1
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Bai Y, Bo D, Bi Y, Areb E, Zhu H, Pan C, Lan X. Analysis of goat PPP6C mRNA profile, detection of genetic variations, and their associations with litter size. Anim Reprod Sci 2024; 268:107544. [PMID: 38981196 DOI: 10.1016/j.anireprosci.2024.107544] [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] [Received: 03/11/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024]
Abstract
The Protein Phosphatase 6 Catalytic Subunit (PPP6C) is evolutionarily a conserved gene in eukaryotes known to play a significant role in mammalian reproduction. This study aimed to investigate expression patterns of PPP6C and explore its association with litter size in Shaanbei white cashmere (SBWC) goats. Initially, we determined the mRNA expression levels of PPP6C in both male and female goats across multiple tissues. The results showed that PPP6C mRNA was expressed in multiple tissues, with higher levels in the testis and fallopian tubes, suggesting its involvement in goat reproduction. Additionally, we identified a novel 19 bp InDel within the PPP6C gene in a population of 1030 SBWC goats, which exhibited polymorphism. Statistical analysis revealed a significant association between the19 bp InDel mutation and litter size (P < 0.05). Subsequent, bioinformatics analysis, including linkage disequilibrium (LD) block and selective scanning, highlighted the linkage tendency among most InDel loci did not stand out within B-8 block, there were still some InDel loci linked to the 19 bp within a relatively narrow region. Furthermore, comparative analysis with Bezoars, these selective signals all indicated that this gene was under higher selection pressure, implying that the 19 bp InDel locus within the PPP6C is potentially associated with domesticated traits, particularly in relation to litter size. The results of the present study suggest that the PPP6C is a vital candidate gene affecting prolificacy in goats, with implications for selective breeding programs for goat breeds.
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Affiliation(s)
- Yangyang Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Didi Bo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yutian Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ebadu Areb
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Central Ethiopia Agricultural Research Institute at Worabe Agricultural Research Center, Worabe, Ethiopia
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi 719000, 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, Shaanxi 712100, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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2
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Song X, Bai Y, Yuan R, Zhu H, Lan X, Qu L. InDel and CNV within the AKAP13 Gene Revealing Strong Associations with Growth Traits in Goat. Animals (Basel) 2023; 13:2746. [PMID: 37685010 PMCID: PMC10487263 DOI: 10.3390/ani13172746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
A-kinase-anchoring protein 13 (AKAP13) is a member of the AKAP protein family that has been found to be associated with bone formation. Thus, we investigated the AKAP13 gene as a potential candidate gene for molecular-marker-assisted selection (MAS) in breeding. Our aim was to explore genetic variations (InDel and CNV) within the AKAP13 gene of Shaanbei white cashmere (SBWC) goats and analyze their relationship with growth traits. Ultimately, we identified three InDel loci (16-bp deletion, 15-bp insertion, and 25-bp deletion) and three CNVs, and the 16-bp and 15-bp loci were significantly associated with goat body length (p < 0.05). Both the 16-bp deletion variant and the 15-bp insertion variant facilitated an increase in body length in goats. In addition to this, there was a certain superposition effect between 16-bp and 15-bp loci, although there was no linkage. Additionally, the CNV1 locus was significantly correlated with body height and body length of goats (p < 0.05), and CNV2 was significantly correlated with chest depth, chest circumference, and cannon circumference of goats (p < 0.05). Individuals with gain type showed excellent growth performance. In conclusion, the InDel and CNV loci that we have identified could possibly serve as effective molecular markers in goat breeding, which is very essential for improving efficiency and success of breeding. Moreover, our findings provide a new avenue for further research into the function of the AKAP13 gene.
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Affiliation(s)
- Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
| | - Yangyang Bai
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Rongrong Yuan
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
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3
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Goat MyoD1: mRNA expression, InDel and CNV detection and their associations with growth traits. Gene 2023; 866:147348. [PMID: 36898510 DOI: 10.1016/j.gene.2023.147348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
The Myogenic differentiation 1 (MyoD1) gene is a crucial regulator of muscle formation and differentiation. However, there are few studies on the mRNA expression pattern of the goat MyoD1 gene and its effect on goat growth and development. To address this, we investigated the mRNA expression of the MyoD1 gene in several tissues of fetal and adult goats, containing heart, liver, spleen, lung, kidney and skeletal muscle. The results focused on the expression of the MyoD1 gene in skeletal muscle of fetal goats was much higher than adult goats, suggesting its important role in skeletal muscle formation and development. Following, a total of 619 Shaanbei White Cashmere goats (SBWCs) were used to monitor the InDel (Insertion/Deletion) and CNV (Copy Number Variation) variations of the MyoD1 gene. Three InDel loci were identified, and there was no significant correlation with goat growth traits. Furthermore, a CNV locus containing the MyoD1 gene exon with three types (Loss type, Normal type, Gain type) were identified. The association analysis results showed that the CNV locus was significantly associated with body weight, height at hip cross, heart girth and hip width in SBWCs (P < 0.05). Meanwhile, the Gain type of CNV exhibited the best growth traits and good consistency among three types in goats, suggesting its potential as a DNA marker for marker-assisted breeding of goats. Overall, our study provided a scientific basis for breeding goats with better growth and development traits.
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Zhong T, Wang X, Huang C, Yang L, Zhao Q, Chen X, Freitas-de-Melo A, Zhan S, Wang L, Dai D, Cao J, Guo J, Li L, Zhang H, Niu L. A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array. Animal 2023; 17:100706. [PMID: 36758301 DOI: 10.1016/j.animal.2023.100706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Tibetan goats, Taihang goats, Jining grey goats, and Meigu goats are the representative indigenous goats in China, found in Qinghai-Tibet Plateau, Western pastoral area, Northern and Southern agricultural regions. Very few studies have conducted a comprehensive analysis of the genomic diversity and selection of these breeds. We genotyped 96 unrelated individuals, using goat 53 K Illumina BeadChip array, of the following goat breeds: Tibetan (TG), Taihang (THG), Jining grey (JGG), and Meigu (MGG). A total of 45 951 single nucleotide polymorphisms were filtered to estimate the genetic diversity and selection signatures. All breeds had a high proportion (over 95%) of polymorphic loci. The observed and excepted heterozygosity ranged from 0.338 (MGG) to 0.402 (JGG) and 0.339 (MGG) to 0.395 (JGG), respectively. Clustering analysis displayed a genetically distinct lineage for each breed, and their Fst were greater than 0.25, indicating that they had a higher genetic differentiation between groups. Furthermore, effective population size reduced in all four populations, indicating a loss of genetic diversity. In addition, runs of homozygosity were mainly distributed in 5-10 Mb. Lastly, we identified signature genes, which were closely related to high-altitude adaptation (ADIRF) and prolificity (CNTROB, SMC3, and PTEN). This study provides a valuable resource for future studies on genome-wide perspectives on the diversity and selection signatures of Chinese indigenous goats.
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Affiliation(s)
- Tao Zhong
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinlu Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunhua Huang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Liu Yang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xiaoyong Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Aline Freitas-de-Melo
- Departamento de Biociencias Veterinarias, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Siyuan Zhan
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dinghui Dai
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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5
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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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6
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Wang Q, Bi Y, Wang Z, Zhu H, Liu M, Wu X, Pan C. Goat SNX29: mRNA expression, InDel and CNV detection, and their associations with litter size. Front Vet Sci 2022; 9:981315. [PMID: 36032302 PMCID: PMC9399746 DOI: 10.3389/fvets.2022.981315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
The sorting nexin 29 (SNX29) gene, a member of the SNX family, is associated with material transport and lipid metabolism. Previous studies have shown that lipid metabolism affects reproductive function in animals. Thus, we hypothesized there is a correlation between the SNX29 gene and reproductive trait. To date, studies on the relationship between the SNX29 gene and reproductive traits are limited. Therefore, the purpose of this study was to examine the polymorphism in the SNX29 gene and its correlation with litter size. Herein, the mRNA expression levels of SNX29 were assayed in various goat tissue. Surprisingly, we found that SNX29 was highly expressed in the corpus luteum, large and small follicles. This result led us to suggest that the SNX29 gene has a critical role in reproduction. We further detected potential polymorphisms in Shaanbei white cashmere (SBWC) goats, including insertion/deletion (InDel, n = 2,057) and copy number variation (CNV, n = 1,402), which were related to fertility. The 17 bp deletion (n = 1004) and the 20 bp deletion (n = 1,053) within the SNX29 gene were discovered to be significantly associated with litter size (P < 0.05), and individuals the ID genotype of P1-Del-17 bp and the DD genotype of P2-Del-20bp had larger litter size. Additionally, the four CNV loci had significant correlations with litter size (P < 0.01) in our detected population. In CNV5, individuals with the median genotype were superior compared to those with loss or gain genotype in term of litter size, and in other three CNVs showed better reproductive trait in the gain genotype. Briefly, these findings suggest that SNX29 could be used as a candidate gene for litter size in goat breeding through marker-assisted selection (MAS).
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Affiliation(s)
- Qian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Yi Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Zhiying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- Life Science Research Center, Yulin University, Yulin, China
| | - Mei Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xianfeng Wu
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, China
- *Correspondence: Chuanying Pan
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
- Xianfeng Wu
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7
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Zhang X, Yuan R, Bai Y, Yang Y, Song X, Lan X, Pan C. A deletion mutation within the goat AKAP13 gene is significantly associated with litter size. Anim Biotechnol 2021; 34:350-356. [PMID: 34431749 DOI: 10.1080/10495398.2021.1968418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A-kinase anchoring protein 13 (AKAP13) is one of the AKAP protein family members, which is correlated with estrogen receptors (ERs) and progesterone receptor (PR) activity. Consequently, the AKAP13 gene is considered to be one of the candidate genes for regulating female fertility. Hence, the objectives of this study were to discover the potential insertion/deletion (indel) variants within the AKAP13 gene and evaluate their associations with litter size of Shaanbei white cashmere goats (SBWC) to screen candidate genes for the molecular marker-assisted selection (MAS). Ultimately, we found the 16-bp deletion of AKAP13 gene which displayed three genotypes (II, ID and DD). However, it was not confirmed to Hardy-Weinberg equilibrium (HWE) in the tested population. Statistical analysis demonstrated that this 16-bp indel locus was significantly associated with litter size in goats (p < 0.05), in which the ID genotype was a key genotype for increasing litter size in goats. Besides, independent χ2 tests between different genotypes and litter size showed that high-prolific groups had higher frequency of the 'D' allele (p < 0.05). Briefly, AKAP13 gene is a candidate gene for improving fertility, and its 16-bp indel locus can be used as a valid DNA molecular marker for the MAS in goat breeding.
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Affiliation(s)
- Xinwei Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rongrong Yuan
- College of Life Sciences, Yulin University, Yulin, China
| | - Yangyang Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuta Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyue Song
- College of Life Sciences, Yulin University, Yulin, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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8
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Erdenee S, Akhatayeva Z, Pan C, Cai Y, Xu H, Chen H, Lan X. An insertion/deletion within the CREB1 gene identified using the RNA-sequencing is associated with sheep body morphometric traits. Gene 2021; 775:145444. [PMID: 33484760 DOI: 10.1016/j.gene.2021.145444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/02/2020] [Accepted: 01/13/2021] [Indexed: 12/31/2022]
Abstract
In a previous study, the cyclic AMP response element-binding protein 1 (CREB1) gene, which is likely involved in the regulation of fat metabolism in sheep adipose tissue, was identified using RNA sequencing. CREB1 is a transcription factor that participates in the regulation of cell proliferation, differentiation, and survival as well as energy metabolism. Therefore, based on preliminary studies, this study aimed to reveal the correlation between the insertion/deletion (indel) polymorphism of the CREB1 gene and sheep growth traits. One insertion variation of the ovine CREB1 gene, C3-ins-26 bp, was investigated in 1847 Chinese and Mongolian sheep breeds. The minor allele frequencies in the CREB1 gene varied from 0.021 to 0.938. Further, statistical analyses indicated that the C3-ins-26 bp indel in the CREB1 gene was significantly related to various body measurements (body length, height, and index; chest width, depth, and width index; cannon circumference index; and height at the hip cross) in a Tan sheep population (p < 0.05). Collectively, these findings may provide important insights into marker-assisted selection of sheep.
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Affiliation(s)
- Sarantsetseg Erdenee
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, 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, Shaanxi 712100, China
| | - Yong Cai
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China; Science Experimental Center, Northwest Minzu University, Lanzhou, Gansu, China.
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China; Science Experimental Center, Northwest Minzu University, Lanzhou, Gansu, China.
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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9
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Akhatayeva Z, Mao C, Jiang F, Pan C, Lin C, Hao K, Lan T, Chen H, Zhang Q, Lan X. Indel variants within the PRL and GHR genes associated with sheep litter size. Reprod Domest Anim 2020; 55:1470-1478. [PMID: 32762057 DOI: 10.1111/rda.13796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/01/2020] [Indexed: 12/27/2022]
Abstract
Growth hormone and prolactin belong to the class of peptide hormones that have a wide range of regulatory functions. In this study, polymorphisms of growth hormone receptor (GHR) and prolactin (PRL) genes were analysed as candidate genes, which are responsible for the litter size in Australian White (AUW) sheep. According to the statistical analyses results, the polymorphism information content (PIC) values of the PRL-P1-ins-23 bp, GHR-P2-del-23 bp and GHR-P8-del-23 bp were 0.371, 0.366 and 0.375, respectively, which indicates the high genetic polymorphism in AUW sheep. Moreover, all indel loci are not conformed to the HWE (p < .05). Further, our findings revealed that the PRL-P1-ins-23 bp polymorphism in the ovine PRL gene was significantly related to the first parity litter size (p = .001) and the DD genotype displaying the highest genotypic mean. Meanwhile, the GHR-P2-del-23 bp and GHR-P8-23 bp indels in the ovine GHR gene were significantly correlated with first parity litter size (p < .05), and the individuals with the genotype II showed significantly higher litter size than others. Collectively, these results demonstrated that our findings could be useful for future sheep breeding strategies based on the molecular-assisted selection (MAS).
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Affiliation(s)
- Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Cui Mao
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Fugui Jiang
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China.,Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 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
| | - Chunjian Lin
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Kunjie Hao
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Tianxin Lan
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Xianyong Lan
- 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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10
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Zou X, Lu T, Zhao Z, Liu G, Lian Z, Guo Y, Sun B, Liu D, Li Y. Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase. BMC Genomics 2020; 21:267. [PMID: 32228439 PMCID: PMC7106838 DOI: 10.1186/s12864-020-6671-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/13/2020] [Indexed: 12/13/2022] Open
Abstract
Background Fertility is an important economic trait in the production of meat goat, and follicular development plays an important role in fertility. Although many mRNAs and microRNAs (miRNAs) have been found to play critical roles in ovarian biological processes, the interaction between mRNAs and miRNAs in follicular development is not yet completely understood. In addition, less attention has been given to the study of single follicle (dominant or atretic follicle) in goats. This study aimed to identify mRNAs, miRNAs, and signaling pathways as well as their interaction networks in the ovarian follicles (large follicles and small follicles) of uniparous and multiple Chuanzhong black goats at estrus phase using RNA-sequencing (RNA-seq) technique. Results The results showed that there was a significant difference in the number of large follicles between uniparous and multiple goats (P < 0.05), but no difference in the number of small follicles was observed (P > 0.05). For the small follicles of uniparous and multiple goats at estrus phase, 289 differentially expressed mRNAs (DEmRNAs) and 16 DEmiRNAs were identified; and for the large follicles, 195 DEmRNAs and 7 DEmiRNAs were identified. The functional enrichment analysis showed that DE genes in small follicles were significantly enriched in ovarian steroidogenesis and steroid hormone biosynthesis, while in large follicles were significantly enriched in ABC transporters and steroid hormone biosynthesis. The results of quantitative real-time polymerase chain reaction were consistent with those of RNA-seq. Analysis of the mRNA-miRNA interaction network suggested that CD36 (miR-122, miR-200a, miR-141), TNFAIP6 (miR-141, miR-200a, miR-182), CYP11A1 (miR-122), SERPINA5 (miR-1, miR-206, miR-133a-3p, miR-133b), and PTGFR (miR-182, miR-122) might be related to fertility, but requires further research on follicular somatic cells. Conclusions This study was used for the first time to reveal the DEmRNAs and DEmiRNAs as well as their interaction in the follicles of uniparous and multiple goats at estrus phase using RNA-seq technology. Our findings provide new clues to uncover the molecular mechanisms and signaling networks of goat reproduction that could be potentially used to increase ovulation rate and kidding rate in goat.
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Affiliation(s)
- Xian Zou
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Tingting Lu
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China
| | - Zhifeng Zhao
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China
| | - Zhiquan Lian
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Wushan Rd., Tianhe Dist, Guangzhou, 510642, Guangdong Province, China.
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11
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E GX, Duan XH, Zhang JH, Huang YF, Zhao YJ, Na RS, Zhao ZQ, Ma YH, Chu MX, Basang WD, Zhu YB, An TW, Luo XL, Han YG, Zeng Y. Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism. 3 Biotech 2019; 9:336. [PMID: 31475088 DOI: 10.1007/s13205-019-1869-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 08/12/2019] [Indexed: 11/24/2022] Open
Abstract
Litter size is considered to be the most important index for estimating domestic animal productivity. The number of indigenous goats in China with higher litter sizes than those of commercial breeds in other countries may be helpful for accelerating genetic improvements in goat breeding. We performed a genome-wide selective sweep analysis of 31 Dazu black goats with extreme standard deviation in litter size within the third fetus to identify significant genomic regions and candidate genes through different analyses. The analysis identified a total of 33,917,703 variants, including 32,262,179 SNPs and 1,655,524 indels. In addition, two novel candidate genes (LRP1B and GLRB), which are related to litter size, were obtained with π, Tajima's D, πA/πB, and F ST at the individual level with a 95% threshold for each parameter. These two genes were annotated in five GO terms (localization, binding, macromolecular complex, membrane part, and membrane) and two pathways (long-term depression and neuroactive ligand-receptor interaction pathway). Regarding the result of linkage disequilibrium (LD) analysis, in LRP1B and GRID2, the high-yield Dazu black goats exhibit significantly different LD patterns from low-yield goats. Litter size variability has low heritability and is related to multiple complex factors found in domestic animals. Obtaining a clear explanation and significant signal by genome-wide selective sweep analysis with a small sample size is difficult. However, we investigated some candidate genes, particularly LRP1B and GLRB, which may provide useful information for further research.
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Affiliation(s)
- Guang-Xin E
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xing-Hai Duan
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Jia-Hua Zhang
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yong-Fu Huang
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yong-Ju Zhao
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Ri-Su Na
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Zhong-Quan Zhao
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yue-Hui Ma
- 2Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 China
| | - Ming-Xing Chu
- 2Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 China
| | - Wang-Dui Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husandry Science, Lasa, 850009 China
| | - Yan-Bin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husandry Science, Lasa, 850009 China
| | - Tian-Wu An
- 4Sichuan Academy of Grassland Sciences, Chengdu, 611731 Sichuan China
| | - Xiao-Lin Luo
- 4Sichuan Academy of Grassland Sciences, Chengdu, 611731 Sichuan China
| | - Yan-Guo Han
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan Zeng
- 1Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
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12
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Yue C, Bai WL, Zheng YY, Hui TY, Sun JM, Guo D, Guo SL, Wang ZY. Correlation analysis of candidate gene SNP for high-yield in Liaoning cashmere goats with litter size and cashmere performance. Anim Biotechnol 2019; 32:43-50. [PMID: 31424321 DOI: 10.1080/10495398.2019.1652188] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This study was designed to identify the relationship of four genes (GDF9, BMPR-IB, FecB and ESR) polymorphisms in the 3'UTR region with litter size and cashmere performance of Liaoning cashmere goats (LCG, n = 1140). The ESR C463T and T575G loci of LCG were genotyped. The results of correlation analysis showed that five effective single nucleotide polymorphisms (SNPs) loci (C47T, C94T, C299T, C463T and T575G) were found in the four genes. The lambing number of CC and CT genotypic individuals at FecB C94T locus was significantly higher than that of TT genotypic individuals (45.7 and 46.8%, respectively); the lambing number of CC genotypic individuals at ESR C463T locus was significantly higher than that of CT, TT genotypic individuals (9 and 15%, respectively); There was a positive correlation between CC genotype at C463T locus and cashmere fineness. In this study, the relationship between FecB C94T and ESR C463T loci C alleles and lambing number in LCG was preliminarily revealed. These results further confirmed that FecB and ESR genes may be significantly correlated with high fecundity of LCG.
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Affiliation(s)
- Chang Yue
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agriculture University, Shenyang, P. R. China
| | - Wen L Bai
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agriculture University, Shenyang, P. R. China
| | - Yuan Y Zheng
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agriculture University, Shenyang, P. R. China
| | - Tai Y Hui
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agriculture University, Shenyang, P. R. China
| | - Jia M Sun
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agriculture University, Shenyang, P. R. China
| | - Dan Guo
- Animal Science Research Institute of Liaoning Province, Liaoyang, P. R. China
| | - Su L Guo
- Prosperous community, Changshun Town, Huade, P. R. China
| | - Ze Y Wang
- College of Animal Husbandry and Veterinary Medicine, Shenyang Agriculture University, Shenyang, P. R. China
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