bone morphogenetic protein 15 (BMP15 ), growth differentiation factor 9 (GDF9 ) and bone morphogenetic protein receptor type 1B (BMPR1B ) from the intra-ovarian signalling pathway contributing to the evidence that signalling from the oocyte is the key driver in follicle regulation rather than circulating gonadotrophin concentrations. Multiple variants in different domains of BMP15 and GDF9 result in partial or complete loss of function of the proteins providing insights into their functional roles and differential regulation contributing to species differences in ovulation rate. Early success encouraged many more studies in prolific strains of sheep, cattle and goats providing a valuable catalogue of genetic variants of large effect increasing ovulation rate and litter size. More recently, genetic association studies are beginning to identify genetic risk factors with smaller effects. Most genes implicated are from pathways with defined roles in regulation of the ovarian function. However, some genomic regions suggest regulation by novel genes. Continuing genetic and related functional studies will add further to our understanding of the detailed regulation of ovulation rate and litter size with implications for health and animal production systems.
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Affiliation(s)
- G W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
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2
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Huang Z, Wang J, Qi D, Li X, Wang J, Zhou J, Ruan Y, Laer Y, Baqian Z, Yang C. Uncovering the genetic diversity and adaptability of Butuo Black Sheep through whole-genome re-sequencing. PLoS One 2024; 19:e0303419. [PMID: 38857228 PMCID: PMC11164371 DOI: 10.1371/journal.pone.0303419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
The Butuo Black Sheep (BBS) is well-known for its ability to thrive at high altitudes, resist diseases, and produce premium-quality meat. Nonetheless, there is insufficient data regarding its genetic diversity and population-specific Single nucleotide polymorphisms (SNPs). This paper centers on the genetic diversity of (BBS). The investigation conducted a whole-genome resequencing of 33 BBS individuals to recognize distinct SNPs exclusive to BBS. The inquiry utilized bioinformatic analysis to identify and explain SNPs and pinpoint crucial mutation sites. The findings reveal that reproductive-related genes (GHR, FSHR, PGR, BMPR1B, FST, ESR1), lipid-related genes (PPARGC1A, STAT6, DGAT1, ACACA, LPL), and protein-related genes (CSN2, LALBA, CSN1S1, CSN1S2) were identified as hub genes. Functional enrichment analysis showed that genes associated with reproduction, immunity, inflammation, hypoxia, PI3K-Akt, and AMPK signaling pathways were present. This research suggests that the unique ability of BBS to adapt to low oxygen levels in the plateau environment may be owing to mutations in a variety of genes. This study provides valuable insights into the genetic makeup of BBS and its potential implications for breeding and conservation efforts. The genes and SPNs identified in this study could serve as molecular markers for BBS.
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Affiliation(s)
| | | | | | | | - Jinkang Wang
- Butuo County Agriculture and Rural Affairs Bureau, Xichang, China
| | - Jingwen Zhou
- Butuo County Forestry and Grassland Bureau, Xichang, China
| | - Yan Ruan
- Butuo County Agriculture and Rural Affairs Bureau, Xichang, China
| | - Youse Laer
- Butuo County Agriculture and Rural Affairs Bureau, Xichang, China
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3
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Zhang Z, Tang X, Li D, Tong X, Min L, Chen W, Ju X, Xu B. The Identification of RPL4 as a Hub Gene Associated with Goat Litter Size via Weighted Gene Co-Expression Network Analysis. Animals (Basel) 2024; 14:1470. [PMID: 38791687 PMCID: PMC11117213 DOI: 10.3390/ani14101470] [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: 04/12/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Reproduction in goats is a highly complex and dynamic process of life regulation, involving coordinated regulation from various aspects such as central nervous system regulation, reproductive system development, oocyte maturation, and fertilized egg development. In recent years, researchers have identified numerous genes associated with goat reproductive performance through high-throughput sequencing, single-cell sequencing, gene knockout, and other techniques. However, there is still an urgent need to explore marker genes related to goat reproductive performance. In this study, a single-cell RNA sequencing dataset of oocytes (GSE136005) was obtained from the Gene Expression Omnibus (GEO) database. Weighted Gene Co-expression Network Analysis (WGCNA) was utilized to identify modules highly correlated with goat litter size. Through gene function enrichment analysis, it was found that genes within the modules were mainly enriched in adhesive junctions, cell cycle, and other signaling pathways. Additionally, the top 30 hub genes with the highest connectivity in WGCNA were identified. Subsequently, using Protein-Protein Interaction (PPI) network analysis, the top 30 genes with the highest connectivity within the modules were identified. The intersection of hub genes, key genes in the PPI network, and differentially expressed genes (DEGs) led to the identification of the RPL4 gene as a key marker gene associated with reproductive capacity in goat oocytes. Overall, our study reveals that the RPL4 gene in oocytes holds promise as a biological marker for assessing goat litter size, deepening our understanding of the regulatory mechanisms underlying goat reproductive performance.
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Affiliation(s)
- Zhifei Zhang
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517500, China
| | - Xueying Tang
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Dagang Li
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
| | - Xiong Tong
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
| | - Li Min
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
| | - Weidong Chen
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517500, China
| | - Xianghong Ju
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Bin Xu
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
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Zhang R, Liu Y, Li W, Wang P, Liu Z, Wen Y, Chu M, Wang L. A mutation in LPAR2 activates the miR-939-5p-LPAR2-PI3K/AKT axis to regulate the proliferation and apoptosis of granulosa cells in sheep. Theriogenology 2024; 219:1-10. [PMID: 38368704 DOI: 10.1016/j.theriogenology.2024.02.010] [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: 09/13/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Lysophosphatidic acid receptor-2 (LPAR2) is a G protein-coupled receptor, which is involved in various physiological processes such as cell development, proliferation, and apoptosis, and is thought to play an important role in follicular development and reproduction. There is evidence that miRNA recognition elements (MRE) in the gene 3'UTR often contain single nucleotide polymorphisms (SNPs) that can alter the binding affinity of the target miRNA, leading to dysregulation of gene expression. In this study, we detected a SNP in LPAR2 3 'UTR (rs410670692, c.*701C > T) in 384 small-tailed Han sheep using Sequenom MassARRAY®SNP genotyping. Association analysis showed that the SNP was significantly associated with litter size. Then, the effect of LPAR2 rs410670692 mutation on gene expression in sheep hosts was studied by molecular biotechnology. The results showed that the expression of LPAR2 in the TT genotype was significantly higher than that in the CC genotype, which confirmed the existence of rs410670692, a functional SNP, in LPAR2 3'UTR. We then used bioinformatics methods and double luciferase reporter gene assay to predict and confirm LPAR2 SNP rs410670692 as the direct targeting regulatory element of miR-939-5p. Cell transfection experiments further found that SNP rs410670692 down-regulated the mRNA and protein levels of LPAR2 by influencing the binding of miR-939-5p. To understand the function and mechanism of miR-939-5p in sheep granulosa cells (GCs), we conducted cell proliferation and apoptosis experiments which showed inhibited GCs proliferation along with promoted GCs apoptosis upon overexpression of miR-939-5p. Moreover, overexpression of miR-939-5p promotes apoptosis of granulosa cells by blocking the LPAR2-dependent PI3K/Akt signaling pathway. In conclusion, these results indicate that the SNP rs410670692 of LPAR2 is related to the litter size of small-tailed cold sheep, and miR-939-5p can act as a regulatory element binding to the C mutation of rs410670692 to regulate the expression of LPAR2, affect the development of GCs, and thus indirectly affect the litter size of sheep. These studies provide evidence for the involvement of LPAR2 polymorphism in sheep reproduction and are expected to provide new insights into the molecular genetic mechanisms of litter size traits in sheep.
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Affiliation(s)
- Runan Zhang
- Key Laboratory of Livestock and Poultry Multiomics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wentao Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Peng Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ziyi Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuliang Wen
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multiomics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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5
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Li J, Gong Y, Wang X, He X, He X, Chu M, Di R. Screening of Litter-Size-Associated SNPs in NOX4, PDE11A and GHR Genes of Sheep. Animals (Basel) 2024; 14:767. [PMID: 38473152 DOI: 10.3390/ani14050767] [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: 01/02/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
In previous studies, NOX4, PDE11A and GHR genes have been screened as important candidate genes for litter size in sheep by using the GWAS method; however, neither their effects on litter size nor the loci associated with litter size have been identified. In this study, three candidate loci (c.1057-4C > T in NOX4, c.1983C > T in PDE11A and c.1618C > T in GHR) were first screened based on our previous resequencing data of 10 sheep breeds. After the three loci were genotyped using Sequenom MassARRAY technology, we carried out population genetics analysis on the three loci and performed association analysis between the polymorphism of the three loci and the litter size of sheep. The results of population genetics analysis suggested that c.1057-4C > T in NOX4 and c.1983C > T in PDE11A may be subject to natural or artificial selection. The results of association analysis indicated that litter size was significantly associated with c.1057-4C > T in NOX4 and c.1983C > T in PDE11A (p < 0.05) in Small Tail Han sheep, and there was no significant interaction effect between the two loci on the litter size. In summary, c.1057-4C > T in NOX4 and c.1983 C > T in PDE11A can be considered candidate molecular markers for improving litter size in sheep.
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Affiliation(s)
- Jiajun Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yiming Gong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xiaolong He
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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6
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Lázaro SF, Tonhati H, Oliveira HR, Silva AA, Scalez DCB, Nascimento AV, Santos DJA, Stefani G, Carvalho IS, Sandoval AF, Brito LF. Genetic parameters and genome-wide association studies for mozzarella and milk production traits, lactation length, and lactation persistency in Murrah buffaloes. J Dairy Sci 2024; 107:992-1021. [PMID: 37730179 DOI: 10.3168/jds.2023-23284] [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: 01/18/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023]
Abstract
Genetic and genomic analyses of longitudinal traits related to milk production efficiency are paramount for optimizing water buffaloes breeding schemes. Therefore, this study aimed to (1) compare single-trait random regression models under a single-step genomic BLUP setting based on alternative covariance functions (i.e., Wood, Wilmink, and Ali and Schaeffer) to describe milk (MY), fat (FY), protein (PY), and mozzarella (MZY) yields, fat-to-protein ratio (FPR), somatic cell score (SCS), lactation length (LL), and lactation persistency (LP) in Murrah dairy buffaloes (Bubalus bubalis); (2) combine the best functions for each trait under a multiple-trait framework; (3) estimate time-dependent SNP effects for all the studied longitudinal traits; and (4) identify the most likely candidate genes associated with the traits. A total of 323,140 test-day records from the first lactation of 4,588 Murrah buffaloes were made available for the study. The model included the average curve of the population nested within herd-year-season of calving, systematic effects of number of milkings per day, and age at first calving as linear and quadratic covariates, and additive genetic, permanent environment, and residual as random effects. The Wood model had the best goodness of fit based on the deviance information criterion and posterior model probabilities for all traits. Moderate heritabilities were estimated over time for most traits (0.30 ± 0.02 for MY; 0.26 ± 0.03 for FY; 0.45 ± 0.04 for PY; 0.28 ± 0.05 for MZY; 0.13 ± 0.02 for FPR; and 0.15 ± 0.03 for SCS). The heritability estimates for LP ranged from 0.38 ± 0.02 to 0.65 ± 0.03 depending on the trait definition used. Similarly, heritabilities estimated for LL ranged from 0.10 ± 0.01 to 0.14 ± 0.03. The genetic correlation estimates across days in milk (DIM) for all traits ranged from -0.06 (186-215 DIM for MY-SCS) to 0.78 (66-95 DIM for PY-MZY). The SNP effects calculated for the random regression model coefficients were used to estimate the SNP effects throughout the lactation curve (from 5 to 305 d). Numerous relevant genomic regions and candidate genes were identified for all traits, confirming their polygenic nature. The candidate genes identified contribute to a better understanding of the genetic background of milk-related traits in Murrah buffaloes and reinforce the value of incorporating genomic information in their breeding programs.
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Affiliation(s)
- Sirlene F Lázaro
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Humberto Tonhati
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Alessandra A Silva
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Daiane C B Scalez
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - André V Nascimento
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | | | - Gabriela Stefani
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Isabella S Carvalho
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Amanda F Sandoval
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
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Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
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8
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Fang X, Yang S, Chen M, Sun R, Zhao L, Gu B, Zhang J, Huang D, Zheng T, Zhao Y, Peng P, Zhao Y. Association analysis of polymorphisms at GLRB, GRIA2, and GASK1B genes with reproductive traits in Dazu Black Goats. Anim Biotechnol 2023; 34:4721-4729. [PMID: 36927330 DOI: 10.1080/10495398.2023.2187406] [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: 03/18/2023]
Abstract
Reproductive traits are essential economic traits in goats. This study aimed to analyze the relationship between single nucleotide polymorphisms (SNPs) within the genes of GLRB, GRIA2, and GASK1B, and reproductive traits (kidding traits and placental traits) in goats. We used the resequencing data of 150 Dazu Black Goats to perform correlation analysis with the average litter size. We screened thirteen SNPs loci in introns and then used the Sanger method to genotype the remaining 150 Dazu Black Goats. The results showed that a total of six SNPs were screened. Three SNPs related to litter size and live litter size (g.28985790T > G, g.28986352A > G, and g.28987976A > G); one SNP related to total cotyledon area (g.29203243G > A); two SNPs related to placental efficiency (g.30189055G > A and g.30193974C > T); one SNP associated with cotyledon support efficiency (g.30193974C > T). The qPCR results showed that GLRB, GRIA2, and GASK1B were all highly expressed in the udder, kidney, uterus, and ovary. It indicated that these three candidate genes might affect the reproductive traits, which could be used as candidate markers for reproductive traits in Dazu Black Goats. Moreover, association studies on a large scale are still needed to figure out what effect these SNPs have on reproductive traits.
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Affiliation(s)
- Xingqiang Fang
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China
| | - Songjian Yang
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China
| | - Meixi Chen
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China
| | - Ruifan Sun
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China
| | - Le Zhao
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China
| | - Bowen Gu
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China
| | - Deli Huang
- Tengda Animal Husbandry Co., Ltd., Chongqing, China
| | | | - Yuanping Zhao
- Dazu County Agriculture and Rural Committee, Chongqing, China
| | - Peng Peng
- Tengda Animal Husbandry Co., Ltd., Chongqing, China
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing, China
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Warburton CL, Costilla R, Engle BN, Moore SS, Corbet NJ, Fordyce G, McGowan MR, Burns BM, Hayes BJ. Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations. Heredity (Edinb) 2023; 131:350-360. [PMID: 37798326 PMCID: PMC10673866 DOI: 10.1038/s41437-023-00651-4] [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: 10/14/2022] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
Many of the world's agriculturally important plant and animal populations consist of hybrids of subspecies. Cattle in tropical and sub-tropical regions for example, originate from two subspecies, Bos taurus indicus (Bos indicus) and Bos taurus taurus (Bos taurus). Methods to derive the underlying genetic architecture for these two subspecies are essential to develop accurate genomic predictions in these hybrid populations. We propose a novel method to achieve this. First, we use haplotypes to assign SNP alleles to ancestral subspecies of origin in a multi-breed and multi-subspecies population. Then we use a BayesR framework to allow SNP alleles originating from the different subspecies differing effects. Applying this method in a composite population of B. indicus and B. taurus hybrids, our results show that there are underlying genomic differences between the two subspecies, and these effects are not identified in multi-breed genomic evaluations that do not account for subspecies of origin effects. The method slightly improved the accuracy of genomic prediction. More significantly, by allocating SNP alleles to ancestral subspecies of origin, we were able to identify four SNP with high posterior probabilities of inclusion that have not been previously associated with cattle fertility and were close to genes associated with fertility in other species. These results show that haplotypes can be used to trace subspecies of origin through the genome of this hybrid population and, in conjunction with our novel Bayesian analysis, subspecies SNP allele allocation can be used to increase the accuracy of QTL association mapping in genetically diverse populations.
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Affiliation(s)
- Christie L Warburton
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia.
| | - Roy Costilla
- Agresearch Limited, Ruakura Research Centre, Hamilton, 3214, New Zealand
| | - Bailey N Engle
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Nicholas J Corbet
- Formerly Central Queensland University, School of Health, Medical and Applied Sciences, Rockhampton, QLD, Australia
| | - Geoffry Fordyce
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Michael R McGowan
- The University of Queensland, School of Veterinary Science, St Lucia, QLD, Australia
| | - Brian M Burns
- Formerly Department of Agriculture and Fisheries, Rockhampton, QLD, Australia
| | - Ben J Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
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10
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Liu LL, Meng J, Ma HY, Cao H, Liu WJ. Candidate genes for litter size in Xinjiang sheep identified by Specific Locus Amplified Fragment (SLAF) sequencing. Anim Biotechnol 2023; 34:3053-3062. [PMID: 36244020 DOI: 10.1080/10495398.2022.2131561] [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: 11/01/2022]
Abstract
The aim of this study was to investigate the selection signatures at a genome-wide level in 'Pishan' sheep using Specific Locus Amplified Fragment (SLAF)-seq. Blood samples from 126 ewes were sequenced using SLAF tags, and the ovarian tissues from 8 ewes (Bashbay sheep, a single litter size group (SG group); 'Pishan' sheep, double litter size group (DG group)) were collected to detect expression levels by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Selection signature analysis was performed using global fixation index (Fst) and nucleotide diversity (π) ratio. A total of 1,192,168 high-quality SLAFs were identified. Notably, 2380 candidate regions under selection using two approaches were identified. A total of 2069 genes were identified, which were involved in dopaminergic synapses, thyroid hormone synthesis, ovarian steroidogenesis and thyroid hormone signalling pathways. Furthermore, Growth Differentiation Factor 9 (GDF9), Period Circadian Regulator 2 (PER2), Thyroid Stimulating Hormone Receptor (TSHR), and Nuclear Receptor Coactivator 1 (NCOA1) reside within these regions and pathways. The expression levels of GDF9 and PER2 genes in sheep tissue of the DG group were significantly higher than those in the SG group. These genes are interesting candidates for litter size and provide a starting point for further identification of conservation strategies for 'Pishan' sheep.
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Affiliation(s)
- Ling-Ling Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jun Meng
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hai-Yu Ma
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hang Cao
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wu-Jun Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
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11
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Wang J, Suo J, Yang R, Zhang CL, Li X, Han Z, Zhou W, Liu S, Gao Q. Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin. Front Genet 2023; 14:1281601. [PMID: 38028584 PMCID: PMC10666172 DOI: 10.3389/fgene.2023.1281601] [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: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Local sheep in the northeastern Tarim Basin can adapt to dry and low-rainfall regional environments. In this study, three local sheep breeds in the northeastern Tarim Basin, LOP (LOP) sheep, Bayinbuluke (BYK) sheep, and Kunlun (KUN, also known as the Qiemo sheep) sheep, and three introduced sheep breeds, Suffolk (SUF) sheep, Dorset (APD) sheep, and Texel (TEX) sheep, were analyzed for genetic diversity, population structure, and selective signature using the Illumina OvineSNP50K BeadChip. We found that LOP, BYK, and KUN had lower observed heterozygosity and expected heterozygosity than TEX, SUF, and ADP, which were differentiated based on geographic distribution. We performed fixation index (FST) analysis on three local sheep breeds in the northeastern Tarim Basin (LOP, BYK, and KUN) and introduced sheep breeds (TEX, SUF, and ADP) to measure genetic differentiation. Nucleotide diversity (PI) analysis was performed on single-nucleotide polymorphism (SNP) data of LOP, BYK, and KUN. A total of 493 candidate genes were obtained by taking the intersection at a threshold of 5%. Among them, SMAD2, ESR2, and HAS2 were related to reproductive traits. PCDH15, TLE4, and TFAP2B were related to growth traits. SOD1, TSHR, and DNAJB5 were related to desert environmental adaptation. Analyzing the genetic patterns of local sheep in the northeastern Tarim Basin can protect the germplasm resources of local sheep and promote the development and utilization of sheep genetic resources.
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Affiliation(s)
- Jieru Wang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Jiajia Suo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Ruizhi Yang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Cheng-Long Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Xiaopeng Li
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Zhipeng Han
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Wen Zhou
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Shudong Liu
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Qinghua Gao
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
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12
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Yang P, Wang G, Jiang S, Chen M, Zeng J, Pang Q, Du D, Zhou M. Comparative analysis of genome-wide copy number variations between Tibetan sheep and White Suffolk sheep. Anim Biotechnol 2023; 34:986-993. [PMID: 34865600 DOI: 10.1080/10495398.2021.2007937] [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: 10/19/2022]
Abstract
The DNA copy number variations (CNVs) are widely involved in affecting various kinds of biological functions, such as environmental adaptation. Tibetan sheep and White Suffolk sheep are two representative indigenous and exotic breeds raised in Sichuan, China, and both of them have many contrasting biological characteristics. In this study, we employed high-throughput sequencing approach to investigate genome-wide CNVs between the two sheep breeds. A total of 11,135 CNV regions (CNVRs) consisting of 6,488 deletions and 4,647 duplications were detected, whose length ranged from 1,599 bp to 0.56 Mb with the mean of 4,658 bp. There were 281 CNVRs segregated between Tibetan sheep and White Suffolk sheep, and 18 of them have been fixed within both breeds. Functional analyses of candidate genes within the segregating CNVRs revealed the thyroid hormone signaling pathway and CTNNB1 gene that would be responsible for differential biological characteristics of breeds, such as energy metabolism, seasonal reproduction, and litter size. Furthermore, the segregating CNVRs identified in this study were overlapped with many known quantitative trait loci that are associated with growth, testis weight, and reproductive seasonality. In conclusion, these results help us better understanding differential biological characteristics between Tibetan sheep and White Suffolk sheep.
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Affiliation(s)
- Pinggui Yang
- Institute of Plateau Animals, Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Shihai Jiang
- Institute of Plateau Animals, Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Minghua Chen
- Institute of Plateau Animals, Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Jie Zeng
- Institute of Plateau Animals, Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Qian Pang
- Institute of Plateau Animals, Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Dan Du
- Institute of Plateau Animals, Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Mingliang Zhou
- Institute of Plateau Animals, Sichuan Academy of Grassland Sciences, Chengdu, China
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13
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Fang X, Gu B, Chen M, Sun R, Zhang J, Zhao L, Zhao Y. Genome-Wide Association Study of the Reproductive Traits of the Dazu Black Goat ( Capra hircus) Using Whole-Genome Resequencing. Genes (Basel) 2023; 14:1960. [PMID: 37895309 PMCID: PMC10606515 DOI: 10.3390/genes14101960] [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: 09/15/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Reproductive traits are the basic economic traits of goats and important indicators in goat breeding. In this study, Dazu black goats (DBGs; n = 150), an important Chinese local goat breed with excellent reproductive performance, were used to screen for important variation loci and genes of reproductive traits. Through genome-wide association studies (GWAS), 18 SNPs were found to be associated with kidding traits (average litter size, average litter size in the first three parity, and average litter size in the first six parity), and 10 SNPs were associated with udder traits (udder depth, teat diameter, teat length, and supernumerary teat). After gene annotation of the associated SNPs and in combination with relevant references, the candidate genes, namely ATP1A1, LRRC4C, SPCS2, XRRA1, CELF4, NTM, TMEM45B, ATE1, and FGFR2, were associated with udder traits, while the ENSCHIG00000017110, SLC9A8, GLRB, GRIA2, GASK1B, and ENSCHIG00000026285 genes were associated with litter size. These SNPs and candidate genes can provide useful biological information for improvement of the reproductive traits of goats.
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Affiliation(s)
- Xingqiang Fang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (X.F.); (B.G.); (M.C.); (R.S.); (J.Z.); (L.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Bowen Gu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (X.F.); (B.G.); (M.C.); (R.S.); (J.Z.); (L.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Meixi Chen
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (X.F.); (B.G.); (M.C.); (R.S.); (J.Z.); (L.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Ruifan Sun
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (X.F.); (B.G.); (M.C.); (R.S.); (J.Z.); (L.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (X.F.); (B.G.); (M.C.); (R.S.); (J.Z.); (L.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Le Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (X.F.); (B.G.); (M.C.); (R.S.); (J.Z.); (L.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (X.F.); (B.G.); (M.C.); (R.S.); (J.Z.); (L.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China
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14
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Zhou F, Quan J, Ruan D, Qiu Y, Ding R, Xu C, Ye Y, Cai G, Liu L, Zhang Z, Yang J, Wu Z, Zheng E. Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS. Animals (Basel) 2023; 13:3243. [PMID: 37893967 PMCID: PMC10603759 DOI: 10.3390/ani13203243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/08/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic architecture of tenderloin weight (TLNW) and rib weight (RIBW)-important components of pig carcass economic value-remain unknown. In this study, we conducted genome-wide association studies (GWAS) for TLNW and RIBW traits in a population of 431 Duroc × Landrace × Yorkshire (DLY) pigs. In our study, the most significant single nucleotide polymorphism (SNP) associated with TLNW was identified as ASGA0085853 (3.28 Mb) on Sus scrofa chromosome 12 (SSC12), while for RIBW, it was Affx-1115046258 (172.45 Mb) on SSC13. Through haplotype block analysis, we discovered a novel quantitative trait locus (QTL) associated with TLNW, spanning a 5 kb region on SSC12, and a novel RIBW-associated QTL spanning 1.42 Mb on SSC13. Furthermore, we hypothesized that three candidate genes, TIMP2 and EML1, and SMN1, are associated with TLNW and RIBW, respectively. Our research not only addresses the knowledge gap regarding TLNW, but also serves as a valuable reference for studying RIBW. The identified SNP loci strongly associated with TLNW and RIBW may prove useful for marker-assisted selection in pig breeding programs.
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Affiliation(s)
- Fuchen Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Yong Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Zhongxin Breeding Technology Co., Ltd., Guangzhou 510642, China
| | - Langqing Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Zebin Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Zhongxin Breeding Technology Co., Ltd., Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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15
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Yang F, Liu Y, Wang P, Wang X, Chu M, Wang P. Mutation of the ETS1 3'UTR interacts with miR-216a-3p to regulate granulosa cell apoptosis in sheep. Theriogenology 2023; 210:133-142. [PMID: 37499371 DOI: 10.1016/j.theriogenology.2023.07.025] [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: 06/08/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 07/29/2023]
Abstract
ETS1, an important member of the ETS transcription factor family, is involved in a variety of physiological processes in living organisms, such as cell development, differentiation, proliferation and apoptosis, and is thought to be associated with embryonic development and reproduction. However, the polymorphism of ETS1 has been rarely studied, and its potential impact on the formation of reproductive traits in sheep remains unclear. Here, we first analyzed polymorphisms of ETS1 in a population of 382 small-tailed Han sheep with a lambing number record using the Kompetitive Allele Specific PCR (KASP) technique. The results showed the presence of a SNP locus rs161611767 (T > C) in the 3'UTR of ETS1. The association analysis showed the lambing number of first, second and third parity in the individuals with the CC genotype (2.51 ± 0.108, 2.51 ± 0.179, 1.27 ± 0.196) was higher than that of individuals with the TT genotype (1.79 ± 0.086, 1.56 ± 0.102, 0.56 ± 0.100) (P < 0.05). Then, molecular biotechnologies were used to investigate the effects of the EST1 rs161611767 mutant locus on host gene expression in sheep and the underlying mechanism of its effect on sheep reproduction. The RT‒qPCR results showed that the expression of ETS1 was higher in individuals with the CC genotype than in those with the TT genotype (P < 0.05). The dual luciferase reporter assay showed that the luciferase activity of ETS1 in sheep with the TT genotype was decreased compared to CC genotype (P < 0.05), confirming the existence of EST1 rs161611767 in the 3'UTR as a functional SNP. Given that the 3'UTR is an important regulatory region of gene transcription and translation, we performed bioinformatics prediction and confirmed that the SNP rs161611767 of ETS1 was a direct functional target of miR-216a-3p using dual luciferase activity assay, and the binding capacity of allele T was stronger than that of allele C. Subsequently, the cell transfection results showed that miR-216a-3p suppressed the endogenous expression of ETS1 in sheep primary granulosa cells (GCs). Finally, CCK-8, EdU, WB detection of marker proteins and flow cytometry were used to detect the effects of miR-216a-3p on GCs viability and proliferation/apoptosis, respectively. The results showed that miR-216a-3p inhibited the proliferation of GCs while promoting apoptosis of GCs. In conclusion, these results demonstrate that the SNP rs161611767 of ETS1 is associated with lambing number in small-tailed Han sheep, and miR-216a-3p can act as a regulatory element binding to the T mutation in rs161611767 to regulate ETS1 expression and affect GCs development, which may indirectly affect the number of lambs in sheep. These studies provide evidence for the involvement of ETS1 polymorphisms in sheep reproduction and are expected to provide new insights to elucidate the molecular genetic mechanisms of lambing traits in sheep.
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Affiliation(s)
- Fan Yang
- College of Bioengineering, Chongqing University, Chongqing, 400044, China; State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Peng Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Pingqing Wang
- College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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16
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Dong J, Jiang X, Liu N, Li H, Zhao J, He J, Gao X. Identification and analysis of differentially expressed microRNAs in endometrium to explore the regulation of sheep fecundity. BMC Genomics 2023; 24:600. [PMID: 37814208 PMCID: PMC10563241 DOI: 10.1186/s12864-023-09681-y] [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: 06/26/2023] [Accepted: 09/15/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) play an important regulatory role in mammalian reproduction. Currently, most studies are primarily concentrated on ovarian miRNAs, ignoring the influence of endometrial miRNAs on the fecundity of female sheep. To uncover potential regulators of sheep fecundity, RNA-seq was used to comparatively analyze miRNA expression profiles of endometrium between high prolificacy sheep (HP, litter size = 3) and low prolificacy sheep (LP, litter size = 1) with FecB genotype. RESULTS Firstly, genomic features of miRNAs from endometrium were analyzed. Furthermore, 58 differentially expressed (DE) miRNAs were found in the endometrium of Hu sheep with different litter size. A co-expression network of DE miRNAs and target genes has been constructed, and hub genes related litter size are included, such as DE miRNA unconservative_NC_019472.2_1229533 and unconservative_NC_019481.2_1637827 target to estrogen receptor α (ESR1) and unconservative_NC_019481.2_1637827 targets to transcription factor 7 (TCF7). Moreover, functional annotation analysis showed that the target genes (NRCAM and NEGR1) of the DE miRNAs were significantly enriched in cell adhesion molecules (CAMs) signaling pathway, which was related to uterine receptivity. CONCLUSION Taken together, this study provides a new valuable resource for understanding the molecular mechanisms underlying Hu sheep prolificacy.
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Affiliation(s)
- Jihong Dong
- College of Animal Science and Technology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong, China
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xuecheng Jiang
- College of Animal Science and Technology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong, China
| | - Nan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong, China
| | - Hegang Li
- College of Animal Science and Technology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong, China
| | - Jinshan Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong, China
| | - Jianning He
- College of Animal Science and Technology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong, China.
| | - Xiaoxiao Gao
- College of Animal Science and Technology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong, China.
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17
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Tsartsianidou V, Pavlidis A, Tosiou E, Arsenos G, Banos G, Triantafyllidis A. Novel genomic markers and genes related to reproduction in prolific Chios dairy sheep: a genome-wide association study. Animal 2023; 17:100723. [PMID: 36801549 DOI: 10.1016/j.animal.2023.100723] [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: 11/01/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 02/07/2023] Open
Abstract
Genetic architecture of sheep reproduction is increasingly gaining scientific interest due to the major impact on sheep production systems. In the present study, we conducted pedigree-based analyses and genome-wide association studies using the Illumina Ovine SNP50K BeadChip to explore the genetic mechanisms underlying the reproduction of the highly prolific Chios dairy sheep. First lambing age, total prolificacy and maternal lamb survival were selected as representative reproductive traits and estimated as significantly heritable (h2 = 0.07-0.21) with no evident genetic antagonism among traits. We identified novel genome-wide and suggestive significant single-nucleotide polymorphisms (SNPs) on chromosomes 2 and 12 associated with age at first lambing. The new variants detected on chromosome 2 span a region of 357.79 kb with high pairwise linkage disequilibrium estimates (r2 = 0.8-0.9). Functional annotation analysis revealed candidate genes, such as the collagen-type genes and the Myostatin gene, that participate in osteogenesis, myogenesis, skeletal and muscle mass development resembling the functionality of major genes affecting the ovulation rate and prolificacy. Additional functional enrichment analysis associated the collagen-type genes with multiple uterine-related disfunctions, such as cervical insufficiency, uterine prolapse and abnormalities of the uterine cervix. Several genes (e.g., KAZN, PRDM2, PDPN, LRRC28) localised close to the SNP marker on chromosome 12 were grouped in annotation enrichment clusters majorly involved in developmental and biosynthetic pathways, apoptosis, and nucleic acid-templated transcription. Our findings may further contribute to unravel the genomic regions that are important for sheep reproduction and could be incorporated into future selective breeding programmes.
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Affiliation(s)
- V Tsartsianidou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 57001 Thessaloniki, Greece.
| | - A Pavlidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - E Tosiou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - G Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - G Banos
- Scotland's Rural College (SRUC), Easter Bush, Midlothian EH25 9RG, UK
| | - A Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 57001 Thessaloniki, Greece
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18
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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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19
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Sánchez-Ramos R, Trujano-Chavez MZ, Gallegos-Sánchez J, Becerril-Pérez CM, Cadena-Villegas S, Cortez-Romero C. Detection of Candidate Genes Associated with Fecundity through Genome-Wide Selection Signatures of Katahdin Ewes. Animals (Basel) 2023; 13:ani13020272. [PMID: 36670812 PMCID: PMC9854690 DOI: 10.3390/ani13020272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
One of the strategies to genetically improve reproductive traits, despite their low inheritability, has been the identification of candidate genes. Therefore, the objective of this study was to detect candidate genes associated with fecundity through the fixation index (FST) and runs of homozygosity (ROH) of selection signatures in Katahdin ewes. Productive and reproductive records from three years were used and the genotypes (OvineSNP50K) of 48 Katahdin ewes. Two groups of ewes were identified to carry out the genetic comparison: with high fecundity (1.3 ± 0.03) and with low fecundity (1.1 ± 0.06). This study shows for the first time evidence of the influence of the CNOT11, GLUD1, GRID1, MAPK8, and CCL28 genes in the fecundity of Katahdin ewes; in addition, new candidate genes were detected for fecundity that were not reported previously in ewes but that were detected for other species: ANK2 (sow), ARHGAP22 (cow and buffalo cow), GHITM (cow), HERC6 (cow), DPF2 (cow), and TRNAC-GCA (buffalo cow, bull). These new candidate genes in ewes seem to have a high expression in reproduction. Therefore, future studies are needed focused on describing the physiological basis of changes in the reproductive behavior influenced by these genes.
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Affiliation(s)
- Reyna Sánchez-Ramos
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | | | - Jaime Gallegos-Sánchez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | - Carlos Miguel Becerril-Pérez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Agroecosistemas Tropicales, Colegio de Postgraduados, Campus Veracruz, Carretera Xalapa-Veracruz Km. 88.5, Manlio Favio Altamirano, Veracruz 91690, Mexico
| | - Said Cadena-Villegas
- Producción Agroalimentaria en Trópico, Colegio de Postgraduados, Campus Tabasco, Periférico Carlos A. Molina, Ranchería Rio Seco y Montaña, Heroica Cárdenas 86500, Mexico
| | - César Cortez-Romero
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Innovación en Manejo de Recursos Naturales, Colegio de Postgraduados, Campus San Luis Potosí, Agustín de Iturbide No. 73, Salinas de Hidalgo, San Luis Potosí 78622, Mexico
- Correspondence: ; Tel.: +52-5959-520-200 (ext. 4000)
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20
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Xiong J, Bao J, Hu W, Shang M, Zhang L. Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat. Front Genet 2023; 13:1044017. [PMID: 36685859 PMCID: PMC9852865 DOI: 10.3389/fgene.2022.1044017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.
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21
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Al-Thuwaini TM, Al-Shuhaib MBS, Kadhem AF, Alkhammas AH. A Missense p.Q>R234 Mutation in the Osteopontin Gene Is Associated With the Prolificacy of Iraqi Awassi Ewes. Bioinform Biol Insights 2023; 17:11779322231172848. [PMID: 37197213 PMCID: PMC10184200 DOI: 10.1177/11779322231172848] [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: 07/13/2022] [Accepted: 04/08/2023] [Indexed: 05/19/2023] Open
Abstract
One of the most valuable traits in production and breeding is a sheep's prolificacy which is influenced by several genes, one of which is the osteopontin (OPN) gene. Thus, this study aimed to determine the effect of genetic variation within the OPN gene on Awassi ewe prolificacy. Genomic DNA was extracted from 123 single-progeny ewes and 109 twin ewes. Polymerase chain reaction (PCR) was used to amplify 4 sequence fragments (289, 275, 338, and 372 bp), representing exons 4, 5, 6, and 7 of the OPN gene. A 372 bp amplicon was identified with 3 different genotypes: TT, TC, and CC. Sequence analysis revealed a novel mutation in TC genotypes p.Q>R234. Statistical analysis revealed that the single nucleotide polymorphism (SNP) p.Q>R234 was associated with prolificacy. Ewes carrying the p.Q>R234 SNP had significantly (P ⩽ .01) lower litter sizes, twinning rates, and lambing rates, and more days to lambing than those with the TC and TT genotypes. The p.Q>R234 SNP was confirmed to be responsible for lower litter size through logistic regression analysis. From these results, we can conclude that the missense variant p.Q>R234 adversely affects the traits of interest and shows that the p.Q>R234 SNP negatively influences the prolificacy of Awassi sheep. Based on this study, it is evident that ewes in this population carrying the p.Q>R234 SNP have a lower litter size and are less prolific.
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Affiliation(s)
- Tahreer M Al-Thuwaini
- Tahreer M Al-Thuwaini, Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq. Emails: ,
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22
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Expression and Polymorphisms of SMAD1, SMAD2 and SMAD3 Genes and Their Association with Litter Size in Tibetan Sheep ( Ovis aries). Genes (Basel) 2022; 13:genes13122307. [PMID: 36553573 PMCID: PMC9777977 DOI: 10.3390/genes13122307] [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: 10/17/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
SMAD1, SMAD2, and SMAD3 are important transcription factors downstream of the TGF-β/SMAD signaling pathway that mediates several physiological processes. In the current study, we used cloning sequencing, RT-qPCR, bioinformatics methods and iMLDR technology to clone the coding region of Tibetan sheep genes, analyze the protein structure and detect the tissue expression characteristics of Tibetan sheep genes, and detect the polymorphisms of 433 Tibetan sheep and analyze their correlation with litter size. The results showed that the ORFs of the SMAD1, SMAD2 and SMAD3 genes were 1398 bp, 1404 bp and 1278 bp, respectively, and encoded 465, 467 and 425 amino acids, respectively. The SMAD1, SMAD2, and SMAD3 proteins were all unstable hydrophilic mixed proteins. SMAD1, SMAD2 and SMAD3 were widely expressed in Tibetan sheep tissues, and all were highly expressed in the uterus, spleen, ovary and lung tissues. Litter sizes of the genotype CC in the SMAD1 gene g.10729C>T locus were significantly higher than that of CT (p < 0.05). In the SMAD3 gene g.21447C>T locus, the genotype TT individuals showed a higher litter size than the CC and CT genotype individuals (p < 0.05). These results preliminarily demonstrated that SMAD1, SMAD2 and SMAD3 were the major candidate genes that affected litter size traits in Tibetan sheep and could be used as a molecular genetic marker for early auxiliary selection for improving reproductive traits during sheep breeding.
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23
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Kang Y, Bi Y, Tang Q, Xu H, Lan X, Zhang Q, Pan C. A 7-nt nucleotide sequence variant within the sheep KDM3B gene affects female reproduction traits. Anim Biotechnol 2022; 33:1661-1667. [PMID: 34081570 DOI: 10.1080/10495398.2021.1929270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lysine demethylase 3B (KDM3B) gene is a histone demethylase, demonstrating specific demethylation of the histone H3 lysine 9. It was detected as a sheep reproductive candidate gene by genome-wide scans, and related studies also showed its significance in female reproductive process. However, rare study researched its polymorphism. Herein, we hypothesized that the polymorphisms of KDM3B gene were associated with sheep reproduction traits. A 7-nt nucleotide sequence variant (rs1088697156) within KDM3B gene was identified in a total of 888 individuals, including the Australian White (AUW) sheep and Lanzhou Fat-tailed (LFT) sheep. II (insertion/insertion) and ID (insertion/deletion) genotypes of 7-nt variant were detected, which were at Hardy-Weinberg equilibrium (HWE) in detected breeds. Association analysis illustrated the 7-nt variant was significantly associated with the litter size, duration of pregnancy, live lamb number, live lamb rate, stillbirth number, stillbirth rate of average and different parity (P < 0.05) in AUW sheep. Moreover, 'ID' was the dominant genotype with excellent consistency in reproductive traits. It is instrumental to select individuals with ID genotype for improving the sheep reproduction traits. These findings suggest that the 7-nt variant within KDM3B gene can be used as a candidate marker of reproduction traits for sheep breeding improvement by marker-assisted selection.
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Affiliation(s)
- Yuxin Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yi Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qi Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China.,Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd, Tianjin, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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24
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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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Identification of Candidate Genes for Twinning Births in Dezhou Donkeys by Detecting Signatures of Selection in Genomic Data. Genes (Basel) 2022; 13:genes13101902. [PMID: 36292787 PMCID: PMC9601833 DOI: 10.3390/genes13101902] [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: 09/09/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Twinning trait in donkeys is an important manifestation of high fecundity, but few reports are available elucidating its genetic mechanism. To explore the genetic mechanism underlying the twin colt trait in Dezhou donkeys, DNA from 21 female Dezhou donkeys that had birthed single or twin colts were collected for whole-genome resequencing. FST, θπ and Tajima’s D were used to detect the selective sweeps between single and twin colt fecundity in the Dezhou donkey groups. Another set of 20 female Dezhou donkeys with single or multiple follicles during estrus were selected to compare concentrations of reproductive hormone including follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2) and progesterone (P4). Four candidate genes including ENO2, PTPN11, SOD2 and CD44 were identified in the present study. The CD44 gene had the highest FST value, and ENO2, PTPN11 and SOD2 were screened by two joint analyses (FST and θπ, θπ and Tajima’s D). There was no significant difference in the LH, FSH and P4 levels between the two groups (p > 0.05); however, the serum E2 content in the multi-follicle group was significantly higher than that in the single-follicle group (p < 0.05). The identified candidate genes may provide new insights into the genetic mechanism of donkey prolificacy and may be useful targets for further research on high reproductive efficiency.
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26
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Giro T, Ilina L, Kulikovsky A, Ziruk I, Giro A. Molecular genetic studies of microbiocenosis and microstructure of jejunum wall in young rams grown on biofortified feed additives. FOODS AND RAW MATERIALS 2022. [DOI: 10.21603/2308-4057-2022-2-541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The research featured the effect of a diet fortified with essential microelements on the ruminal microbiota of young rams. Ruminal microbiota is largely responsible for feed digestibility and body functioning of cattle.
The study involved the contents of the rumens and jejuna of seven-month-old rams of the Edilbaev breed, which were subjected to a biofortified diet. The diet included the Russian feed additives Yoddar-Zn and DAFS-25 represent a protein-carbohydrate complex with plant silicon. The microflora of the digestive tract was tested using the molecular genetic method of terminal restriction fragment length polymorphism (T-RFLP) sequestration. The microstructural studies of the jejunum samples exploited light microscopy.
The feed additives increased the population of cellulolytic and lactate-fermenting bacteria, as well as the Prevotella sp. microbiome and bifidobacteria in the rumen samples. The data obtained revealed the effect of essential microelements on the taxonomic pattern of microorganisms and the microflora profile. The research revealed the ratio of normal, opportunistic, pathogenic, nonculturable, and transit microflora. The jejunum wall samples obtained from the experimental group that fed on Yoddar-Zn and DAFS-25 had a more distinct micropicture of mucous membrane. Their rumen microflora balance had fewer pathogenic and opportunistic microorganisms, which was also confirmed by the jejunum morphology.
The feed additives DAFS-25 and Yoddar-Zn proved beneficial for ram diet and inhibited the negative effect of pathogenic treponemas on the rumen. The additives improved digestion, absorption, and assimilation of food nutrients, as well as increased the livestock yield.
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Affiliation(s)
| | | | | | - Irina Ziruk
- N.I. Vavilov Saratov State Agrarian University
| | - Anna Giro
- N.I. Vavilov Saratov State Agrarian University
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Wijayanti D, Zhang S, Yang Y, Bai Y, Akhatayeva Z, Pan C, Zhu H, Qu L, Lan X. Goat SMAD family member 1 (SMAD1): mRNA expression, genetic variants, and their associations with litter size. Theriogenology 2022; 193:11-19. [PMID: 36116245 DOI: 10.1016/j.theriogenology.2022.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 12/20/2022]
Abstract
SMAD family member 1 (SMAD1) is phosphorylated and activated by the BMP receptors, which help regulate ovulation rate, cell growth, apoptosis, and development. Previously, the genome-wide association study revealed that it has been associated with fecundity in sheep. However, its effect on litter size has not been investigated in goats. Therefore, this study aimed to determine the level of SMAD1 mRNA expression in various tissues and to identify its polymorphisms and their association with litter size in Shaanbei white cashmere goat (SBWC). As a result, RT-qPCR analysis showed that SMAD1 was expressed in various tissues in female SBWC goats, including the ovary (P < 0.05). Importantly, the mRNA expression level in the ovaries of mothers of multi-lambs had a higher level than the mothers of single lambs (P < 0.05). Moreover, two InDels (18-bp and 7-bp) in intron 1 of SMAD1 were polymorphic among ten potential loci. Both 18-bp and 7-bp InDels were significantly correlated with litter size (P = 0.014) and (P = 0.0001), respectively. As shown by the chi-squared test, genotypic distributions of 18-bp and 7-bp were significantly distinct between single-lamb (P = 0.02) and multi-lamb mothers (P = 0.002). Our findings confirm that two InDels in SMAD1 were significantly associated with litter size and suggest that they could be used to improve fertility traits in goat breeding strategies.
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Affiliation(s)
- Dwi Wijayanti
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China; Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, West Java, 46115, Indonesia.
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yuta Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yangyang Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China.
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China.
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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28
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Sadeghi M, Bahrami A, Hasankhani A, Kioumarsi H, Nouralizadeh R, Abdulkareem SA, Ghafouri F, Barkema HW. lncRNA-miRNA-mRNA ceRNA Network Involved in Sheep Prolificacy: An Integrated Approach. Genes (Basel) 2022; 13:genes13081295. [PMID: 35893032 PMCID: PMC9332185 DOI: 10.3390/genes13081295] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding the molecular pattern of fertility is considered as an important step in breeding of different species, and despite the high importance of the fertility, little success has been achieved in dissecting the interactome basis of sheep fertility. However, the complex mechanisms associated with prolificacy in sheep have not been fully understood. Therefore, this study aimed to use competitive endogenous RNA (ceRNA) networks to evaluate this trait to better understand the molecular mechanisms responsible for fertility. A competitive endogenous RNA (ceRNA) network of the corpus luteum was constructed between Romanov and Baluchi sheep breeds with either good or poor genetic merit for prolificacy using whole-transcriptome analysis. First, the main list of lncRNAs, miRNAs, and mRNA related to the corpus luteum that alter with the breed were extracted, then miRNA−mRNA and lncRNA−mRNA interactions were predicted, and the ceRNA network was constructed by integrating these interactions with the other gene regulatory networks and the protein−protein interaction (PPI). A total of 264 mRNAs, 14 lncRNAs, and 34 miRNAs were identified by combining the GO and KEGG enrichment analyses. In total, 44, 7, 7, and 6 mRNAs, lncRNAs, miRNAs, and crucial modules, respectively, were disclosed through clustering for the corpus luteum ceRNA network. All these RNAs involved in biological processes, namely proteolysis, actin cytoskeleton organization, immune system process, cell adhesion, cell differentiation, and lipid metabolic process, have an overexpression pattern (Padj < 0.01). This study increases our understanding of the contribution of different breed transcriptomes to phenotypic fertility differences and constructed a ceRNA network in sheep (Ovis aries) to provide insights into further research on the molecular mechanism and identify new biomarkers for genetic improvement.
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Affiliation(s)
- Masoumeh Sadeghi
- Environmental Health, Zahedan University of Medical Sciences, Zahedan 98, Iran;
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, 80333 Munich, Germany
- Correspondence: (A.B.); (R.N.); Tel.: +98-9199300065 (A.B.)
| | - Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
| | - Hamed Kioumarsi
- Department of Animal Science Research, Gilan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Rasht 43, Iran;
| | - Reza Nouralizadeh
- Department of Food and Drug Control, Faculty of Pharmacy, Jundishapour University of Medical Sciences, Ahvaz 63, Iran
- Correspondence: (A.B.); (R.N.); Tel.: +98-9199300065 (A.B.)
| | - Sarah Ali Abdulkareem
- Department of Computer Science, Al-Turath University College, Al Mansour, Baghdad 10011, Iraq;
| | - Farzad Ghafouri
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N4Z6, Canada;
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29
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Liu Y, Zhou Z, He X, Jiang Y, Ouyang Y, Hong Q, Chu M. Differentially Expressed Circular RNA Profile Signatures Identified in Prolificacy Trait of Yunshang Black Goat Ovary at Estrus Cycle. Front Physiol 2022; 13:820459. [PMID: 35492611 PMCID: PMC9049588 DOI: 10.3389/fphys.2022.820459] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/10/2022] [Indexed: 01/10/2023] Open
Abstract
CircRNAs acting as miRNA sponges play important roles in the growth process of animal individuals. The prolificacy trait of goats is involved in many pathways, however, the variation of circRNA expression profiles in the different phases of the estrus cycle at high and low fecundity groups is still unknown. Here, we analyzed the circRNA profiles of ovarian tissues among high and low fecundity groups in the follicular phase (HF vs LF), high and low fecundity groups in the luteal phase (HL vs LL), and high and low fecundity in the whole estrus cycle (HF vs HL and LF vs LL) using RNA-seq. A total of 283 (114 upregulated and 169 downregulated), 559 (299 upregulated and 260 downregulated), 449 (254 upregulated and 195 downregulated), and 314 (210 upregulated and 104 downregulated) differentially expressed (DE) circRNAs were screened in HF vs LF, HF vs HL, HL vs LL, and LF vs LL groups, respectively. Enrichment analysis suggested that the targeting of DE circRNAs was mainly enriched in oocyte meiosis, the GnRH signaling pathway, and estrogen signaling pathway. After integrating our previous study of miRNA-seq, there were 56 miRNAs that could target to 192 DE circRNAs, including the miR-133 family (including miR-133a-3p and miR-133b), miR-129-3p, and miR-21, which also had important influence on the prolificacy trait of goats. Then, 18 circRNAs with coding potential were obtained by four software predictions, and 9 circRNAs were validated by RT-qPCR. Together, circRNAs play a key role in the prolificacy trait and the transformation of the follicular phase to the luteal phase in the estrus cycle of goats.
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Affiliation(s)
- Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Zuyang Zhou
- 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, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yina Ouyang
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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30
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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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31
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Xu SS, Gao L, Shen M, Lyu F. Whole-Genome Selective Scans Detect Genes Associated With Important Phenotypic Traits in Sheep (Ovis aries ). Front Genet 2021; 12:738879. [PMID: 34868210 PMCID: PMC8637624 DOI: 10.3389/fgene.2021.738879] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Sheep (Ovis aries) is one of the important livestock with diverse phenotypic traits. However, little is known about the molecular mechanism of diverse phenotypic traits in domestic sheep. Using the genome-wide high-density SNP data (600K) in 253 samples from 13 populations, we conducted the tests of selective sweeps (i.e., pairwise FST and XP-CLR) associated with several important phenotypic traits (e.g., tail types, horn morphology, prolificacy, coat pigmentation, ear size, milk production, meat production, body size and wool fineness). We identified strong selective signatures in previously reported (e.g., T, RXFP2, BMPR1B, TYRP1, MSRB3, TF, CEBPA, GPR21 and HOXC8) and novel genes associated with the traits, such as CERS6, BTG1, RYR3, SLC6A4, NNAT and OGT for fat deposition in the tails, FOXO4 for fertility, PTCH1 and EMX2 for ear size, and RMI1 and SCD5 for body size. Further gene annotation analysis showed that these genes were identified to be the most probable genes accounting for the diverse phenotypic traits. Our results provide novel insights into the genetic mechanisms underlying the traits and also new genetic markers for genetic improvement in sheep and other livestock.
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Affiliation(s)
- Song-Song Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Shenzhen Branch, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lei Gao
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Min Shen
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Fenghua Lyu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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32
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33
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The statistical power of genome-wide association studies for threshold traits with different frequencies of causal variants. Genetica 2021; 150:51-57. [PMID: 34705138 DOI: 10.1007/s10709-021-00140-8] [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: 06/14/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022]
Abstract
This study aimed to investigate the effects of incidence rate, heritability, and polygenic variance on the statistical power of genome-wide association studies (GWAS) for threshold traits. Different incidence rates of threshold trait (1, 3, 5, 10, 25, 40, 50, 60, 75 and 90%), heritability (10 and 25%), and polygenic variance ratio (0 and 25%) were simulated separately for common (MAF ≥ 0.05), low-frequency (0.05 > MAF ≥ 0.01), and rare (MAF < 0.01) variants. Association studies were performed by logistic and linear mixed models. The highest statistical powers were observed in common and low-frequency variants with an incidence of 25-50% and 10-40%, respectively, but for rare variants, the highest statistical power was observed at low incidence. For all causal variant frequencies, the estimated heritability decline with an increase in incidence rate. We found high statistical power for traits with high heritability. In contrast, those with a high polygenic variance ratio have lower statistical power to detect common causal variants using a linear mixed model. These results demonstrate that the incidence rate of threshold traits, heritability, and polygenic variance may affect the statistical power of GWAS. Therefore, it is recommended that the effect of incidence rate, heritability, and polygenic variance be considered in designing GWAS for threshold traits.
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34
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Zhang S, Gao X, Jiang Y, Shen Y, Xie H, Pan P, Huang Y, Wei Y, Jiang Q. Population validation of reproductive gene mutation loci and association with the litter size in Nubian goat. Arch Anim Breed 2021; 64:375-386. [PMID: 34584939 PMCID: PMC8461558 DOI: 10.5194/aab-64-375-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/20/2021] [Indexed: 01/05/2023] Open
Abstract
Litter size is an important component trait of doe
reproduction. By improving it, production efficiency and economic benefits
can be significantly provided. Genetic marker-assisted selection (MAS) based
on proven molecular indicators could enhance the efficacy of goat selection,
as well as litter size trait. Many molecular markers have been identified
that they can be used to improve litter size in different goat breeds.
However, the presence and value of these markers vary among goat breeds. In
the present study, we used the reported loci on other breeds of goat as
candidate loci to detect whether these loci appear in this Nubian goat
population; then we proceed to genotype and detect surrounding loci (50 bp)
by multiplex PCR and sequencing technology. As a result, 69
mutations (59 SNPs and 10 indels) were screened out from 23 candidate genes
in Nubian goat population, 12 loci were significantly associated with
the litter size of first-parity individuals; 5 loci were significantly
associated with the litter size of second-parity individuals; 3 loci
were significantly associated with the litter size of third-parity
individuals. In addition, five loci were significantly associated with the
average litter size. The additive effect value of KITLG: g.18047318 G>A in first parity, KITLG: g.18152042G>A in third parity, KISS-1: g.1341674
C>G in first parity, and GHR: g.32134187G>A in
second parity exceed more than 0.40, and the preponderant alleles are G, C,
A and G, respectively. Further, linkage disequilibrium analysis of 21 mutation
loci shows that 3 haplotype blocks are formed, and the litter size of
combination type AACC in KISS-1 gene and AAGG in KITLG gene are significantly lower
than that of other combinations genotype in first parity (P<0.05). These findings
can provide effective candidate DNA markers for selecting superior
individuals in Nubian goat breeding.
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Affiliation(s)
- Sanbao Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Xiaotong Gao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yuhang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yujian Shen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Hongyue Xie
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Peng Pan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yanna Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yingming Wei
- Institute for New Rural Development, Guangxi University, Nanning 530004, Guangxi, China
| | - Qinyang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
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35
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Tao L, Wang X, Zhong Y, Liu Q, Xia Q, Chen S, He X, Di R, Chu M. Combined approaches identify known and novel genes associated with sheep litter size and non-seasonal breeding. Anim Genet 2021; 52:857-867. [PMID: 34494299 DOI: 10.1111/age.13138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 01/29/2023]
Abstract
Improvement of ewe reproduction is considerable by appropriately increasing litter size and sustaining non-seasonal breeding. However, their genetic makeups have not been entirely elucidated. Genome-wide analyses of 821 individuals were performed by combining three genomic approaches (genome-wide association study, XP-nSL, and runs of homozygosity). Consequently, 35 candidate genes including three domestication genes (TSHR, GTF2A1, and KITLG) were identified. Other than the FecB mutation at BMPR1B, we described a significant association of a missense mutation rs406686139 at seasonal lambing-associated TSHR gene with litter size. Some promising novel genes may be relevant for sheep reproduction by multitude biological processes, such as FETUB functioning in fertilization, HNRNPA1 in oogenesis, DCUN1D1 in spermatogenesis, and HRG in fertility outcome. The present study suggests that improvement of ewe reproduction is attributed to selective breeding, and casts light on the genetic basis and improvement of sheep reproduction.
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Affiliation(s)
- Lin Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangyu 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
| | - Yingjie Zhong
- 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
| | - Qiuyue Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing Xia
- 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
| | - Si Chen
- 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
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ran 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
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Wang ZH, Zhu QH, Li X, Zhu JW, Tian DM, Zhang SS, Kang HL, Li CP, Dong LL, Zhao WM, Li MH. iSheep: an Integrated Resource for Sheep Genome, Variant and Phenotype. Front Genet 2021; 12:714852. [PMID: 34490043 PMCID: PMC8418083 DOI: 10.3389/fgene.2021.714852] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Zhong-Huang Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Qiang-Hui Zhu
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China.,CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xin Li
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China.,CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jun-Wei Zhu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation), Beijing, China
| | - Dong-Mei Tian
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation), Beijing, China
| | - Si-Si Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation), Beijing, China
| | - Hai-Long Kang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Cui-Ping Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation), Beijing, China
| | - Li-Li Dong
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation), Beijing, China
| | - Wen-Ming Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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37
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Wang R, Wang Z, Wang X, Li Y, Qu L, Lan X. A novel 4-bp insertion within the goat CFAP43 gene and its association with litter size. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Jian L, Xue Y, Gao Y, Wang B, Qu Y, Li S, Li H, Li Z, Wang B, Luo H. Vitamin E Can Ameliorate Oxidative Damage of Ovine Hepatocytes In Vitro by Regulating Genes Expression Associated with Apoptosis and Pyroptosis, but Not Ferroptosis. Molecules 2021; 26:molecules26154520. [PMID: 34361674 PMCID: PMC8348559 DOI: 10.3390/molecules26154520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 01/31/2023] Open
Abstract
(1) Background: the current research was conducted to investigate the potential non-antioxidant roles of vitamin E in the protection of hepatocysts from oxidative damage. (2) Methods: primary sheep hepatocytes were cultured and exposed to 200, 400, 600, or 800 μmol/L hydrogen peroxide, while their viability was assessed using a CCK-8 kit. Then, cells were treated with 400 μmol/L hydrogen peroxide following a pretreatment with 50, 100, 200, 400, and 800 μmol/L vitamin E and their intracellular ROS levels were determined by means of the DCF-DA assay. RNA-seq, verified by qRT-PCR, was conducted thereafter: non-treated control (C1); cells treated with 400 μmol/L hydrogen peroxide (C2); and C2 plus a pretreatment with 100 μmol/L vitamin E (T1). (3) Results: the 200-800 μmol/L hydrogen peroxide caused significant cell death, while 50, 100, and 200 μmol/L vitamin E pretreatment significantly improved the survival rate of hepatocytes. ROS content in the cells pretreated with vitamin E was significantly lower than that in the control group and hydrogen-peroxide-treated group, especially in those pretreated with 100 μmol/L vitamin E. The differentially expressed genes (DEGs) concerning cell death involved in apoptosis (RIPK1, TLR7, CASP8, and CASP8AP2), pyroptosis (NLRP3, IL-1β, and IRAK2), and ferroptosis (TFRC and PTGS2). The abundances of IL-1β, IRAK2, NLRP3, CASP8, CASP8AP2, RIPK1, and TLR7 were significantly increased in the C1 group and decreased in T1 group, while TFRC and PTGS2 were increased in T1 group. (4) Conclusions: oxidative stress induced by hydrogen peroxide caused cellular damage and death in sheep hepatocytes. Pretreatment with vitamin E effectively reduced intracellular ROS levels and protected the hepatocytes from cell death by regulating gene expression associated with apoptosis (RIPK1, TLR7, CASP8, and CASP8AP2) and pyroptosis (NLRP3, IL-1β, and IRAK2), but not ferroptosis (TFRC and PTGS2).
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Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations. Animals (Basel) 2021; 11:ani11061510. [PMID: 34071004 PMCID: PMC8224610 DOI: 10.3390/ani11061510] [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: 04/19/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary In the local populations, the increase in inbreeding is a relevant problem for the reduction in production, reproduction, and adaptive traits. The application of genomic technologies has facilitated the assessment of inbreeding in these populations. The current study aims to investigate the patterns of homozygosity in five Italian local goat populations. The results showed the different selection histories and breeding schemes of these goat populations. The analysis also indicated the importance of this information to avoid future loss of diversity and to produce information for designing optimal breeding and conservation programs. Abstract The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.
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Salehian-Dehkordi H, Xu YX, Xu SS, Li X, Luo LY, Liu YJ, Wang DF, Cao YH, Shen M, Gao L, Chen ZH, Glessner JT, Lenstra JA, Esmailizadeh A, Li MH, Lv FH. Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World's Sheep. Front Genet 2021; 12:670582. [PMID: 34093663 PMCID: PMC8175073 DOI: 10.3389/fgene.2021.670582] [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: 02/22/2021] [Accepted: 03/31/2021] [Indexed: 11/19/2022] Open
Abstract
Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (∼10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1, WNT7B, HMX1, and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3, KHDRBS2, and SDCCAG3 in Hu sheep; NOS3, BMP1, and SLC19A1 in Icelandic; CDK2 in Finnsheep; MICA in Romanov; and REEP4 in Texel sheep for litter size. These CNVs and associated genes are important markers for molecular breeding of sheep and other livestock species.
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Affiliation(s)
- Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ya-Xi Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Jing Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Shen
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Joseph T Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Ali Esmailizadeh
- Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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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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Tao L, He X, Jiang Y, Liu Y, Ouyang Y, Shen Y, Hong Q, Chu M. Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep. Genes (Basel) 2021; 12:480. [PMID: 33810234 PMCID: PMC8065816 DOI: 10.3390/genes12040480] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
The litter size of domestic goats and sheep is an economically important trait that shows variation within breeds. Strenuous efforts have been made to understand the genetic mechanisms underlying prolificacy in goats and sheep. However, there has been a paucity of research on the genetic convergence of prolificacy between goats and sheep, which likely arose because of similar natural and artificial selection forces. Here, we performed comparative genomic and transcriptomic analyses to identify the genetic convergence of prolificacy between goats and sheep. By combining genomic and transcriptomic data for the first time, we identified this genetic convergence in (1) positively selected genes (CHST11 and SDCCAG8), (2) differentially expressed genes (SERPINA14, RSAD2, and PPIG at follicular phase, and IGF1, GPRIN3, LIPG, SLC7A11, and CHST15 at luteal phase), and (3) biological pathways (genomic level: osteoclast differentiation, ErbB signaling pathway, and relaxin signaling pathway; transcriptomic level: the regulation of viral genome replication at follicular phase, and protein kinase B signaling and antigen processing and presentation at luteal phase). These results indicated the potential physiological convergence and enhanced our understanding of the overlapping genetic makeup underlying litter size in goats and sheep.
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Affiliation(s)
- Lin Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
- College of Life Science and Food Engineering, Hebei University of Engineering, Handan 056038, China
| | - Yina Ouyang
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Yezhen Shen
- Annoroad Gene Technology Co., Ltd., Beijing 100176, China;
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
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A genome-wide association study for prolificacy in three Polish sheep breeds. J Appl Genet 2021; 62:323-326. [PMID: 33608865 PMCID: PMC8032615 DOI: 10.1007/s13353-021-00615-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 11/02/2020] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
Reproductive traits (especially litter size) are usually characterized by low heritability, and thus, phenotypic selection is often ineffective and slow. In order to improve fertility characteristics such as ovulation rate and litter size, it seems more effective to select breeding animals based on their genotype. The aim of the study was to use genome-wide association study (GWAS) in three sheep breeds to identify the genetic variants affecting the litter size in sheep. The study allowed us to identify one genome-wide significant SNP (rs402032081—located in ephrin type-A receptor 6, EPHA6) showing an association with litter size in Polish Mountain Sheep. We suggest that the EPHA6 gene can be a candidate gene for prolificacy trait in selected breeds of sheep; however, it needs further functional data for validation.
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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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Tao L, He X, Wang X, Di R, Chu M. Litter Size of Sheep ( Ovis aries): Inbreeding Depression and Homozygous Regions. Genes (Basel) 2021; 12:109. [PMID: 33477586 PMCID: PMC7831309 DOI: 10.3390/genes12010109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Ovine litter size (LS) is an important trait showing variability within breeds. It remains largely unknown whether inbreeding depression on LS exists based on genomic homozygous regions, and whether the homozygous regions resulted from inbreeding are significantly associated with LS in sheep. We here reanalyze a set of single nucleotide polymorphism (SNP) chip of six breeds to characterize the patterns of runs of homozygosity (ROH), to evaluate inbreeding levels and inbreeding depressions on LS, and to identify candidate homozygous regions responsible for LS. Consequently, unique ROH patterns were observed among six sheep populations. Inbreeding depression on LS was only found in Hu sheep, where a significant reduction of 0.016, 0.02, and 0.02 per 1% elevated inbreeding FROH4-8, FROH>8 and the total inbreeding measure was observed, respectively. Nine significantly homozygous regions were found for LS in Hu sheep, where some promising genes for LS possibly via regulation of the development of oocytes (NGF, AKT1, and SYCP1), fertilization (SPAG17, MORC1, TDRD9, ZFYVE21, ADGRB3, and CKB), embryo implantation (PPP1R13B, INF2, and VANGL1) and development (DPPA2, DPPA4, CDCA4, CSDE1, and ADSSL1), and reproductive health (NRG3, BAG5, CKB, and XRCC3) were identified. These results from the present study would provide insights into the genetic management and complementary understandings of LS in sheep.
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Affiliation(s)
| | | | | | | | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (X.W.); (R.D.)
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Krivoruchko AY, Yatsyk OA, Safaryan EY. Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed. Vavilovskii Zhurnal Genet Selektsii 2020; 24:836-843. [PMID: 35087996 PMCID: PMC8763718 DOI: 10.18699/vj20.681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/15/2020] [Accepted: 10/29/2020] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study
of individuals with outstanding productivity indicators – exhibition animals, representatives of the super-elite class.
The aim of this study was to identify new candidate genes for economically valuable traits based on the search for
single nucleotide polymorphisms (SNPs) associated with belonging to different evaluation classes in rams of the Russian meat merino breed. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v. 1.07 software. Highly reliable associations were found between animals
belonging to different evaluation classes and the frequency of occurrence of individual SNPs on chromosomes 2, 6,
10, 13, and 20. Most of the substitutions with high association reliability are concentrated on chromosome 10 in the
region 10: 30859297–31873769. To search for candidate genes, 15 polymorphisms with the highest association reliability were selected (–log10(р) > 9). Determining the location of the analyzed SNPs relative to the latest annotation
Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex
of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA,
EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and
DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development
of the inflammatory process and the work of circadian rhythms. Thus, the candidate genes under consideration can
influence the formation of exterior features and productive qualities of sheep. However, further research is needed
to confirm the influence of genes and determine the exact mechanisms for implementing this influence on the phenotype.
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Affiliation(s)
- A. Y. Krivoruchko
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
| | - O. A. Yatsyk
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
| | - E. Y. Safaryan
- All-Russian Research Institute of Sheep and Goat Breeding – Branch of the North Caucasus Federal Agricultural Research Center
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Zhang H, Zhang Y, Peng A, Nie H, Wang F, Elsabagh M, Loor JJ, Amini NC. Determination of the trace minerals requirements for maintenance and growth of 35–50 kg Dorper × Hu crossbred ram lambs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1719910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Hao Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Ying Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Along Peng
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Haitao Nie
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing, China
| | - Mabrouk Elsabagh
- Department of Animal Production and Technology, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Nigde, Turkey
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Juan J. Loor
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Nthanda C. Amini
- Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
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Tao L, He X, Wang F, Zhong Y, Pan L, Wang X, Gan S, Di R, Chu M. Luzhong mutton sheep: inbreeding and selection signatures. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:777-789. [PMID: 33987559 PMCID: PMC7721573 DOI: 10.5187/jast.2020.62.6.777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/11/2020] [Accepted: 10/02/2020] [Indexed: 01/13/2023]
Abstract
Intense artificial selection has been imposed to Luzhong mutton sheep population
in the past years. Improvements on growth and reproductive performance are two
breeding goals in the present herd. Although some progresses were phenotypically
observed possibly due to inbreeding induced by strong selection in terms of
these traits, the genomic evaluation was poorly understood. Therefore, a
high-density SNP array was used to characterize the pattern of runs of
homozygosity (ROH), estimate inbreeding and inbreeding depressions on early
growth performance and litter size based upon ROH, and scan positive selection
signatures of recent population. Consequently, a low inbreeding level was
observed which had negative effects on litter size, but not on early growth
performance. And 160 genes were under selection, of which some were reported to
be linked to several traits of sheep including body weight, litter size, carcass
and meat quality, milk yield and composition, fiber quality and health, and the
top genes were associated with growth (growth hormone [GH]- growth hormone
receptor [GHR]- Insulin-like growth factor 1 [IGF1] axis) and litter size (bone
morphogenic proteins [BMPs]-associated). The effectiveness of previous breeding
measures was highlighted, but purging selection was proposed to alleviate the
inbreeding depression on litter size, providing some genomic insights to
breeding management of Luzhong mutton sheep.
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Affiliation(s)
- Lin Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengyan 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
| | - Yingjie Zhong
- 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
| | - Linxiang Pan
- Ji'nan Laiwu Yingtai Agriculture and Animal Husbandry Technology, Ji'nan, Shandong 271114, China
| | - Xiangyu 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
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China
| | - Ran 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
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Tao L, He XY, Jiang YT, Lan R, Li M, Li ZM, Yang WF, Hong QH, Chu MX. Combined approaches to reveal genes associated with litter size in Yunshang black goats. Anim Genet 2020; 51:924-934. [PMID: 32986880 DOI: 10.1111/age.12999] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 01/25/2023]
Abstract
Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two subpopulations (polytocous group, PG, and monotocous group, MG) with evident differences of litter size. Following the mapping to reference genome, and SNP calling and pruning, three approaches - GWAS, ROH analysis and detection of signatures of selection - were employed to unveil candidate genes responsible for litter size. Consequently, 12 candidate genes containing OSBPL8 with the minimum P-value were uncovered by GWAS. Differences were observed in the pattern of ROH between two subpopulations that shared similar low inbreeding coefficients. Two ROH hotspots and 12 corresponding genes emerged from ROH pool association analysis. Based on the nSL statistic, 15 and 61 promising genes were disclosed under selection for MG and PG respectively. Of them, some promising genes participate in ovarian function (PPP2R5C, CDC25A, ESR1, RPS26 and SERPINBs), seasonal reproduction (DIO3, BTG1 and CRYM) and metabolism (OSBPL8, SLC39A5 and SERPINBs). Our study pinpointed some novel promising genes influencing litter size, provided a comprehensive insight into genetic makeup of litter size and might facilitate selective breeding in goats.
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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
| | - Y T Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - R Lan
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - M Li
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Z M Li
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - W F Yang
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Q H Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, 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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Akhatayeva Z, Mao C, Jiang F, Pan C, Lin C, Hao K, Lan T, Chen H, Zhang Q, Lan X. Indel variants within the PRL and GHR genes associated with sheep litter size. Reprod Domest Anim 2020; 55:1470-1478. [PMID: 32762057 DOI: 10.1111/rda.13796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/01/2020] [Indexed: 12/27/2022]
Abstract
Growth hormone and prolactin belong to the class of peptide hormones that have a wide range of regulatory functions. In this study, polymorphisms of growth hormone receptor (GHR) and prolactin (PRL) genes were analysed as candidate genes, which are responsible for the litter size in Australian White (AUW) sheep. According to the statistical analyses results, the polymorphism information content (PIC) values of the PRL-P1-ins-23 bp, GHR-P2-del-23 bp and GHR-P8-del-23 bp were 0.371, 0.366 and 0.375, respectively, which indicates the high genetic polymorphism in AUW sheep. Moreover, all indel loci are not conformed to the HWE (p < .05). Further, our findings revealed that the PRL-P1-ins-23 bp polymorphism in the ovine PRL gene was significantly related to the first parity litter size (p = .001) and the DD genotype displaying the highest genotypic mean. Meanwhile, the GHR-P2-del-23 bp and GHR-P8-23 bp indels in the ovine GHR gene were significantly correlated with first parity litter size (p < .05), and the individuals with the genotype II showed significantly higher litter size than others. Collectively, these results demonstrated that our findings could be useful for future sheep breeding strategies based on the molecular-assisted selection (MAS).
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Affiliation(s)
- Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Cui Mao
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Fugui Jiang
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China.,Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chunjian Lin
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Kunjie Hao
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Tianxin Lan
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - 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
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, 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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