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Ren H, Tang Q, Xue T, Wang Q, Xu H, Zhang Q, Pan C. A 24-bp indel within the sheep AHR gene is associated with litter size. Anim Biotechnol 2022; 33:1533-1538. [PMID: 33947312 DOI: 10.1080/10495398.2021.1914071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aryl Hydrocarbon Receptor (AHR) is a member of the PER-ARNT-SIM (PAS) family, which could mediate various biological processes, for instance, the balance of the immune system, cell proliferation, differentiation, vascular tissue remodeling and reproduction ability regulation. A previous research showed that the AHR gene exerted important functions on the pig reproduction, implying that it could serve as a candidate gene related to animal reproductive traits. Here, the aim of this work was to identify potential insertion/deletion (indel) mutations of the AHR gene in three sheep breeds and analyze the associations between these mutations and reproductive traits. Results showed that a 24-bp indel was uncovered three genotypes (II, ID and DD) in the Australian White sheep (AuW) and Lanzhou fat-tail sheep (LZFT) population, while there were only two genotypes (ID and DD) in Luxi black-headed sheep (LXBH). Moreover, the Fisher's exact test showed that the 24-bp indel mutation was significantly associated with litter size and live litter size in AuW sheep (Fisher's p < 0.05). Therefore, the 24-bp indel of sheep AHR gene can contribute to sheep marker-assisted selection breeding and further improve the sheep reproductive performance.
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Affiliation(s)
- Hongying Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Tao Xue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China.,Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry co., Ltd, Tianjin, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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2
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Liu N, Cui W, Chen M, Zhang X, Song X, Pan C. A 21-bp indel within the LLGL1 gene is significantly associated with litter size in goat. Anim Biotechnol 2019; 32:213-218. [PMID: 31646948 DOI: 10.1080/10495398.2019.1677682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The scribble cell polarity complex component (LLGL1) is part of the cytoskeletal network and is involved in maintaining cell polarity and epithelial integrity. Based on the whole-genome sequencing analysis in goat, LLGL1 gene is suggested as a putative important candidate gene affecting litter size in Shaanbei White Cashmere Goats (SBWC). Therefore, the objective of this study was to uncover the possible novel insertion/deletion (Indel) variant in goat LLGL1 gene and to evaluate its association with litter size of SBWC (n = 827). Using the PCR detection and DNA sequencing, the 21-bp indel in the upstream of LLGL1 was firstly founded and two genotypes were identified: II (insertion/insertion) and ID (insertion/deletion), respectively. Association analyses revealed that the 21-bp indel was significantly correlated with litter size (p = 0.017). Notably, the individuals with II genotype were significantly greater than that of the genotype ID, and the 'I' allele was dominant. Additionally, the remarkable influence of the indel on traits might be related to the change of DEAF-1-related (NUDR) binding site through bioinformatics analysis. Briefly, the 21-bp indel within the goat LLGL1 gene could be an effective DNA molecular marker and provide valuable theoretical basis for marker-assisted selection (MAS) in goat industry.
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Affiliation(s)
- Nuan Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenbo Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingyue Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuelian Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, China.,Life Science Research Center, Yulin University, Yulin, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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Cui W, Liu N, Zhang X, Zhang Y, Qu L, Yan H, Lan X, Dong W, Pan C. A 20-bp insertion/deletion (indel) polymorphism within the CDC25A gene and its associations with growth traits in goat. Arch Anim Breed 2019; 62:353-360. [PMID: 31807646 PMCID: PMC6852853 DOI: 10.5194/aab-62-353-2019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/17/2019] [Indexed: 12/28/2022] Open
Abstract
Cell division cycle 25A (CDC25A), a member of the CDC25 family of phosphatases, is
required for progression from G1 to the S phase of the cell cycle. CDC25A provides an essential function during early embryonic development in mice,
suggesting that it plays an important role in growth and development. In
this study, we used mathematical expectation (ME) methods to identify a
20-bp insertion/deletion (indel) polymorphism of CDC25A gene in Shaanbei White
Cashmere (SBWC) goats. We also investigated the association between this
20-bp indel and growth-related traits in SBWC goats. Association results
showed that the indel was related to growth traits (height at hip cross,
cannon circumference, and cannon circumference index) in SBWC goats. The
height at hip cross of individuals with insertion/insertion (II) genotype
was higher than those with insertion/deletion (ID) genotype (P=0.02); on
the contrary, the cannon circumference and cannon circumference index of
individuals with ID genotype were superior when compared with those with II
genotype (P=0.017 and P=0.009). These findings suggest that the 20-bp
indel in the CDC25A gene significantly affects growth-related traits, and could be
utilized as a candidate marker for marker-assisted selection (MAS) in
the cashmere goat industry.
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Affiliation(s)
- Wenbo Cui
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Nuan Liu
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Xuelian Zhang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Yanghai Zhang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China.,Life Science Research Center, Yulin University, Yulin, China
| | - Hailong Yan
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China.,Life Science Research Center, Yulin University, Yulin, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China.,College of Animals Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
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Zhao H, He S, Wang S, Zhu Y, Xu H, Luo R, Lan X, Cai Y, Sun X. Two New Insertion/Deletion Variants of the PITX2 Gene and their Effects on Growth Traits in Sheep. Anim Biotechnol 2017; 29:276-282. [PMID: 29200321 DOI: 10.1080/10495398.2017.1379415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In China, Tong sheep (TS) and Lanzhou fat-tailed sheep (LFTS) are two closely relative endanger breeds for low meat production and low fecundity, finding some marker-assisted selected (MAS) is our first priority for improving their growth traits. For this purpose, Hu sheep (HS) and small-tailed Han sheep (STHS) were compared with two endangered breeds (TS and LFTS). Paired-liked homeodomain transcription factor 2 (PITX2) gene was the important member of PITX family, which could adjust animal growth through hypothalamic-pituitary-adrenal axis. During the past years, insertion/deletion (indel) has become increasingly popular in application as MAS. In this study, two novel indel loci were identified, and five significant differences, including chest width, hip width, chest depth, chest circumference, and body height, were found between different breeds. Interestingly, there was no DD genotype and smaller number of ID genotye. All the ID genotypes were significantly greater than II genotype, which was to say the allele of "D" was dominant variation and its frequency was lower, which demonstrated that it has huge space for selection. Briefly, the two indel were potential and useful DNA markers for selecting excellent individuals in relation to growth traits in sheep.
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Affiliation(s)
- Haidong Zhao
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Shuai He
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Shuhui Wang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Yanjiao Zhu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Hongwei Xu
- b Science Experimental Center , Northwest University for Nationalities , Lanzhou , China
| | - Renyun Luo
- c Ruilin Sci-Tech Culture and Breeding Limit Company , Yongjing , China
| | - Xianyong Lan
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Yong Cai
- c Ruilin Sci-Tech Culture and Breeding Limit Company , Yongjing , China.,d College of Life Science and Engineering , Northwest University for Nationalities , Lanzhou , China
| | - Xiuzhu Sun
- a College of Animal Science and Technology , Northwest A&F University , Yangling , China
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5
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Ren F, Yu S, Chen R, Lv X, Pan C. Identification of a novel 12-bp insertion/deletion (indel) of iPS-related Oct4 gene and its association with reproductive traits in male piglets. Anim Reprod Sci 2017; 178:55-60. [PMID: 28139300 DOI: 10.1016/j.anireprosci.2017.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 01/01/2023]
Abstract
As a key factor of cellular reprogramming, Oct4 is one of vital transcription factors for induced pluripotent stem cells (iPSCs). Loss of its function or deletion causes apoptosis in primordial germ cells (PGCs), which affect reproductive traits in mammals. In this study, a novel 12-bp insertion/deletion (indel) polymorphism (NC_010449:g.2759-2760insGGTTTTTGTCTA) within the Oct4 gene was identified in 442 pigs of Large White (LW) and Landrace (LD) breeds, showing three genotypes designated as II, ID, and DD. The frequencies of allele "I" in LW and LD pigs were 0.587 and 0.648, respectively. The male piglets with homozygous II or DD genotypes of Oct4 gene exhibited better reproductive traits than those with heterozygous ID genotype. Moreover, there were two significant associations between this 12-bp indel polymorphism and testis long circumference (TLC) (P=0.005) and testis short girth (TSG) (P=0.003) as well as 15-day testis weight (TW) (P=0.013) in the LW male piglets. These findings suggest that the 12-bp indel polymorphism of the Oct4 gene might be a potential DNA marker for selecting preferred individuals in relation to reproductive traits in pig marker-assisted selection (MAS) breeding, which could contribute to the breeding and genetics in male piglets.
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Affiliation(s)
- Fa Ren
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Shuai Yu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Rui Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Xiaoyan Lv
- National Swine Foundation Seed Farm of Ankang Yangchen Modern Agriculture Group Co. Ltd, Ankang, 725000 PR China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
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6
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Goh SK, Musafer A, Witkowski T, Muralidharan V, Christophi C, Do H, Dobrovic A. Comparison of 3 Methodologies for Genotyping of Small Deletion and Insertion Polymorphisms. Clin Chem 2016; 62:1012-9. [DOI: 10.1373/clinchem.2016.256388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/16/2022]
Abstract
Abstract
BACKGROUND
The quantification of genomic chimerism is increasingly recognized for its clinical significance after transplantation. Before the measurement of chimerism, accurate genotyping of genetic polymorphisms for informative alleles that can distinguish donor DNA from recipient DNA is essential. The ease of allelic discrimination of small deletion and insertion polymorphisms (DIPs) makes DIPs attractive markers to track chimerism. Current methodologies for the genotyping of DIPs are largely based on “open-tube” approaches. “Closed-tube” approaches involving no or minimal post-PCR handling are preferred. We compared 3 distinct methodologies to determine an optimal platform for DIP genotyping.
METHODS
Genomic DNA from 19 normal individuals was genotyped for 6 small biallelic DIPs using high-resolution melting analysis (HRMA), probe-free droplet digital PCR (ddPCR), and microfluidic electrophoresis of PCR products. For HRMA, 3 different platforms were compared.
RESULTS
Our newly developed probe-free ddPCR approach allowed the genotype of each DIP to be determined by fluorescence intensity based on amplicon size. Microfluidic electrophoresis also allowed genotypes to be determined by amplicon size. HRMA assays allowed the genotype of each DIP to be determined by melting profile. Genotyping results were concordant between the 3 methodologies. HRMA was the most readily performed methodology and was robust across 3 separate HRMA-capable platforms.
CONCLUSIONS
We demonstrated the effectiveness of probe-free ddPCR to accurately genotype small biallelic DIPs. Nevertheless, HRMA proved to be the optimal approach for genotyping small DIPs because closed-tube approaches are preferred owing to rapid and less laborious workflows and least risk of PCR contamination.
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Affiliation(s)
- Su Kah Goh
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Ashan Musafer
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - Tom Witkowski
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | | | - Christopher Christophi
- Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Victoria, Australia
- Department of Pathology, University of Melbourne, Victoria, Australia
| | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Victoria, Australia
- Department of Pathology, University of Melbourne, Victoria, Australia
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