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Zhang Y, Song Y, Zhang W, Xiao T, Peng H. Effect of NLR family pyrin domain containing 9 gene polymorphism on litter size in large white pigs. Anim Biotechnol 2023; 34:4547-4552. [PMID: 36651576 DOI: 10.1080/10495398.2023.2166840] [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: 01/19/2023]
Abstract
NLR family pyrin domain containing 9 (NLRP9) is a mammalian reproduction-related gene. In this study, we researched the associations between polymorphisms located in the coding sequence (CDS) of the NLRP9 gene, and both the total number of piglets born per litter (TNB) and the number of piglets born alive per litter (NBA) in Canada Large White pigs (CLW). We detected a single nucleotide polymorphism (SNP) within exon 3 (g.10910C > T). The allele frequencies at the NLRP9 locus were 0.474 for the C allele and 0.526 for the T allele. Three genotypes, CC, CT, and TT, occurred with frequencies of 0.216, 0.515, and 0.269, respectively. Sows with the CC genotype had the largest TNB and NBA, sows with TT had the smallest, and those with CT were in-between. This difference was statistically significant (p < 0.05). Furthermore, CC females grew faster than CT or TT females, and there was a significant relationship between NLRP9 polymorphism and the average daily gain (p < 0.05). Here, we provide the first evidence for a novel SNP in NLRP9 associated with litter size in CLW sows, which could be used as a genetic marker to improve litter size in pig breeding and production.
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Affiliation(s)
- Yanyan Zhang
- College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yongqi Song
- Ruzhou Vocational and Technical College, Ruzhou, Henan, China
| | - Wenchang Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Tianfang Xiao
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Hui Peng
- College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
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Mojodi E, Mosadegh Mehrjardi A, Naeimzadeh Y, Ghasemi N, Falahati A, Mohammad Moshtaghioun S. The sequence variation of mitochondrial tRNA tyrosine and cysteine among Iranian women with idiopathic recurrent miscarriage: A case-control study. Int J Reprod Biomed 2023; 21:567-576. [PMID: 37727391 PMCID: PMC10505698 DOI: 10.18502/ijrm.v21i7.13894] [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: 04/24/2022] [Revised: 12/08/2022] [Accepted: 06/07/2023] [Indexed: 09/21/2023] Open
Abstract
Background Recurrent miscarriage is one of the most prevalent reproductive diseases. This phenomenon has several reasons, including maternal, hormonal, immunological, and parental genetic factors. Idiopathic recurrent miscarriage (IRM), with no distinctive etiology, involves about half of the recurrent miscarriage cases. Some mutations in mitochondrial DNA can lead to miscarriage. Mitochondrial tRNA (mt-tRNA) mutations cause nearly half of the mitochondrial disorders. Objective To identify mt- tRNAC y s & T y r gene mutations in Iranian women with IRM. Materials and Methods In this case-control study, 100 Iranian women with IRM and 100 women as control without any history of miscarriage were investigated by polymerase chain reaction-single strand conformation polymorphism technique followed by gene sequencing. Bioinformatics analysis were done using human mitochondrial genome database, molecular evolutionary genetics analysis, mammalian mitochondrial-tRNA, etc. Results Results showed 4 mt-tRNA mutations including 1 cysteine mt-tRNA mutation (5824C> T) and 3 tyrosine mt-tRNA mutations (5868T> A, 5849C> T, and 5836T> C) in our cases. Conclusion Amongst the 4 mutations found, one was novel that is still not reported. Our bioinformatics analysis revealed that these mutations can be pathogenic. They occurred in tRNA-conserved regions and their secondary structure was changed, which can result in mitochondrial dysfunction. Mutations of these genes may help in the assessment of IRM. Further study of all 22 mt-tRNAs possible mutations is recommended to describe their etiologic role in IRM.
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Affiliation(s)
- Elham Mojodi
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - Alimohammad Mosadegh Mehrjardi
- Department of Traditional Pharmacy, Faculty of Traditional Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yasaman Naeimzadeh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasrin Ghasemi
- Abortion Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ali Falahati
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
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Sharma S, Sandhir R, Ganju L, Kumar B, Singh Y. Unique mutations in mitochondrial DNA and associated pathways involved in high altitude pulmonary edema susceptibility in Indian lowlanders. J Biomol Struct Dyn 2022:1-16. [PMID: 35666092 DOI: 10.1080/07391102.2022.2081610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
High altitude pulmonary edema (HAPE) is a life threatening non-cardiogenic pulmonary edema that occurs in an otherwise healthy individuals travelling to altitude above 2500 m. Earlier studies have reported association of mutations in nuclear (nDNA) and mitochondrial DNA (mtDNA) with HAPE susceptibility. However, the molecular mechanisms involved in the pathobiology of HAPE have not been fully understood. The present study investigates the genetic predisposition to HAPE by analyzing the mtDNA mutations in HAPE susceptibles (n = 23) and acclimatized controls (n = 23) using next generation sequencing. Structural analysis of mutations was done using SWISS Model server and stability was determined using ΔΔG values. Meta-analysis of GSE52209 dataset was done to identify differentially expressed genes (DEGs) in HAPE susceptibles and acclimatized controls. Fourteen non-synonymous, conserved and pathogenic mutations were predicted using SIFT and PolyPhen scoring in protein coding genes, whereas six mutations in mt-tRNA genes showed association with HAPE (p ≤ 0.05). The structural analysis of these mutations revealed conformational changes in critical regions in Complexes I-V which are involved in subunit assembly and proton pumping activity. The protein-protein interaction network analysis of DEGs showed that HIF1α, EGLN2, EGLN3, PDK1, TFAM, PPARGC1α and NRF1 genes form highly interconnected cluster. Further, pathway enrichment analysis using DAVID revealed that "HIF-1 signaling", "oxidative phosphorylation" and "Metabolic pathways" had strong association with HAPE. Based on the findings it appears that the identified mtDNA mutations may be a potential risk factor in development of HAPE with the associated pathways providing mechanistic insight into the understanding of pathobiology of HAPE and sites for development of therapeutic targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swati Sharma
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi, India.,Department of Biochemistry, Basic Medical Sciences Block II, Panjab University, Chandigarh, India
| | - Rajat Sandhir
- Department of Biochemistry, Basic Medical Sciences Block II, Panjab University, Chandigarh, India
| | - Lilly Ganju
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi, India
| | - Bhuvnesh Kumar
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi, India
| | - Yamini Singh
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi, India
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Wang D, Yang L, Ning C, Liu JF, Zhao X. Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs. BMC Genomics 2021; 22:736. [PMID: 34641784 PMCID: PMC8507312 DOI: 10.1186/s12864-021-08030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Background Reference sequences play a vital role in next-generation sequencing (NGS), impacting mapping quality during genome analyses. However, reference genomes usually do not represent the full range of genetic diversity of a species as a result of geographical divergence and independent demographic events of different populations. For the mitochondrial genome (mitogenome), which occurs in high copy numbers in cells and is strictly maternally inherited, an optimal reference sequence has the potential to make mitogenome alignment both more accurate and more efficient. In this study, we used three different types of reference sequences for mitogenome mapping, i.e., the commonly used reference sequence (CU-ref), the breed-specific reference sequence (BS-ref) and the sample-specific reference sequence (SS-ref), respectively, and compared the accuracy of mitogenome alignment and SNP calling among them, for the purpose of proposing the optimal reference sequence for mitochondrial DNA (mtDNA) analyses of specific populations Results Four pigs, representing three different breeds, were high-throughput sequenced, subsequently mapping reads to the reference sequences mentioned above, resulting in a largest mapping ratio and a deepest coverage without increased running time when aligning reads to a BS-ref. Next, single nucleotide polymorphism (SNP) calling was carried out by 18 detection strategies with the three tools SAMtools, VarScan and GATK with different parameters, using the bam results mapping to BS-ref. The results showed that all eighteen strategies achieved the same high specificity and sensitivity, which suggested a high accuracy of mitogenome alignment by the BS-ref because of a low requirement for SNP calling tools and parameter choices. Conclusions This study showed that different reference sequences representing different genetic relationships to sample reads influenced mitogenome alignment, with the breed-specific reference sequences being optimal for mitogenome analyses, which provides a refined processing perspective for NGS data. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08030-1.
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Affiliation(s)
- Dan Wang
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Liu Yang
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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Liu H, Wang J, Wang D, Kong M, Ning C, Zhang X, Xiao J, Zhang X, Liu J, Zhao X. Cybrid Model Supports Mitochondrial Genetic Effect on Pig Litter Size. Front Genet 2020; 11:579382. [PMID: 33384712 PMCID: PMC7770168 DOI: 10.3389/fgene.2020.579382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/23/2020] [Indexed: 11/13/2022] Open
Abstract
In pigs, mitochondrial DNA (mtDNA) polymorphism and the correlation to reproductive performance across breeds and individuals have been largely reported, however, experimental proof has never been provided. In this study, we analyzed 807 sows for correlation of total number born (TNB) and mitotype, which presented the maximum of 1.73 piglets for mtDNA contribution. Cybrid models representing different mitotypes were generated for identification of the mtDNA effect. Results indicated significant differences on cellular and molecular characteristics among cybrids, including energy metabolic traits, mtDNA copy numbers and transcriptions, mRNA and protein expressions on mitochondrial biogenesis genes and reproduction-related genes. Referring to mitotypes, the cybrids with prolific mitotypes presented significantly higher oxygen consumption rate (OCR) productions, mtDNA transcriptions and copy numbers than those with common mitotypes, while both mRNA and protein expressions of PPARA, TFAM, ER1, ER2, and ESRRG in prolific cybrids were significantly higher than those with common mitotypes. Cybrid models reflected the mtDNA effect on pig litter size, suggesting the potential application of mtDNA polymorphism in pig selection and breeding practices.
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Affiliation(s)
- Hao Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Wenshang Professor Workstation of China Agricultural University, Jining, China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
| | - Dan Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Minghua Kong
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Xing Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Wenshang Professor Workstation of China Agricultural University, Jining, China
| | - Jinlong Xiao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Wenshang Professor Workstation of China Agricultural University, Jining, China
| | - Xin Zhang
- Wenshang Professor Workstation of China Agricultural University, Jining, China.,Jining Animal Husbandry Station, Jining, China
| | - Jianfeng Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xingbo Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Wenshang Professor Workstation of China Agricultural University, Jining, China
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Wang D, Xiang H, Ning C, Liu H, Liu JF, Zhao X. Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses. Brief Bioinform 2020; 21:1368-1377. [PMID: 31204429 DOI: 10.1093/bib/bbz060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/19/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic associations between mitochondrial DNA (mtDNA) and economic traits have been widely reported for pigs, which indicate the importance of mtDNA. However, studies on mtDNA heteroplasmy in pigs are rare. Next generation sequencing (NGS) methodologies have emerged as a promising genomic approach for detection of mitochondrial heteroplasmy. Due to the short reads, flexible bioinformatic analyses and the contamination of nuclear mitochondrial sequences (NUMTs), NGS was expected to increase false-positive detection of heteroplasmy. In this study, Sanger sequencing was performed as a gold standard to detect heteroplasmy with a detection sensitivity of 5% in pigs and then one whole-genome sequencing method (WGS) and two mtDNA enrichment sequencing methods (Capture and LongPCR) were carried out. The aim of this study was to determine whether mitochondrial heteroplasmy identification from NGS data was affected by NUMTs. We find that WGS generated more false intra-individual polymorphisms and less mapping specificity than the two enrichment sequencing methods, suggesting NUMTs indeed led to false-positive mitochondrial heteroplasmies from NGS data. In addition, to accurately detect mitochondrial diversity, three commonly used tools-SAMtools, VarScan and GATK-with different parameter values were compared. VarScan achieved the best specificity and sensitivity when considering the base alignment quality re-computation and the minimum variant frequency of 0.25. It also suggested bioinformatic workflow interfere in the identification of mtDNA SNPs. In conclusion, intra-individual polymorphism in pig mitochondria from NGS data was confused with NUMTs, and mtDNA-specific enrichment is essential before high-throughput sequencing in the detection of mitochondrial genome sequences.
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Affiliation(s)
- Dan Wang
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hai Xiang
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong 528231, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Liu
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
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