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Wu S, Xie J, Zhong T, Shen L, Zhao Y, Chen L, Gan M, Zhang S, Zhu L, Niu L. Genetic polymorphisms in ESR and FSHβ genes and their association with litter traits in Large White pigs. Anim Biotechnol 2023; 34:4713-4720. [PMID: 36927230 DOI: 10.1080/10495398.2023.2187405] [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
The estrogen receptor (ESR) gene and follicle-stimulating hormone β (FSHβ) gene are responsible for litter traits. The present study aimed to verify the polymorphisms of ESR and FSHβ and assess their effects on the litter traits in 201 Large White pigs. Four SNPs (g.C669T, g.A1296G, g.C1665T and g.A1755G) were found in ESR. The TT genotype at g.C1665T locus and AA genotype at g.A1755G locus could significantly increase the total litter size of the first litter of American Large White pigs (p < 0.05). Eight SNPs were found in exon 3 of FSHβ. The AA genotype at g.A511G locus, AA and AG genotypes at g.A617G locus, CC and CT genotypes at g.C630T locus, CT and TT genotypes at g.C652T locus, CT and TT genotypes at g.C735T locus, AA and AG genotypes at g.A746G, AA and AG genotypes at g.A921G and CT genotype at g.C678T could significantly increase the litter size of different strains of Large White pigs (p < 0.05). Our study revealed that the genetic variations of ESR and FSHβ were closely related to the litter trait of Large White pigs. Therefore, ESR and FSHβ genes could be used as molecular markers for the genetic selection of Large White pigs.
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Affiliation(s)
- Shun Wu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jingjing Xie
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Tao Zhong
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linyuan Shen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ye Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lei Chen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mailin Gan
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shunhua Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Zhu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lili Niu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Chen SY, Schenkel FS, Melo ALP, Oliveira HR, Pedrosa VB, Araujo AC, Melka MG, Brito LF. Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes. BMC Genomics 2022; 23:331. [PMID: 35484513 PMCID: PMC9052698 DOI: 10.1186/s12864-022-08555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Background Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic. Results There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits. Conclusions These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08555-z.
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Affiliation(s)
- Shi-Yi Chen
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ana L P Melo
- Department of Reproduction and Animal Evaluation, Rural Federal University of Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Andre C Araujo
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA
| | - Melkaye G Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI, 54022, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA. .,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Mao H, Chen L, Bao R, Weng S, Wang M, Xu N, Qi L, Wang J. Mechanisms of Oogenesis-Related Long Non-coding RNAs in Porcine Ovaries Treated With Recombinant Pig Follicle-Stimulating Hormone. Front Vet Sci 2022; 8:838703. [PMID: 35281430 PMCID: PMC8908959 DOI: 10.3389/fvets.2021.838703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 11/17/2022] Open
Abstract
Reproductive efficiency is of significant importance in pork production for it has a great impact on economic success. Ovulation rate is an early component of reproduction efficiency of pigs, and it contributes to the upper limit of litter size. In this study, we used the newly developed recombinant pig follicle stimulating hormone (rpFSH) instead of traditional PMSG to increase ovulation rate of pigs in order to achieve higher litter size, for it was better at stimulating ovulation, and showed more cheaper and greener. However, relatively little is known about the underlying genetic bases and molecular mechanisms. Consequently, an experiment was carried out in ovaries of replacement gilts to screen the key genes and lncRNAs that affect the fecundity of pigs by RNA-seq technology. Twenty gilts were divided into two groups, including 10 rpFSH treatment pigs and 10 control animals. After slaughtering and collecting the phenotypic data, ovaries of five pigs in each group were selected for RNA-seq. Total RNA was extracted to construct the library and then sequence on an Illumina Hiseq 4000 system. A comprehensive analysis of mRNAs and long non-coding RNAs (lncRNAs) from 10 samples was performed with bioinformatics. The phenotypic data showed that rpFSH treatment groups had the higher (P < 0.01) ovarian weight and more mature follicles. The RNA-seq results showed that a total of 43,499 mRNAs and 21,703 lncRNAs were identified, including 21,300 novel lncRNAs and 403 known lncRNAs, of which 585 mRNAs and 398 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the two groups of rpFSH treatment group and controlled group. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to prolactin receptor activity, mitophagy by induced vacuole formation, and meiotic spindle. Moreover, we found that NR5A2 (nuclear receptor subfamily 5, group A, member 2), a target gene of lncRNA MSTRG.3902.1, was involved in regulating follicular development, ovulation, and estrogen production. Our study provided a catalog of lncRNAs and mRNAs associated with ovulation of rpFSH treatment, and they deserve further study to deepen the understanding of biological processes in the regulation of ovaries of rpFSH treatment pigs.
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Affiliation(s)
- Haiguang Mao
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Lu Chen
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Rupo Bao
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Shiqiao Weng
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Mengting Wang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Ningying Xu
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Lili Qi
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
- *Correspondence: Lili Qi
| | - Jinbo Wang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
- Jinbo Wang
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Vanvanhossou SFU, Yin T, Scheper C, Fries R, Dossa LH, König S. Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin. Front Genet 2021; 12:657282. [PMID: 34956303 PMCID: PMC8694269 DOI: 10.3389/fgene.2021.657282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.
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Affiliation(s)
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
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Abousoliman I, Reyer H, Oster M, Murani E, Mohamed I, Wimmers K. Genome-Wide Analysis for Early Growth-Related Traits of the Locally Adapted Egyptian Barki Sheep. Genes (Basel) 2021; 12:genes12081243. [PMID: 34440417 PMCID: PMC8394750 DOI: 10.3390/genes12081243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Sheep play a critical role in the agricultural and livestock sector in Egypt. For sheep meat production, growth traits such as birth and weaning weights are very important and determine the supply and income of local farmers. The Barki sheep originates from the northeastern coastal zone of Africa, and due to its good adaptation to the harsh environmental conditions, it contributes significantly to the meat production in these semi-arid regions. This study aimed to use a genome-wide SNP panel to identify genomic regions that are diversified between groups of individuals of Egyptian Barki sheep with high and low growth performance traits. In this context, from a phenotyped population of 140 lambs of Barki sheep, 69 lambs were considered for a genome-wide scan with the Illumina OvineSNP50 V2 BeadChip. The selected lambs were grouped into divergent subsets with significantly different performance for birth weight and weaning weight. After quality control, 63 animals and 40,383 SNPs were used for analysis. The fixation index (FST) for each SNP was calculated between the groups. The results verified genomic regions harboring some previously proposed candidate genes for traits related to body growth, i.e., EYA2, GDF2, GDF10, MEF2B, SLC16A7, TBX15, TFAP2B, and TNNC2. Moreover, novel candidate genes were proposed with known functional implications on growth processes such as CPXM2 and LRIG3. Subsequent association analysis showed significant effects of the considered SNPs on birth and weaning weights. Results highlight the genetic diversity associated with performance traits and thus the potential to improve growth traits in the Barki sheep breed.
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Affiliation(s)
- Ibrahim Abousoliman
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
- Desert Research Center, Department of Animal and Poultry Breeding, 1 Mathaf El-Matareya St., El-Matareya, Cairo 11753, Egypt;
| | - Henry Reyer
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Michael Oster
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Ismail Mohamed
- Desert Research Center, Department of Animal and Poultry Breeding, 1 Mathaf El-Matareya St., El-Matareya, Cairo 11753, Egypt;
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 7, 18059 Rostock, Germany
- Correspondence: ; Tel.: +49-382-08-68-600
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Norseeda W, Liu G, Teltathum T, Supakankul P, Sringarm K, Naraballobh W, Khamlor T, Chomdej S, Nganvongpanit K, Krutmuang P, Mekchay S. Association of IL-4 and IL-4R Polymorphisms with Litter Size Traits in Pigs. Animals (Basel) 2021; 11:ani11041154. [PMID: 33920608 PMCID: PMC8073830 DOI: 10.3390/ani11041154] [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: 03/25/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/01/2022] Open
Abstract
Simple Summary The IL-4 and IL-4R cytokine genes are responsible for immune response in the reproductive system and are related to embryonic implantation and fetal survival during pregnancy in females. However, to date, their effects on litter size traits in pigs have been not elucidated. Therefore, the present study was conducted to verify the porcine IL-4 and IL-4R polymorphisms and assess how they affect litter size traits in commercial pigs. The findings suggested that the porcine IL-4 g.134993898T > C and IL-4R c.1577A > T polymorphisms were associated with the litter size traits. Therefore, the porcine IL-4 and IL-4R genes may be potentially effective genetic markers to improve the litter size traits in pigs. Abstract The interleukin-4 (IL-4) and interleukin-4 receptor (IL-4R) are cytokines that are involved in the immune and reproductive systems. This study aimed to verify the polymorphisms in the porcine IL-4 and IL-4R genes and to assess their effects on litter size traits in commercial pigs. Single nucleotide polymorphisms (SNPs) in the porcine IL-4 and IL-4R genes were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. A non-coding SNP of IL-4 g.134993898T > C and a non-synonymous SNP of IL-4R c.1577A > T (amino acid change at position 526, Q526L) were found to be segregating in Landrace sows. The IL-4 g.134993898T > C polymorphism was significantly associated with the number of piglets weaned alive (NWA) trait. The IL-4R c.1577A > T polymorphism was significantly associated with the number born alive (NBA) and NWA traits. Moreover, the accumulation of favorable alleles of these two SNP markers revealed significant associations with the NBA, NWA, and mean weight of piglets at weaning (MWW) traits. These findings indicate that the porcine IL-4 and IL-4R genes may contribute to the reproductive traits of pigs and could be used as candidate genes to improve litter size traits in the pig breeding industry.
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Affiliation(s)
- Worrarak Norseeda
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (W.N.); (K.S.); (W.N.); (T.K.)
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guisheng Liu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Tawatchai Teltathum
- Mae Hong Son Livestock Research and Breeding Center, Mae Hong Son 58000, Thailand;
| | - Pantaporn Supakankul
- Division of Animal Science, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand;
| | - Korawan Sringarm
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (W.N.); (K.S.); (W.N.); (T.K.)
- Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Watcharapong Naraballobh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (W.N.); (K.S.); (W.N.); (T.K.)
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Trisadee Khamlor
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (W.N.); (K.S.); (W.N.); (T.K.)
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Korakot Nganvongpanit
- Department of Veterinary Bioscience and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand;
| | - Patcharin Krutmuang
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (W.N.); (K.S.); (W.N.); (T.K.)
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
- Correspondence:
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Bai Y, Li J, Zhu H, Liu J, Dong S, Li L, Qu L, Chen H, Song X, Lan X. Deletion mutation within the goat PPP3CA gene identified by GWAS significantly affects litter size. Reprod Fertil Dev 2021; 33:476-483. [PMID: 33883061 DOI: 10.1071/rd20337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/18/2021] [Indexed: 12/20/2022] Open
Abstract
The protein phosphatase 3 catalytic subunit α (PPP3CA) gene is a high reproduction traits candidate gene for goats as revealed by a genome-wide association study. The aim of this work was to explore the genetic variations of the goat PPP3CA as well as to evaluate the genetic effects on litter size. Three novel insertions/deletions (indels) within the goat PPP3CA were found and their minor allelic frequencies (MAF) were 0.105, 0.066, and 0.042, respectively. The results showed that only the 20bp indel polymorphism was significantly associated with litter size in Shaanbei white cashmere goats (P<0.05) and individuals with deletion/deletion (DD) genotypes demonstrated the junior phenotypes when compared with those with other genotypes. These findings suggested that the 20bp indel is a potential DNA marker for selecting superior individuals in marker-assisted selection for breeding concerning fecundity in goats.
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Affiliation(s)
- Yangyang Bai
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling Shaanxi 712100, China; and Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin Shaanxi 719000, China; and Life Science Research Center, Yulin University, Yulin Shaanxi 719000, China
| | - Jie Li
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, 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, China; and Life Science Research Center, Yulin University, Yulin Shaanxi 719000, China; and Shaanxi Province 'Four Subjects One Union' Sheep and Goat Engineering & Technology University & Enterprise Alliance Research Center, Yulin, Shaanxi 719000, PR China; and Shaanxi Haoli cashmere goat Technology Development Co., Ltd, Yulin, Shaanxi, PR China, 719000
| | - Jinwang Liu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin Shaanxi 719000, China; and Life Science Research Center, Yulin University, Yulin Shaanxi 719000, China; and Shaanxi Province 'Four Subjects One Union' Sheep and Goat Engineering & Technology University & Enterprise Alliance Research Center, Yulin, Shaanxi 719000, PR China
| | - Shuwei Dong
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin Shaanxi 719000, China; and Life Science Research Center, Yulin University, Yulin Shaanxi 719000, China; and Shaanxi Province 'Four Subjects One Union' Sheep and Goat Engineering & Technology University & Enterprise Alliance Research Center, Yulin, Shaanxi 719000, PR China
| | - Longping Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin Shaanxi 719000, China; and Life Science Research Center, Yulin University, Yulin Shaanxi 719000, China; and Shaanxi Province 'Four Subjects One Union' Sheep and Goat Engineering & Technology University & Enterprise Alliance Research Center, Yulin, Shaanxi 719000, PR China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin Shaanxi 719000, China; and Life Science Research Center, Yulin University, Yulin Shaanxi 719000, China
| | - Hong Chen
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin Shaanxi 719000, China; and Life Science Research Center, Yulin University, Yulin Shaanxi 719000, China; and Shaanxi Province 'Four Subjects One Union' Sheep and Goat Engineering & Technology University & Enterprise Alliance Research Center, Yulin, Shaanxi 719000, PR China
| | - Xianyong Lan
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling Shaanxi 712100, China; and Corresponding author.
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Hu H, Jia Q, Xi J, Zhou B, Li Z. Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows. BMC Genomics 2020; 21:636. [PMID: 32928107 PMCID: PMC7490888 DOI: 10.1186/s12864-020-07055-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/06/2020] [Indexed: 01/20/2023] Open
Abstract
Background Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics. Results In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log2 (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data. Conclusions These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.
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Affiliation(s)
- Huiyan Hu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Qing Jia
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China. .,Engineering Research Center for Agriculture in Hebei Mountainous Areas, Baoding, 071000, Hebei, China.
| | - Jianzhong Xi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Bo Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Zhiqiang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
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Integrated Analysis of miRNA-mRNA Network Reveals Different Regulatory Patterns in the Endometrium of Meishan and Duroc Sows during Mid-Late Gestation. Animals (Basel) 2020; 10:ani10030420. [PMID: 32138165 PMCID: PMC7143271 DOI: 10.3390/ani10030420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 02/29/2020] [Accepted: 03/01/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Meishan pigs have a lower fetal loss rate during mid-late gestation compared to Duroc pigs. Differentially expressed mRNAs and miRNAs detected in endometrial tissue from Meishan and Duroc sows at mid-late gestation are involved in regulating hormone and oxygen levels, blood vessel development, and developmental processes affecting reproduction. In addition, ssc-miR-503 and ssc-miR-671-5p were shown to target the EGF and ESR1 genes, respectively. These findings provided an important resource for studying embryonic mortality during mid-late gestation in pigs. Abstract Embryo loss is a major factor affecting profitability in the pig industry. Embryonic mortality occurs during peri-implantation and mid-late gestation in pigs. Previous investigations have shown that the embryo loss rate in Meishan pigs is significantly lower than in commercial breeds. Most studies have focused on embryonic mortality during early gestation, but little is known about losses during mid-late gestation. In this study, we performed a transcriptome analysis of endometrial tissue in mid-late gestation sows (gestation days 49 and 72) sampled from two breeds (Meishan (MS) and Duroc (DU)) that have different embryo loss rates. We identified 411, 1113, 697, and 327 differentially expressed genes, and 14, 36, 57, and 43 differentially expressed miRNAs in four comparisons (DU49 vs. DU72, DU49 vs. MS49, DU72 vs. MS72, and MS49 vs. MS72), respectively. Subsequently; seven differentially expressed mRNAs and miRNAs were validated using qPCR. Functional analysis suggested the differentially expressed genes and miRNAs target genes mainly involved in regulation of hormone levels, blood vessel development, developmental process involved in reproduction, embryonic placenta development, and the immune system. A network analysis of potential miRNA-gene interactions revealed that differentially expressed miRNAs in Meishan pigs are involved in the response to estradiol and oxygen levels, and affect angiogenesis and blood vessel development. The binding site on ssc-miR-503 for epidermal growth factor (EGF) and the binding site on ssc-miR-671-5p for estrogen receptor α (ESR1) were identified using a dual luciferase assay. The results of this study will enable further exploration of miRNA-mRNA interactions important in pig pregnancy and will help to uncover molecular mechanisms affecting embryonic mortality in pigs during mid-late gestation.
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Ogawa S, Konta A, Kimata M, Ishii K, Uemoto Y, Satoh M. Genetic parameter estimation for number born alive at different parities in Landrace and Large White pigs. Anim Sci J 2019; 90:1111-1119. [DOI: 10.1111/asj.13252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Shinichiro Ogawa
- Graduate School of Agricultural Science Tohoku University Sendai Japan
| | - Ayane Konta
- Faculty of Agriculture Tohoku University Sendai Japan
| | | | - Kazuo Ishii
- Division of Animal Breeding and Reproduction, Institute of Livestock and Grassland Science NARO Tsukuba Japan
| | - Yoshinobu Uemoto
- Graduate School of Agricultural Science Tohoku University Sendai Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science Tohoku University Sendai Japan
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