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Xiao M, Ruan Y, Huang J, Dai L, Xu J, Xu H. Association analysis between Acetyl-Coenzyme A Acyltransferase-1 gene polymorphism and growth traits in Xiangsu pigs. Front Genet 2024; 15:1346903. [PMID: 38756449 PMCID: PMC11096523 DOI: 10.3389/fgene.2024.1346903] [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: 11/30/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction Acetyl-Coenzyme A Acyltransferase-1 (ACAA1) is a peroxisomal acyltransferase involved in fatty acid metabolism. Current evidence does not precisely reveal the effect of the ACAA1 gene on pig growth performance. Methods The present study assessed the mRNA expression levels of the ACAA1 gene in the heart, liver, spleen, lung, kidney of 6-month-old Xiangsu pigs and in the longissimus dorsi muscle at different growth stages (newborn, 6 months and 12 months of age) using RT-qPCR. The relationship between single-nucleotide polymorphisms (SNPs) of ACAA1 gene and growth traits in 6-month-old and 12-month-old Xiangsu pigs was investigated on 184 healthy Xiangsu pigs using Sanger sequencing. Results The ACAA1 gene was expressed in heart, liver, spleen, lung, kidney, and longissimus dorsi muscle of 6-month-old pigs, with the highest level of expression in the liver. ACAA1 gene expression in the longissimus dorsi muscle decreased with age (p < 0.01). In addition, four SNPs were identified in the ACAA1 gene, including exon g.48810 A>G (rs343060194), intron g.51546 T>C (rs319197012), exon g.55035 T>C (rs333279910), and exon g.55088 C>T (rs322138947). Hardy-Weinberg equilibrium (p > 0.05) was found for the four SNPs, and linkage disequilibrium (LD) analysis revealed a strong LD between g.55035 T>C (rs333279910) and g.55088 C>T (rs322138947) (r 2 = 1.000). Association analysis showed that g.48810 A>G (rs343060194), g.51546 T>C (rs319197012), g.55035 T>C (rs333279910), and g.55088 C>T (rs322138947) varied in body weight, body length, body height, abdominal circumference, leg and hip circumference and living backfat thickness between 6-month-old and 12-month-old Xiangsu pigs. Conclusion These findings strongly demonstrate that the ACAA1 gene can be exploited for marker-assisted selection to improve growth-related phenotypes in Xiangsu pigs and present new candidate genes for molecular pig breeding.
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Affiliation(s)
- Meimei Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Jiajin Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Lingang Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Jiali Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
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Huang J, Ruan Y, Xiao M, Dai L, Jiang C, Li J, Xu J, Chen X, Xu H. Association between polymorphisms in NOBOX and litter size traits in Xiangsu pigs. Front Vet Sci 2024; 11:1359312. [PMID: 38523712 PMCID: PMC10959092 DOI: 10.3389/fvets.2024.1359312] [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: 12/21/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
The newborn ovary homeobox gene (NOBOX) regulates ovarian and early oocyte development, and thus plays an essential role in reproduction. In this study, the mRNA expression level and single nucleotide polymorphism (SNP) of NOBOX in various tissues of Xiangsu pigs were studied to explore the relationship between its polymorphism and litter size traits. Also, bioinformatics was used to evaluate the effects of missense substitutions on protein structure and function. The results revealed that NOBOX is preferentially expressed in the ovary. Six mutations were detected in the NOBOX sequence, including g.1624 T>C, g.1858 G>A, g.2770 G>A, g.2821 A>G, g.5659 A>G, and g.6025 T>A, of which g.1858 G>A was a missense mutation. However, only g.1858 G>A, g.5659 A>G, and g.6025 T>A were significantly associated with litter size traits (p < 0.05). Further prediction of the effect of the missense mutation g.1858 G>A on protein function revealed that p.V82M is a non-conservative mutation that significantly reduces protein stability and thus alters protein function. Overall, these findings suggest that NOBOX polymorphism is closely related to the litter size of Xiangsu pigs, which may provide new insights into pig breeding.
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Affiliation(s)
- Jiajin Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Meimei Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Lingang Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Chuanmei Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Jifeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Jiali Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
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Gong T, Mu Q, Xu Y, Wang W, Meng L, Feng X, Liu W, Ao Z, Zhang Y, Chen X, Xu H. Expression of the umami taste receptor T1R1/T1R3 in porcine testis of: Function in regulating testosterone synthesis and autophagy in Leydig cells. J Steroid Biochem Mol Biol 2024; 236:106429. [PMID: 38035949 DOI: 10.1016/j.jsbmb.2023.106429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023]
Abstract
Testosterone is a vital male hormone responsible for male sexual characteristics. The taste receptor family 1 subunit 3 (T1R3) regulates testosterone synthesis and autophagy in non-taste cells, and the links with the taste receptor family 1 subunit 1 (T1R1) for umami perception. However, little is known about these mechanisms. Thus, we aimed to determine the relationship between the umami taste receptor (T1R1/T1R3) and testosterone synthesis or autophagy in testicular Leydig cells of the Xiang pig. There was a certain proportion of spermatogenic tubular dysplasia in the Xiang pig at puberty, in which autophagy was enhanced, and the testosterone level was increased with a weak expression of T1R3. Silenced T1R3 decreased testosterone level and intracellular cyclic adenosine monophosphate (cAMP) content and inhibited the messenger RNA (mRNA) expression levels of testosterone synthesis enzyme genes [steroidogenic acute regulatory protein (StAR), hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 (3β-HSD1), cytochrome P450 family 17 subfamily A member 1 (CYP17A1) and hydroxysteroid 17-beta dehydrogenase 3 (17β-HSD3)]. In addition, T1R3 increased the number of acidic autophagy bubbles and upregulated the expression levels of autophagy markers [Microtubule-associated protein 1 A/1B-light chain 3 (LC3) and Beclin-1] in testicular Leydig cells of the Xiang pig. Using an umami tasting agonist (10 mM L-glutamate for 6 h), the activation of T1R1/T1R3 enhanced the testosterone synthesis ability by increasing the intracellular cAMP level and upregulated the expression levels of StAR, 3β-HSD1, CYP17A1 and 17β-HSD3 in Leydig cells. Furthermore, the number of acidic autophagy bubbles decreased in the T1R1/T1R3-activated group with the downregulation of the expression levels of the autophagy markers, including LC3 and Beclin-1. These data suggest that the function of T1R1/T1R3 expressed in testicular Leydig cells of the Xiang pig is related to testosterone synthesis and autophagy.
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Affiliation(s)
- Ting Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China.
| | - Qi Mu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
| | - Yongjian Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Qiannan Buyi and Miao Autonomous Prefecture Bureau of Agriculture and Rural Affairs, PR China
| | - Weiyong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
| | - Lijie Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
| | - Xianzhou Feng
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
| | - Wenjiao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
| | - Zheng Ao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
| | - Yiyu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, Guizhou, PR China; College of Animal Science, Guizhou University, Guiyang 550025, Guizhou, PR China
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Xu J, Ruan Y, Sun J, Shi P, Huang J, Dai L, Xiao M, Xu H. Association Analysis of PRKAA2 and MSMB Polymorphisms and Growth Traits of Xiangsu Hybrid Pigs. Genes (Basel) 2022; 14:genes14010113. [PMID: 36672854 PMCID: PMC9858937 DOI: 10.3390/genes14010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, Xiangsu hybrid pig growth traits were evaluated via PRKAA2 and MSMB as candidate genes. Sanger sequencing revealed three mutation sites in PRKAA2, namely, g.42101G>T, g.60146A>T, and g.61455G>A, and all these sites were intronic mutations. Moreover, six mutation sites were identified in MSMB: intronic g.4374G>T, exonic g.4564T>C, exonic g.6378G>A, exonic g.6386C>T, intronic g.8643G>A, and intronic g.8857A>G. Association analysis revealed that g.42101G>T, g.60146A>T, g.61455G>A, g.4374G>T, g.4564T>C, g.6378G>A, g.6386C>T, g.8643G>A, and g.8857A>G showed different relationship patterns among body weight, body length, body height, chest circumference, abdominal circumference, tube circumference, and chest depth. Real-time polymerase chain reaction results revealed that the expression of PRKAA2 was highest in the longissimus dorsi muscle, followed by that in the heart, kidney, liver, lung, and spleen. The expression of MSMB was highest in the spleen, followed by that in the liver, kidney, lung, heart, and longissimus dorsi muscle. These results suggest that PRKAA2 and MSMB can be used in marker-assisted selection to improve growth related traits in Xiangsu hybrid pigs, providing new candidate genes for Pig molecular breeding.
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Affiliation(s)
- Jiali Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jinkui Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Pengfei Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jiajin Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Lingang Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Meimei Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
- Correspondence:
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Li X, Zhang X, Luo Y, Liu R, Sun Y, Zhao S, Yu M, Cao J. Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells. Genes (Basel) 2022; 13:genes13091515. [PMID: 36140681 PMCID: PMC9498719 DOI: 10.3390/genes13091515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/25/2022] Open
Abstract
The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the CD163 had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection.
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Affiliation(s)
- Xiaolong Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yandong Luo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ru Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianhua Cao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
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Wang X, Ran X, Niu X, Huang S, Li S, Wang J. Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs. Sci Rep 2022; 12:11823. [PMID: 35821031 PMCID: PMC9276726 DOI: 10.1038/s41598-022-14686-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.
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Affiliation(s)
- Xiying Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.,Tongren University, Tongren, 554300, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
| | - Xi Niu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Shihui Huang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Sheng Li
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jiafu Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
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7
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Ma H, Jiang J, He J, Liu H, Han L, Gong Y, Li B, Yu Z, Tang S, Zhang Y, Duan Y, Yin Y, Zeng Q, Yi J, He X, Zeng Y, Kim KS, Xu K, Liang F, He J. Long-read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds. Mol Ecol Resour 2021; 22:1508-1520. [PMID: 34758184 DOI: 10.1111/1755-0998.13550] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]
Abstract
Advances in long-read sequencing technology and genome assembly provide an opportunity to improve the pig genome and reveal the full range of structural variations (SVs) between local Chinese and European pigs. To date, little is known about the genomes of some unique Chinese indigenous breeds, such as the Ningxiang pig. Here, we report the sequencing and assembly of a highly contiguous Ningxiang pig genome (NX) via an integration of PacBio single-molecule real-time sequencing, Illumina next-generation sequencing, BioNano optical mapping and Hi-C (chromosome conformation capture) approaches. The assembled genome comprises 2.44 Gb with a contig N50 of 26.1 Mb and 418 contigs in total. These contigs are organized into 121 scaffolds with a scaffold N50 of 139.0 Mb. More than 99.1% of the assembled sequence could be localized to 19 pseudochromosomes and is annotated with 20,914 protein-coding genes and 34.04% repetitive sequences. Comparisons between the NX and European Duroc assemblies revealed many SVs in genes involved in the immune system, nervous system, lipid metabolism and environmental adaptation. The genetic variants include 47 Chinese domestic pig-specific SVs and the associated 74 genes may contribute to the differences in domestic traits compared to European pigs. Moreover, single nucleotide polymorphisms (SNPs) identified from whole genome resequencing data of 73 Chinese pigs, representing 17 geographically isolated breeds, showed their specific genetic variations, population structure and evolutionary patterns. Finally, we explore transcriptional regulation in the first intron of the MYL4 gene, as the genomic SV (281-bp deletion) in Ningxiang pig promotes its subcutaneous fat compared to European pig breeds. This work identifies a set of Asian-specific SVs and SNPs, which will be important resources for modern pig breeding and genetic conservation.
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Affiliation(s)
- Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Juan Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | | | | | - Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Shengguo Tang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
| | - Yehui Duan
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, PR China
| | - Yulong Yin
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, PR China
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China.,Ningxiang Pig Farm of Dalong Livestock Technology Co., Ltd, Ningxiang, PR China
| | | | - Xinglong He
- Bureau of Animal Husbandry, Veterinary and Fisheries in Ningxiang City, Ningxiang, PR China
| | - Yongbo Zeng
- Bureau of Animal Husbandry, Veterinary and Fisheries in Ningxiang City, Ningxiang, PR China
| | - Kung Seok Kim
- Department of Natural Resources Ecology and Management, Iowa State University, Ames, Iowa, USA
| | - Kang Xu
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, PR China
| | - Fan Liang
- Grandomics Biosciences, Wuhan, PR China
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, PR China
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8
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Ran X, Hu F, Mao N, Ruan Y, Yi F, Niu X, Huang S, Li S, You L, Zhang F, Tang L, Wang J, Liu J. Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs. Porcine Health Manag 2021; 7:52. [PMID: 34470660 PMCID: PMC8411529 DOI: 10.1186/s40813-021-00226-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although lots of quantitative trait loci (QTLs) and genes present roles in litter size of some breeds, the information might not make it clear for the huge diversity of reproductive capability in pig breeds. To elucidate the inherent mechanisms of heterogeneity of reproductive capability in litter size of Xiang pig, we performed transcriptome analysis for the expression profile in ovaries using RNA-seq method. RESULTS We identified 1,419 up-regulated and 1,376 down-regulated genes in Xiang pigs with large litter size. Among them, 1,010 differentially expressed genes (DEGs) were differently spliced between two groups with large or small litter sizes. Based on GO and KEGG analysis, numerous members of genes were gathered in ovarian steroidogenesis, steroid biosynthesis, oocyte maturation and reproduction processes. CONCLUSIONS Combined with gene biological function, twelve genes were found out that might be related with the reproductive capability of Xiang pig, of which, eleven genes were recognized as hub genes. These genes may play a role in promoting litter size by elevating steroid and peptide hormones supply through the ovary and facilitating the processes of ovulation and in vivo fertilization.
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Affiliation(s)
- Xueqin Ran
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fengbin Hu
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Ning Mao
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Yiqi Ruan
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fanli Yi
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Xi Niu
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Shihui Huang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Sheng Li
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Longjiang You
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fuping Zhang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Liangting Tang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Jiafu Wang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China.
| | - Jianfeng Liu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
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9
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Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers. Animals (Basel) 2021; 11:ani11041136. [PMID: 33921134 PMCID: PMC8071531 DOI: 10.3390/ani11041136] [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: 03/11/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Our previous studies suggested that the short interspersed nuclear element (SINE) retrotransposon insertion polymorphisms (RIPs), as a new type of molecular marker developed very recently, are ideal molecular markers and have the potential to be used for population genetic analysis and molecular breeding in pigs and possibly it can be extended to other livestock animals as well. However, no report is available for the application of SINE RIPs in population genetic analysis in livestock, including pigs. Here, we evaluated 30 SINE RIPs in several indigenous Chinese miniature pig breeds, including three subpopulations of Bama pigs (BM-cov, BM-clo, and BM-inb). BM-cov is a subpopulation conserved in the national conservation farm, and BM-clo is a closed population maintained over 30 years with only 2 boars and 14 sows imported from its original area, while BM-inb herd is an 18 generation continuous inbreeding line based on the BM-clo population. To our knowledge, it is the first time to report the genetic diversity, breed differentiation, and population structures for these populations by using SINE RIPs, and which suggests the feasibility of SINE RIPs in pig genetic analysis. Abstract RIPs have been developed as effective genetic markers and popularly applied for genetic analysis in plants, but few reports are available for domestic animals. Here, we established 30 new molecular markers based on the SINE RIPs, and applied them for population genetic analysis in seven Chinese miniature pigs. The data revealed that the closed herd (BM-clo), inbreeding herd (BM-inb) of Bama miniature pigs were distinctly different from the BM-cov herds in the conservation farm, and other miniature pigs (Wuzhishan, Congjiang Xiang, Tibetan, and Mingguang small ear). These later five miniature pig breeds can further be classified into two clades based on a phylogenetic tree: one included BM-cov and Wuzhishan, the other included Congjiang Xiang, Tibetan, and Mingguang small ear, which was well-supported by structure analysis. The polymorphic information contents estimated by using SINE RIPs are lower than the predictions based on microsatellites. Overall, the genetic distances and breed-relationships between these populations revealed by 30 SINE RIPs generally agree with their evolutions and geographic distributions. We demonstrated the potential of SINE RIPs as new genetic markers for genetic monitoring and population structure analysis in pigs, which can even be extended to other livestock animals.
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Gong T, Wang W, Xu H, Yang Y, Chen X, Meng L, Xu Y, Li Z, Wan S, Mu Q. Longitudinal Expression of Testicular TAS1R3 from Prepuberty to Sexual Maturity in Congjiang Xiang Pigs. Animals (Basel) 2021; 11:ani11020437. [PMID: 33567555 PMCID: PMC7916009 DOI: 10.3390/ani11020437] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/05/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Taste receptor type 1 subunit 3 (T1R3), a sweet/umami taste receptor, is widely expressed from the tongue to the testis, and testis expression is associated with male sterility. In Congjiang Xiang pigs, T1R3 is expressed in elongating/elongated spermatids and Leydig cells in a stage-dependent manner during postnatal development and the spermatogenic cycle. T1R3 may contribute to regulation of spermatid differentiation and Leydig cell function, and may therefore help limit the incidence of various male reproductive pathologies. Abstract Testicular expression of taste receptor type 1 subunit 3 (T1R3), a sweet/umami taste receptor, has been implicated in spermatogenesis and steroidogenesis in mice. We explored the role of testicular T1R3 in porcine postnatal development using the Congjiang Xiang pig, a rare Chinese miniature pig breed. Based on testicular weights, morphology, and testosterone levels, four key developmental stages were identified in the pig at postnatal days 15–180 (prepuberty: 30 day; early puberty: 60 day; late puberty: 90 day; sexual maturity: 120 day). During development, testicular T1R3 exhibited stage-dependent and cell-specific expression patterns. In particular, T1R3 levels increased significantly from prepuberty to puberty (p < 0.05), and expression remained high until sexual maturity (p < 0.05), similar to results for phospholipase Cβ2 (PLCβ2). The strong expressions of T1R3/PLCβ2 were observed at the cytoplasm of elongating/elongated spermatids and Leydig cells. In the eight-stage cycle of the seminiferous epithelium in pigs, T1R3/PLCβ2 levels were higher in the spermatogenic epithelium at stages II–VI than at the other stages, and the strong expressions were detected in elongating/elongated spermatids and residual bodies. The message RNA (mRNA) levels of taste receptor type 1 subunit 1 (T1R1) in the testis showed a similar trend to levels of T1R3. These data indicate a possible role of T1R3 in the regulation of spermatid differentiation and Leydig cell function.
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Affiliation(s)
- Ting Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Weiyong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
- Correspondence: ; Tel.: +86-0851-88298005
| | - Yi Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Lijie Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Yongjian Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Ziqing Li
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Sufang Wan
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Qi Mu
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
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11
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Getmantseva LV, Bakoev SY, Shevtsova VS, Kolosov AY, Bakoev NF, Kolosova MA. Assessing the Effect of SNPs on Litter Traits in Pigs. SCIENTIFICA 2020; 2020:5243689. [PMID: 32802554 PMCID: PMC7414332 DOI: 10.1155/2020/5243689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 06/04/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
The reproductive ability of sows is the principle of continuous and efficient production, based on such traits as the number of piglets, the total number of parities, and the period of economic use. Currently, SNPs associated with the TNB and NBA are presented in the PigQTLdb. The aim of this work was the assessment of the SNP effects on the litter traits in Large White (LW, n = 502) and Landrace (LN, n = 432) sow breeds in a farm in Russia. 9 SNPs (SNP_1: rs80956812; SNP_2: rs81471381; SNP_3: rs80891106; SNP_4: rs81399474; SNP_5: rs81421148; SNP_6: rs81242222; SNP_7: rs81319839; SNP_8: rs81312912; SNP_9: rs80962240) were selected for the study. Associative analysis was performed using the GLM procedure in R version 3.5.1. The analysis of reproductive traits was carried out according to the results of the first parity, the second and subsequent parities, and totals for lifetime of sows. The significant effect on litter traits in LW was determined for SNP rs80956812, SNP rs81471381, SNP rs81421148, and SNP rs81399474. The significant effect on litter traits in LN was determined for SNP rs81421148 and SNP rs81319839. AKT3 gene was identified as perspective candidate gene, whose biological functions, as well as the results obtained in our work and in other studies, indicate its potential role in the reproductive process regulation in pigs. In general, the data obtained help to explain the genetic mechanisms of reproductive traits.
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Affiliation(s)
- Lyubov V. Getmantseva
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russia
| | - Siroj Yu Bakoev
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russia
| | | | - Anatoly Yu Kolosov
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russia
- Don State Agrarian University, Persianovski 346493, Russia
| | - Neckruz F. Bakoev
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russia
| | - Maria A. Kolosova
- Southern Federal University, Rostov-on-Don 344006, Russia
- Don State Agrarian University, Persianovski 346493, Russia
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