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Zhang B, Wang C, Yang W, Zhang H, Meng Q, Shi B, Shan A. Transcriptome analysis of the effect of pyrroloquinoline quinone disodium (PQQ·Na 2) on reproductive performance in sows during gestation and lactation. J Anim Sci Biotechnol 2019; 10:62. [PMID: 31406573 PMCID: PMC6685232 DOI: 10.1186/s40104-019-0369-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023] Open
Abstract
Background Pyrroloquinoline quinone (PQQ), which is a water soluble, thermo-stable triglyceride-quinone, is widely distributed in nature and characterized as a mammalian vitamin-like redox cofactor. The objective of this study was to investigate the effects of pyrroloquinoline quinone disodium (PQQ·Na2) on reproductive performance in sows. Results Dietary supplementation with PQQ·Na2 significantly increased the total number of piglets born, the number of piglets born alive and the born alive litter weight. It also increased the antioxidant status in the placenta, plasma and milk. The concentration of NO was significantly increased in the plasma and placenta. RNA-seq analysis showed that 462 unigenes were differentially expressed between the control (Con) treatment and PQQ treatment groups. Among these unigenes, 199 were upregulated, while 263 unigenes were downregulated. The assigned functions of the unigenes covered a broad range of GO categories. Reproduction (27, 7.03%) and the reproduction process (27, 7.03%) were assigned to the biological process category. By matching DEGs to the KEGG database, we identified 29 pathways. Conclusions In conclusion, dietary supplementation with PQQ·Na2 in gestating and lactating sows had positive effects on their reproductive performance. Electronic supplementary material The online version of this article (10.1186/s40104-019-0369-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Boru Zhang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Chenxi Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Wei Yang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Hongyun Zhang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Qingwei Meng
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Baoming Shi
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
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An SM, Kwon S, Hwang JH, Yu GE, Kang DG, Park DH, Kim TW, Park HC, Ha J, Kim CW. Hypomethylation in the promoter region of ZPBP as a potential litter size indicator in Berkshire pigs. Arch Anim Breed 2019; 62:69-76. [PMID: 31807615 PMCID: PMC6852858 DOI: 10.5194/aab-62-69-2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 03/01/2019] [Indexed: 01/09/2023] Open
Abstract
In pigs, litter size is typically defined as the total number of piglets born (TNB) or the number of piglets born alive (NBA). Increasing pig litter size is of great economic interest as a means to increase productivity. The capacity of the uterus is a critical component of litter size and may play a central role in prolificacy. In this study, we investigated litter-size-related epigenetic markers in uterine tissue from Berkshire pigs with smaller litter size groups (SLGs) and larger litter size groups (LLGs) using genome-wide bisulfite sequencing (GWBS). A total of 3269 differentially methylated regions (DMRs) were identified: 1566 were hypermethylated and 1703 hypomethylated in LLG compared to SLG. The zona pellucida binding protein (ZPBP) gene was significantly hypomethylated in the LLG promoter region, and its expression was significantly upregulated in uterine tissue. Thus, the methylation status of ZPBP gene was identified as a potential indicator of litter size. Furthermore, we verified its negative correlation with litter size traits (TNB and NBA) in whole blood samples from 172 Berkshire sows as a blood-based biomarker by a porcine methylation-specific restriction enzyme polymerase chain reaction (PMP) assay. The results suggest that the methylation status of the ZPBP gene can serve as a valuable epigenetic biomarker for hyperprolific sows.
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Affiliation(s)
- Sang Mi An
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Seulgi Kwon
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Jung Hye Hwang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Go Eun Yu
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Deok Gyeong Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Da Hye Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Tae Wan Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | | | - Jeongim Ha
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Chul Wook Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
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Genome-wide genetic structure and differentially selected regions among Landrace, Erhualian, and Meishan pigs using specific-locus amplified fragment sequencing. Sci Rep 2017; 7:10063. [PMID: 28855565 PMCID: PMC5577042 DOI: 10.1038/s41598-017-09969-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
As typical Chinese indigenous pig breeds, Erhualian and Meishan have been widely used to produce new strain or breed in the world. However, the genetic basis of characteristics of these pig breeds is still limited. Moreover, considering cost and output of sequencing, it is necessary to further develop cost-effective method for pig genome screening. To contribute on this issue, we developed a SLAF-seq (specific-locus amplified fragment sequencing) method for pigs and applied it to analyze the genetic difference among Landrace, Erhualian, and Meishan pigs. A total of 453.75 million reads were produced by SLAF-seq. After quality-control, 165,670 SNPs (single nucleotide polymorphisms) were used in further analysis. The results showed that Landrace had distinct genetic relationship compared to Erhualian (FST = 0.5480) and Meishan (FST = 0.5800), respectively, while Erhualian and Meishan held the relatively close genetic relationship (FST = 0.2335). Furthermore, a genome-wide scanning revealed 268 differentially selected regions (DSRs) with 855 genes and 256 DSRs with 347 genes between Landrace and the two Chinese indigenous pig breeds and between Erhualian and Meishan, respectively. This study provides a new cost-effective method for pig genome study and might contribute to a better understanding on the formation mechanism of genetic difference among pigs with different geographical origins.
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Huang L, Yin ZJ, Feng YF, Zhang XD, Wu T, Ding YY, Ye PF, Fu K, Zhang MQ. Identification and differential expression of microRNAs in the ovaries of pigs (Sus scrofa) with high and low litter sizes. Anim Genet 2016; 47:543-51. [PMID: 27435155 DOI: 10.1111/age.12452] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2016] [Indexed: 12/01/2022]
Abstract
Litter size affects profitability in the swine industry. Mammalian ovaries play important roles during reproduction, including ovulation and hormone secretion, which are tightly regulated by specific microRNAs (miRNAs). In this study, we investigated the effects of specific miRNAs on porcine litter size. We compared the ovarian miRNAs of Yorkshire pigs with high (YH) and low (YL) litter sizes using Solexa sequencing technology. We identified 327 and 320 miRNAs in the ovaries of YH and YL pigs respectively. A total of 297 miRNAs were co-expressed; 30 and 23 miRNAs respectively were specifically expressed in the two libraries. A total of 83 novel miRNAs were predicted; 37 specific miRNAs were obtained, of which 21 miRNAs were upregulated and 16 miRNAs were downregulated in YH compared with YL. Additionally, 19 628 and 19 250 target genes were predicted in the two libraries respectively. The results revealed that specific miRNAs (i.e., miR-224, miR-99a, let-7c, miR-181c, miR-214 and miR-21) may affect porcine litter size. The results of this study will help in gaining understanding of the role of miRNAs in porcine litter size regulation.
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Affiliation(s)
- L Huang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China
| | - Z J Yin
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China
| | - Y F Feng
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China
| | - X D Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China.
| | - T Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China
| | - Y Y Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China
| | - P F Ye
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China
| | - K Fu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China
| | - M Q Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R. China
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Sato S, Kikuchi T, Uemoto Y, Mikawa S, Suzuki K. Effect of candidate gene polymorphisms on reproductive traits in a Large White pig population. Anim Sci J 2016; 87:1455-1463. [DOI: 10.1111/asj.12580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/24/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Shuji Sato
- National Livestock Breeding Center; Nishigo Fukushima Japan
| | | | | | - Satoshi Mikawa
- National Institute of Agrobiological Sciences; Tsukuba Ibaraki Japan
| | - Keiichi Suzuki
- Graduate School of Agricultural Science; Tohoku University; Sendai Miyagi Japan
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Yang M, Yang B, Yan X, Ouyang J, Zeng W, Ai H, Ren J, Huang L. Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene. BMC Genet 2012; 13:57. [PMID: 22793500 PMCID: PMC3505144 DOI: 10.1186/1471-2156-13-57] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 06/28/2012] [Indexed: 11/24/2022] Open
Abstract
Background MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD) within this gene in Chinese indigenous breeds and Western commercial breeds. Results A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb) in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Conclusions Chinese and Western breeds have similar nucleotide diversity but evolve divergently in the MUC4 region. Western breeds exhibited unusual low LD extent at the MUC4 locus, reflecting the complexity of nucleotide variability of pig genome. The finding suggests that high density (e.g. 1SNP/10 kb) markers are required to capture the underlying causal variants at such regions.
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Affiliation(s)
- Ming Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
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