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Han B, Tian D, Li X, Liu S, Tian F, Liu D, Wang S, Zhao K. Multiomics Analyses Provide New Insight into Genetic Variation of Reproductive Adaptability in Tibetan Sheep. Mol Biol Evol 2024; 41:msae058. [PMID: 38552245 PMCID: PMC10980521 DOI: 10.1093/molbev/msae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
Domestication and artificial selection during production-oriented breeding have greatly shaped the level of genomic variability in sheep. However, the genetic variation associated with increased reproduction remains elusive. Here, two groups of samples from consecutively monotocous and polytocous sheep were collected for genome-wide association, transcriptomic, proteomic, and metabolomic analyses to explore the genetic variation in fecundity in Tibetan sheep. Genome-wide association study revealed strong associations between BMPR1B (p.Q249R) and litter size, as well as between PAPPA and lambing interval; these findings were validated in 1,130 individuals. Furthermore, we constructed the first single-cell atlas of Tibetan sheep ovary tissues and identified a specific mural granulosa cell subtype with PAPPA-specific expression and differential expression of BMPR1B between the two groups. Bulk RNA-seq indicated that BMPR1B and PAPPA expressions were similar between the two groups of sheep. 3D protein structure prediction and coimmunoprecipitation analysis indicated that mutation and mutually exclusive exons of BMPR1B are the main mechanisms for prolific Tibetan sheep. We propose that PAPPA is a key gene for stimulating ovarian follicular growth and development, and steroidogenesis. Our work reveals the genetic variation in reproductive performance in Tibetan sheep, providing insights and valuable genetic resources for the discovery of genes and regulatory mechanisms that improve reproductive success.
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Affiliation(s)
- Buying Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Dehong Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xue Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Dehui Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Song Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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Yue C, Wang J, Shen Y, Zhang J, Liu J, Xiao A, Liu Y, Eer H, Zhang QE. Whole-genome DNA methylation profiling reveals epigenetic signatures in developing muscle in Tan and Hu sheep and their offspring. Front Vet Sci 2023; 10:1186040. [PMID: 37388464 PMCID: PMC10301830 DOI: 10.3389/fvets.2023.1186040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction The Tan sheep is a popular local breed in China because of its tenderness and flavor. The Hu sheep breed is also famous for its high litter size, and its muscle growth rate is faster than that of Tan sheep. However, the epigenetic mechanism behind these muscle-related phenotypes is unknown. Methods In this study, the longissimus dorsi tissue from 18 6 month-old Tan sheep, Hu sheep, and Tan-Hu F2 generation (6 sheep per population) were collected. After genomic DNA extraction, whole-genome bisulfite sequencing (WGBS) and bioinformatics analysis were performed to construct genome-wide DNA methylome maps for the Tan sheep, Hu sheep and their Tan-Hu F2 generation. Results Distinct genome-wide DNA methylation patterns were observed between Tan sheep and Hu sheep. Moreover, DNA methylated regions were significantly increased in the skeletal muscle from Tan sheep vs. the F2 generation compared to the Hu sheep vs. F2 generation and the Tan sheep vs. Hu sheep. Compared with Hu sheep, the methylation levels of actin alpha 1 (ACTA1), myosin heavy chain 11 (MYH11), Wiskott-Aldrich syndrome protein (WAS), vav guanine nucleotide exchange factor 1 (VAV1), fibronectin 1 (FN1) and Rho-associated protein kinase 2 (ROCK2) genes were markedly distinct in the Tan sheep. Furthermore, Gene Ontology analysis indicated that these genes were involved in myotube differentiation, myotube cell development, smooth muscle cell differentiation and striated muscle cell differentiation. Conclusion The findings from this study, in addition to data from previous research, demonstrated that the ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 genes may exert regulatory effects on muscle development.
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Affiliation(s)
- Caijuan Yue
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jiakang Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yifei Shen
- Institute of Marxism, China University of Geosciences, Wuhan, Hubei, China
| | - Junli Zhang
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jian Liu
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Aiping Xiao
- Animal Husbandry Extension Station, Yinchuan, Ningxia, China
| | - Yisha Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
| | - Hehua Eer
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Qiao-e Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
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Di R, Wang F, Yu P, Wang X, He X, Mwacharo JM, Pan L, Chu M. Detection of Novel Variations Related to Litter Size in BMP15 Gene of Luzhong Mutton Sheep ( Ovis aries). Animals (Basel) 2021; 11:ani11123528. [PMID: 34944305 PMCID: PMC8698048 DOI: 10.3390/ani11123528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/02/2021] [Accepted: 12/05/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary BMP15 is a critical gene in sheep reproduction. Most of its variations have been reported in European sheep. In this study, the entire open reading frame (ORF) region of BMP15 was sequenced in 154 Luzhong mutton sheep. Among 13 identified variations, six were novel. Four SNPs (ENSOART00000010201.1:c.352+342C>A, c.352+1232T>C, c.352+1165A>G and c.353-2036T>A) were significantly associated with litter size, and could be used as candidate genetic markers for improving litter size. The results also suggested possible interaction between BMP15 and FecB/GDF9. Abstract Litter size is an important economic trait in the mutton sheep industry. BMP15 is one of the key candidate genes for litter size in sheep. In this study, the entire ORF region of BMP15 was sequenced in 154 Luzhong mutton ewes, and the novel variations were determined. The association between polymorphism in BMP15 and litter size was analyzed using a general linear model. Six out of a total of thirteen variations were identified to be novel. Association analysis indicated that four (SNPs ENSOART00000010201.1:c.352+342C>A, c.352+1232T>C, c.352+1165A>G and c.353-2036T>A) were significantly associated with litter size. The joint analysis among three major genes (BMP15, BMPR1B and GDF9) exhibited significant interaction effects in three combinations (FecB and c.352+1232T>C of BMP15; FecB and c.352+1165A>G of BMP15; c.352+342C>A of BMP15 and ENSOART00000014382.1:c.994G>A of GDF9). For the SNPs c.352+1232T>C and c.352+342C>A, the global distribution of allele frequencies showed that the highest variation frequency occurs in Western Europe. In conclusion, the results demonstrated that BMP15 is a major gene for litter size in Luzhong mutton sheep and candidate SNPs associated with litter size were identified.
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Affiliation(s)
- 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; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - 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; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - Ping Yu
- 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; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - 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; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - 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; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - Joram Mwashigadi Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa P.O. Box 5689, Ethiopia;
- Animal and Veterinary Sciences, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Midlothian EH25 9RG, UK
| | - Linxiang Pan
- Shandong Yingtai Agriculture and Animal Husbandry Technology Co., Ltd., Jinan 271114, 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; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
- Correspondence: ; Tel.: +86-010-6281-9850
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Mohamadipoor Saadatabadi L, Mohammadabadi M, Amiri Ghanatsaman Z, Babenko O, Stavetska R, Kalashnik O, Kucher D, Kochuk-Yashchenko O, Asadollahpour Nanaei H. Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds. BMC Vet Res 2021; 17:369. [PMID: 34861880 PMCID: PMC8641187 DOI: 10.1186/s12917-021-03077-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sheep were among the first animals to be domesticated. They are raised all over the world and produce a major scale of animal-based protein for human consumption and play an important role in agricultural economy. Iran is one of the important locations for sheep genetic resources in the world. Here, we compared the Illumina Ovine SNP50 BeadChip data of three Iranian local breeds (Moghani, Afshari and Gezel), as a population that does not undergone artificial breeding programs as yet, and five other sheep breeds namely East Friesian white, East Friesian brown, Lacaune, DorsetHorn and Texel to detect genetic mechanisms underlying economical traits and daptation to harsh environments in sheep. RESULTS To identify genomic regions that have been targeted by positive selection, we used fixation index (Fst) and nucleotide diversity (Pi) statistics. Further analysis indicated candidate genes involved in different important traits such as; wool production included crimp of wool (PTPN3, NBEA and KRTAP20-2 genes), fiber diameter (PIK3R4 gene), hair follicle development (LHX2 gene), the growth and development of fiber (COL17A1 gene)), adaptation to hot arid environments (CORIN gene), adaptive in deficit water status (CPQ gene), heat stress (PLCB4, FAM107B, NBEA, PIK3C2B and USP43 genes) in sheep. CONCLUSIONS We detected several candidate genes related to wool production traits and adaptation to hot arid environments in sheep that can be applicable for inbreeding goals. Our findings not only include the results of previous researches, but also identify a number of novel candidate genes related to studied traits. However, more works will be essential to acknowledge phenotype- genotype relationships of the identified genes in our study.
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Affiliation(s)
| | | | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Shiraz, Iran
| | - Olena Babenko
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Ruslana Stavetska
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Oleksandr Kalashnik
- Department of Animal Science, Sumy National Agrarian University, Sumy, Ukraine
| | - Dmytro Kucher
- Department of Breeding, Animal Genetics and Biotechnology, Polissia National University, Zhytomyr, Ukraine
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Li H, Xu H, Akhatayeva Z, Liu H, Lin C, Han X, Lu X, Lan X, Zhang Q, Pan C. Novel indel variations of the sheep FecB gene and their effects on litter size. Gene 2020; 767:145176. [PMID: 33002573 DOI: 10.1016/j.gene.2020.145176] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/02/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
Various studies had shown that the FecB gene (also known as BMPRIB, BMPR1B or ALK-6) was the major gene influencing sheep litter size, for which its SNPs' variations were reportedly linked. Yet, surprisingly, there was no published information on the insertion/deletion (indel) variation of this gene. Herein, using a population of Chinese Australian White sheep (n = 932), we identified five novel indels in the different introns of the FecB gene. Among them, the 12-bp indel was distinguished as a splicing region variation that was completely linked to the 17-bp indel. Analysis of variance revealed that only the 10-bp indel was significantly associated with sheep litter size (P = 0.010), for which the deletion/deletion (DD) genotype was the harmful one for fecundity. Nevertheless, the combined genotypes of these five indels were significantly (P = 0.033) correlated with the litter size. These findings would provide fresh insight into developing a sounder basis to accelerate molecular breeding in sheep via DNA markers in a marker-assisted selection strategy.
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Affiliation(s)
- Haixia Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu 730030, China
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongfei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunjian Lin
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China
| | - Xufei Han
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China
| | - Xiaofang Lu
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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He X, Li B, Fu S, Wang B, Qi Y, Da L, Te R, Sun S, Liu Y, Zhang W. Identification of piRNAs in the testes of Sunite and Small-tailed Han sheep. Anim Biotechnol 2019; 32:13-20. [PMID: 31318630 DOI: 10.1080/10495398.2019.1640717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
P-element-induced wimpy testis-interacting RNAs (piRNAs) are small RNAs that are essential for mammalian spermatogenesis and testicular development. Comparative analyses of the molecular mechanisms of spermatogenesis among different organisms are therefore dependent on accurate piRNA characterizations. In this study, we identified piRNAs in the testes of two breeds of Mongolian sheep: the Sunite (SN), which has a low reproductive rate, and Small-tailed Han (STH), which has a high reproductive rate. A thorough understanding of the mechanisms underlying the differences in fecundity between the two breeds might provide insights for the improvement of fertility and reproductive success in these and other sheep breeds. We identified 835 piRNAs and 206 piRNA clusters across the two breeds. Of these, 29 putative piRNAs were expressed in the SN samples only, and 229 putative piRNAs were expressed in the STH samples only. In addition, 206 piRNA clusters were upregulated in STH sheep as compared to the SN sheep. Functional pathway analysis indicated that the genes neighboring the predicted piRNAs were likely associated with spermatogenesis. piRNAs might thus be linked to male fecundity in sheep. Our results increase knowledge of the association between piRNAs and male fertility.
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Affiliation(s)
- Xiaolong He
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, PR China
| | - Bei Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Shaoyin Fu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, PR China
| | - Biao Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, PR China
| | - Yunxia Qi
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, PR China
| | - Lai Da
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, PR China
| | - Rigele Te
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, PR China
| | - Suzhen Sun
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, PR China
| | - Yongbin Liu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, PR China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, PR China
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Li L, Lu S, Ma Q, Wan P, Liu C, Yang H, Yang H, Yang Y, Dai R, Shi G. The comparison of reproductive hormone receptor expressions of the sheep ovary and hormone concentrations in two Chinese breeds. Reprod Domest Anim 2019; 54:892-901. [PMID: 31002198 DOI: 10.1111/rda.13441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 04/06/2019] [Indexed: 12/25/2022]
Abstract
The aim of this research was to investigate the changes in reproductive hormone receptor expressions of the ovary and hormone concentrations between oestrous cycle pattern of two different sheep breeds in China. Ovarian tissues were collected from Chinese Merino (Junken type) and Hu sheep with different reproductive states in spring and autumn. Serum samples were assayed for oestrogen (E2), progesterone (P), luteinizing hormone (LH) and follicle-stimulating hormone (FSH) concentrations by radioimmunoassay during spring. The ovarian expression of hormone receptors (ERα, ERβ, PR, LHR and FSHR) was analysed using real-time reverse transcription polymerase chain reaction (RT-PCR). In Chinese Merino, there was no corpora lutea and ovulation point on the surfaces of ovaries in spring and low basal levels of both LH and P in serum. ERα, ERβ and FSHR were expressed significantly higher in Merino ovaries during anoestrus compared with oestrous or luteal phases of Hu sheep (p < 0.05 or p < 0.01). However, both varieties of sheep exhibited a similar tendency to secrete E2 and FSH. Compared with Hu sheep, FSH levels were slightly higher in Merino serum. In Hu sheep, ERα, ERβ, FSHR, LHR and PR expressed in luteal phase ovaries during spring were significantly lower (p < 0.05, p < 0.01 or p < 0.001) than autumn. Interestingly, LHR and PR expressed in anoestrous ovaries were similar to that in oestrous phase of both sheep breeds. The above results suggest that seasonal reproductive sheep increased the expression of E2 and FSH receptors in ovary during spring may enhance the effects of E2 and FSH on follicular development. It is likely that this enhancement prevents the ovary from progressing to the luteal phase.
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Affiliation(s)
- Liangyuan Li
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Shouliang Lu
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Qiman Ma
- College of Medicine, Shihezi University, Shihezi, China
| | - Pengcheng Wan
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Changbin Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Hanyulu Yang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Hua Yang
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yonglin Yang
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Rong Dai
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Guoqing Shi
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
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Nosrati M, Asadollahpour Nanaei H, Amiri Ghanatsaman Z, Esmailizadeh A. Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep. Reprod Domest Anim 2018; 54:358-364. [PMID: 30359467 DOI: 10.1111/rda.13368] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022]
Abstract
Ovulation rate and prolificacy are the most important reproductive traits that have major impact on the efficiency of lamb meat production. Here, we compared the whole genomes of the Romanov sheep, known as one of the high prolific breeds, and four other sheep breeds namely Assaf, Awassi, Cambridge and British du cher, to identify genetic mechanisms underlying prolificacy in sheep. Selection signature analysis revealed 637 and 477 protein-coding genes under positive selection from FST and nucleotide diversity (Pi) statistics, respectively. Further analysis showed that several candidate genes including LEPR, PDGFRL and KLF5 genes are involved in sheep prolificacy. The identified candidate genes in the selected regions are novel and provide new insights into the genetic mechanisms underlying prolificacy in sheep and can be useful in sheep breeding programmes to develop improved breeds for high reproductive efficiency.
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Affiliation(s)
- Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.,Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.,Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
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Xu SS, Gao L, Xie XL, Ren YL, Shen ZQ, Wang F, Shen M, Eyϸórsdóttir E, Hallsson JH, Kiseleva T, Kantanen J, Li MH. Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds. Front Genet 2018; 9:118. [PMID: 29692799 PMCID: PMC5902979 DOI: 10.3389/fgene.2018.00118] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/23/2018] [Indexed: 12/11/2022] Open
Abstract
Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.
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Affiliation(s)
- 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, Beijing, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xing-Long Xie
- 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, Beijing, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Emma Eyϸórsdóttir
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Jón H. Hallsson
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Tatyana Kiseleva
- All-Russian Research Institute of Genetics and Farm Animal Breeding, Russian Academy of Sciences, Moscow, Russia
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland
| | - Meng-Hua 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, Beijing, China
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Zhang Y, Li F, Feng X, Yang H, Zhu A, Pang J, Han L, Zhang T, Yao X, Wang F. Genome-wide analysis of DNA Methylation profiles on sheep ovaries associated with prolificacy using whole-genome Bisulfite sequencing. BMC Genomics 2017; 18:759. [PMID: 28969601 PMCID: PMC5625832 DOI: 10.1186/s12864-017-4068-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/16/2017] [Indexed: 12/15/2022] Open
Abstract
Background Ovulation rate and litter size are important reproductive traits in sheep with high economic value. Recent work has revealed a potential link between DNA methylation and prolificacy. However, a genome-wide study that sought to identify potential DNA methylation sites involved in sheep prolificacy indicated that it is still unknown. Here, we aimed to investigate the genome-wide DNA methylation profiles of Hu sheep ovaries by comparing a high-prolificacy group (HP, litter size of three for at least 2 consecutive lambings) and low prolificacy group (LP, litter size of one for at least 2 consecutive lambings) using deep whole-genome bisulfite sequencing (WGBS). Results First, our results demonstrated lower expression levels of DNA methyltransferase (DNMT) genes in the ovaries of the HP group than that in the ovaries of the LP group. Both groups showed similar proportions of methylation at CpG sites but different proportions at non-CpG sites. Subsequently, we identified 70,899 differential methylated regions (DMRs) of CG, 16 DMRs of CHG, 356 DMRs of CHH and 12,832 DMR-related genes(DMGs). Gene Ontology (GO) analyses revealed that some DMGs were involved in regulating female gonad development and ovarian follicle development. Finally, we found that 10 DMGs, including BMP7, BMPR1B, CTNNB1, FST, FSHR, LHCGR, TGFB2 and TGFB3, are more likely to be involved in prolificacy of Hu sheep, as assessed by correlation analysis and listed in detail. Conclusions This study revealed the global DNA methylation pattern of sheep ovaries associated with high and low prolificacy groups, which may contribute to a better understanding of the epigenetic regulation of sheep reproductive capacity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4068-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanli Zhang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Fengzhe Li
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Xu Feng
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Hua Yang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Aoxiang Zhu
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Jing Pang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Le Han
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Tingting Zhang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Xiaolei Yao
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Feng Wang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, China.
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