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Yang Y, Wang C, Chen S, Liu Y, Jia H, Wang H, He D. Identifying candidate genes and biological pathways in muscle development through multi-tissue transcriptome comparisons between male and female geese. Sci Rep 2024; 14:16474. [PMID: 39014195 PMCID: PMC11252291 DOI: 10.1038/s41598-024-67560-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/12/2024] [Indexed: 07/18/2024] Open
Abstract
Males and females have long shown disparities in body weight and height; yet, the underlying mechanisms influencing growth and development remain unclear. Male and female Zhedong White Geese (ZDW) geese have long been selected for large body size and egg production, respectively. This led to a large difference in body weight between males and females, making them a unique model for studying the effects of sex on growth and development. This study aimed to elucidate these mechanisms by comparing the transcriptomes of muscle and pituitary tissues in male and female ZDW geese to identify the critical genes responsible for the effects of sex on growth performance. Our analysis revealed 1101 differentially expressed genes (DEGs) in leg musculature (507 upregulated, 594 downregulated), 773 DEGs in breast musculature (311 upregulated, 462 downregulated), and 517 DEGs in the pituitary gland (281 upregulated, 236 downregulated) between male and female geese. These DEGs were significantly enriched in gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with endocrine metabolism (e.g., hormonal activities), muscle formation (e.g., sarcomere and myofibril), and bone formation (e.g., bone morphogenesis and cartilage formation). The upregulated genes in males were enriched in KEGG pathways involving nutrient digestion and absorption (vitamin and protein), as well as the secretion of digestive juices (gastric acid and bile). Through protein-protein interaction analyses, we also observed high-density gene networks related to muscle fiber development, calcium ion metabolism, mitochondrial respiratory chain, and bone development. Therefore, our multi-tissue transcriptome analysis provides a deeper understanding of the complex and systematic gender-driven effects on growth and development in geese. IGF1, GHRHR, and NCAPG-LCORL and pathways related to myogenesis might play vital roles in gender differences before hormones exert their effect.
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Affiliation(s)
- Yunzhou Yang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China
| | - Cui Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China
| | - Shufang Chen
- Institute of Animal and Poultry Science, Ningbo Academy of Agricultural Sciences, Ningbo, 315040, China
| | - Yi Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China
| | - Huiyan Jia
- Institute of Animal and Poultry Science, Ningbo Academy of Agricultural Sciences, Ningbo, 315040, China
| | - Huiying Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China.
| | - Daqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China.
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2
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Zhao J, Mu Y, Gong P, Liu B, Zhang F, Zhu L, Shi C, Lv X, Luo J. Whole-genome resequencing of native and imported dairy goat identifies genes associated with productivity and immunity. Front Vet Sci 2024; 11:1409282. [PMID: 39040818 PMCID: PMC11260678 DOI: 10.3389/fvets.2024.1409282] [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: 03/29/2024] [Accepted: 05/23/2024] [Indexed: 07/24/2024] Open
Abstract
Understanding the differences in genetic variation between local Chinese dairy goat breeds and imported breeds can help germplasm innovation and molecular breeding. However, the research is limited in this area. In this study, whole-genome resequencing data from 134 individuals of both local and imported dairy goat breeds were analyzed, and their differences in genomic genetic variation, genetic diversity, and population structure were subsequently identified. We also screened candidate genes associated with important traits of dairy goats such as milk production (STK3, GHR, PRELID3B), reproduction (ATP5E), growth and development (CTSZ, GHR), and immune function (CTSZ, NELFCD). Furthermore, we examined allele frequency distributions for the genes of interest and found significant differences between the two populations. This study provides valuable resources for the study of genetic diversity in dairy goats and lays the foundation for the selective breeding of dairy goats in the future.
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Affiliation(s)
- Jianqing Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yuanpan Mu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Baolong Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Fuhong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Lu Zhu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chenbo Shi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xuefeng Lv
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
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3
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Zuo P, Zhang C, Gao Y, Zhao L, Guo J, Yang Y, Yu Q, Li Y, Wang Z, Yang H. Genome-wide unraveling SNP pairwise epistatic effects associated with sheep body weight. Anim Biotechnol 2023; 34:3416-3427. [PMID: 36495095 DOI: 10.1080/10495398.2022.2152349] [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: 12/14/2022]
Abstract
Epistatic effects are an important part of the genetic effect of complex traits in livestock. In this study, we used 218 synthetic ewes from the Xinjiang Academy of Agricultural Reclamation in China to identify interacting paired with genome-wide single nucleotide polymorphisms (SNPs) associated with birth weight, weaning weight, and one-yearling weight. We detected 2 and 66 SNP-SNP interactions of sheep birth weight and weaning weight, respectively. No significant epistatic interaction of one-year-old body weight was detected. The genetic interaction of sheep body weight is dynamic and time-dependent. Most significant interactions of weaning body weight contributed 1% or higher. In the weaning weight trait, 66 significant SNP pairs consisted of 98 single SNPs covering 23 chromosomes, 5 of which were nonsynonymous SNPs (nsSNPs), resulting in single amino acid substitution. We found that genes that interact with transcription factors (TFs) are target genes for the corresponding TFs. Four epitron networks affecting weaning weight, including subnetworks of HIVEP3 and BACH2 transcription factors, constructed using significant SNP pairs, were also analyzed and annotated. These results suggest that transcription factors may play an important role in explaining epistatic effects. It provides a new idea to study the genetic mechanism of weight developing.
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Affiliation(s)
- Peng Zuo
- College of Science, Northeast Agricultural University, Harbin
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Chaoxin Zhang
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yupeng Gao
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Engineering, Northeast Agricultural University, Harbin, China
| | - Lijunyi Zhao
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Information and Electrical Engineering, Northeast Agricultural University, Harbin, China
| | - Jiaxu Guo
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation, Shihezi, Hebei, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation, Shihezi, Hebei, China
| | - Yunna Li
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhipeng Wang
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation, Shihezi, Hebei, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation, Shihezi, Hebei, China
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Wang X, Li J, Bai J, Chen M, Wang L, Fan H, Zeng F, Lu X, He Y. Exploring the Impact of Insertion/Deletion in FTO and PLIN1 Genes on Morphometric Traits in Sheep. Animals (Basel) 2023; 13:3032. [PMID: 37835645 PMCID: PMC10571888 DOI: 10.3390/ani13193032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023] Open
Abstract
This study aimed to identify InDels from the FTO and PLIN1 genes and to analyze their association with morphometric traits in Hu sheep (HS), Dupor sheep (DS), and Small Tail Han sheep (STHS). The FTO and PLIN1 genes were genotyped using the insertion/deletion (InDel) method. A one-way ANOVA with SPSS 26.0 software (IBM Corp, Armonk, NY, USA) was used to assess the effect of the InDel FTO and PLIN1 genes on morphometric traits. The results revealed significant associations between certain InDels and the morphometric traits in different breeds of sheep. Specifically, FTO-2 was significantly associated with cannon circumference (CaC) in HS rams and body height (BoH) in HS ewes (p < 0.05). FTO-2 was also significantly associated with chest width (ChW), CaC, head length (HeL), and coccyx length (CoL) in the STHS breed (p < 0.05). FTO-3 showed significant associations with BoH in HS rams and BoH, back height (BaH), ChW, and chest depth (ChD) in HS ewes (p < 0.05). FTO-3 was also significantly associated with ChW in the DS and STHS breeds (p < 0.05). FTO-5 was significantly associated with body weight (BoW) in the DS breed and BoH in the STHS breed (p < 0.05). Furthermore, PLIN1 was significantly related to BoW in the DS breed and was significantly associated with CoL and forehead width (FoW) in the STHS breed (p < 0.05). In conclusion, the study suggested that InDels in the FTO and PLIN1 genes could provide practical information to improve morphometric traits in sheep breeding.
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Affiliation(s)
| | | | - Junyan Bai
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (X.W.)
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Sun X, Niu Q, Jiang J, Wang G, Zhou P, Li J, Chen C, Liu L, Xu L, Ren H. Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers. Genes (Basel) 2023; 14:1183. [PMID: 37372363 DOI: 10.3390/genes14061183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the Youzhou dark (YZD) goat population (n = 206) using the Illumina GoatSNP54 BeadChip. In the GWAS, we identified one SNP (snp54094-scaffold824-899720) on chromosome 11 for litter size, two SNPs on chromosome 26 (snp11508-scaffold142-1990450, SORCS3) and chromosome 12 (snp55048-scaffold842-324525, LOC102187779) for coat colour and one SNP on chromosome 18 (snp56013-scaffold873-22716, TCF25) for the black middorsal stripe. In contrast, no SNPs were identified for skin colour. In selection signature analysis, 295 significant iHS genomic regions with a mean |iHS| score > 2.66, containing selection signatures encompassing 232 candidate genes were detected. In particular, 43 GO terms and one KEGG pathway were significantly enriched in the selected genes, which may contribute to the excellent environmental adaptability and characteristic trait formation during the domestication of YZD goats. In ROH detection, we identified 4446 ROH segments and 282 consensus ROH regions, among which nine common genes overlapped with those detected using the iHS method. Some known candidate genes for economic traits such as reproduction (TSHR, ANGPT4, CENPF, PIBF1, DACH1, DIS3, CHST1, COL4A1, PRKD1 and DNMT3B) and development and growth (TNPO2, IFT80, UCP2, UCP3, GHRHR, SIM1, CCM2L, CTNNA3 and CTNNA1) were revealed by iHS and ROH detection. Overall, this study is limited by the small population size, which affects the results of GWAS to a certain extent. Nevertheless, our findings could provide the first overview of the genetic mechanism underlying these important traits and provide novel insights into the future conservation and utilisation of Chinese goat germplasm resources.
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Affiliation(s)
- Xiaoyan Sun
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Qunhao Niu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Jiang
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Peng Zhou
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Jie Li
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Cancan Chen
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Liangjia Liu
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
| | - Lingyang Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hangxing Ren
- Chongqing Academy of Animal Sciences, Rongchang 402460, China
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6
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Yang Y, Sun X, Cui W, Liu N, Wang K, Qu L, Pan C. The detection of mutation within goat cell division cycle 25 A and its effect on kidding number. Anim Biotechnol 2022; 33:1504-1509. [PMID: 33879023 DOI: 10.1080/10495398.2021.1910519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cell division cycle 25 A (CDC25A) accounts for an essential function on early folliculogenesis of female mammals, especially regulating the function of intra-ovarian, thus this gene is pinpointed as a candidate gene that influences the kidding number of goat. On this ground, the purpose of this study was to investigate whether the reported 20-nt nucleotide variants locus (rs639467625) of the CDC25A gene influences kidding number in Shaanbei white cashmere goat (SBWC). The χ2-test showed that there were more ID genotypes in mothers of multiple lambs than in mothers of single lambs. Interestingly, this indel locus was related to the first-born kidding number in the group of SBWC goats (p < 0.05). Similarly, the result of the t-test was consistent with the result of the χ2-test, showed the kidding number of ID genotype individuals was large than that of II individuals (p < 0.05). These findings proved that the different genotypes of CDC25A have impacts on goat kidding numbers. Thus, the results led us to speculate that the ID genotype of CDC25A was one of the main indel influencing goat kidding numbers. Simultaneously, this study was expected to provide useful DNA markers for superior individuals selection by marker-assisted selection (MAS) and make a contribution to goats breeding.
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Affiliation(s)
- Yuta Yang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaomei Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Wenbo Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Nuan Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Qu
- College of Life Sciences, Yulin University, Yulin, Shaanxi, PR China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, 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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7
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Yuan Y, Yang B, He Y, Zhang W, E G. Genome-Wide Selection Signal Analysis of Australian Boer Goat by Insertion/Deletion Variants. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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8
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Selionova M, Aibazov M, Mamontova T, Malorodov V, Sermyagin A, Zinovyeva N, Easa AA. Genome-wide association study of live body weight and body conformation traits in young Karachai goats. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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9
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Kang Y, Zhu Q, Meng F, Xu H, Guo Z, Pan C. Rapid detection of InDel within the KDM3B gene in five sheep breeds using the mathematical expectation (ME) method. Gene 2022; 834:146598. [PMID: 35598684 DOI: 10.1016/j.gene.2022.146598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/02/2022] [Accepted: 05/16/2022] [Indexed: 12/20/2022]
Abstract
Lysine demethylase 3B (KDM3B), a candidate gene associated with bone formation and growth, and differentiation of osteoblast, might affect the animal growth traits. Herein, the insertion/deletion (InDel) of the KDM3B gene was quickly detected in 882 sheep from five breeds using the mathematical expectation (ME) method. The results showed that there were two genotypes of 7-bp variation in KDM3B, including II (insertion/insertion) and ID (insertion/deletion), and the frequency of two genotypes varied among the five sheep breeds. Association analysis results demonstrated that the 7-bp indel was significantly associated with chest depth of LFT sheep (P = 0.012), and body weight (P = 0.006), body height (P = 0.030), chest depth (P = 0.043), chest circumference (P = 0.016), abdominal width (P = 0.035) and height at hip cross (P = 0.022) in LXBH sheep. Moreover, II genotype was the predominant genotype with excellent consistency in sheep growth traits (P < 0.05). Collectively, the above results suggest that this locus can be used as an effective molecular marker to improve the sheep growth traits and provide a scientific basis for the development of sheep breeding.
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Affiliation(s)
- Yuxin Kang
- 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.
| | - Qihui Zhu
- 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.
| | - Fanxin Meng
- 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.
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China; Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China.
| | - Zhengang Guo
- Animal Husbandry and Veterinary Science Institute, Bijie, Guizhou 551700, China; Guizhou New Wumeng Ecological Animal Husbandry Development Limited Company, Hezhang, Guizhou 553200, 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.
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Zhou Z, Jiang T, Zhu Y, Ling Z, Yang B, Huang L. A comparative investigation on
H3K27ac
enhancer activities in the brain and liver tissues between wild boars and domesticated pigs. Evol Appl 2022; 15:1281-1290. [PMID: 36051459 PMCID: PMC9423090 DOI: 10.1111/eva.13461] [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: 02/14/2022] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
Dramatic phenotypic differences between domestic pigs and wild boars (Sus scrofa) provide opportunities to investigate molecular mechanisms underlying the formation of complex traits, including morphology, physiology and behaviour. Most studies comparing domestic pigs and wild boars have focused on variations in DNA sequences and mRNA expression, but not on epigenetic changes. Here, we present a genome‐wide comparative study on H3K27ac enhancer activities and the corresponding mRNA profiling in the brain and liver tissues of adult Bama Xiang pigs (BMXs) and Chinese wild boars (CWBs). We identified a total of 1,29,487 potential regulatory elements, among which 11,241 H3K27ac peaks showed differential activity between CWBs and BMXs in at least one tissue. These peaks were overrepresented by binding motifs of FOXA1, JunB, ATF3 and BATF, and overlapped with differentially expressed genes that are involved in female mating behaviour, response to growth factors and hormones, and lipid metabolism. We also identified 4118 nonredundant super‐enhancers from ChIP‐Seq data on H3K27ac. Notably, we identified differentially active peaks located close to or within candidate genes, including TBX19, MSTN, AHR and P2RY1, which were identified in DNA sequence‐based population differentiation studies. This study generates a valuable dataset on H3K27ac profiles of the brain and liver from domestic pigs and wild boars, which helps gain insights into the changes in enhancer activities from wild boars to domestic pigs.
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Affiliation(s)
- Zhimin Zhou
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Tao Jiang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yaling Zhu
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Ziqi Ling
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Bin Yang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Lusheng Huang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
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Polymorphisms of the Growth Hormone Releasing Hormone Receptor Gene Affect Body Conformation Traits in Chinese Dabieshan Cattle. Animals (Basel) 2022; 12:ani12131601. [PMID: 35804502 PMCID: PMC9265053 DOI: 10.3390/ani12131601] [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: 05/12/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
This study was performed to expose the polymorphisms of the growth hormone-releasing hormone receptor gene in Chinese Dabieshan cattle, evaluate its effect on body conformation traits, and find potential molecular markers in Chinese cattle. The GHRHR structure and the phylogenetic tree were analyzed using bioinformatics software. The polymorphism of the GHRHR gene in 486 female cattle was genotyped by PCR-RFLP and DNA sequencing, and the association between SNPs and body conformation traits of Chinese Dabieshan cattle was analyzed by one-way ANOVA in SPSS software. GHRHR was often conserved in nine species, and its sequence of cattle was closest to sheep and goats. Six polymorphic SNPs were identified, g.10667A > C and g.10670A > C were missense mutation. The association analysis indicated that the six SNPs significantly influenced the body conformation traits of Chinese Dabieshan cattle (p < 0.05). Six haplotypes were identified and Hap1 (-CAACGA-) had the highest frequency (36.10%). The Hap3/5 (-GCCCCCGGAAGG-) exhibited a significantly greater wither height (WH), hip height (HH), heart girth (HG), and hip width (HW) (p < 0.05). Overall, the polymorphisms of GHRHR affected the body conformation traits of Chinese Dabieshan cattle, and the GHRHR gene could be used as a molecular marker in Dabieshan cattle breeding programs.
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12
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Liu Z, Bai C, Shi L, He Y, Hu M, Sun H, Peng H, Lai W, Jiao S, Zhao Z, Ma H, Yan S. Detection of selection signatures in South African Mutton Merino sheep using whole-genome sequencing data. Anim Genet 2022; 53:224-229. [PMID: 35099062 DOI: 10.1111/age.13173] [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] [Received: 11/21/2021] [Revised: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Abstract
The South African Mutton Merino (SAMM), a dual-purpose (meat and wool) sheep breed, is characterized by its excellent performance on growth, carcass traits and meat quality compared to other fine-wool Merino breeds. Nowadays, the SAMM breed has been widely used to cross with commercial and indigenous fine-wool or coarse-wool breeds to improve the growth and meat performance in many countries. To date, however, little is known about the genetic basis for its prominent characteristics. In this study, whole-genome sequences of 10 SAMM were sequenced and the selection signatures were analyzed together with those of 39 Australian Merino and Chinese Merino (wool-type Merino) by FST , iHS, and XP-EHH methods. In total, 313 genes in 277 regions were identified by at least 2 methods with the signal of selection and 21 of them were identified by all three methods. We highlighted a list of interesting genes, including GHR, LCORL, SMO, NCAPG, DCC, IBSP, PPARGC1A, PACRGL, PRDM5, XYLB, AHCYL2, TEFM, AFG1L, and FAM184B, which have been shown to be involved in growth, carcass traits, and meat quality by previous studies. Herein, GHR, encoding a transmembrane receptor for growth hormone, is the most notable one. We report the first study on selection signatures analysis of SAMM at whole-genome sequence level. These results provide new insights into the genetic mechanisms underlying the growth and carcass traits in SAMM.
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Affiliation(s)
- Zhengxi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Chunyan Bai
- College of Animal Science, Jilin University, Changchun, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Yu He
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun, China
| | - Hongyang Peng
- College of Animal Science, Jilin University, Changchun, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun, China
| | - Shuyu Jiao
- College of Animal Science, Jilin University, Changchun, China
| | - Zhongli Zhao
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Huihai Ma
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
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Mo F, Sun W, Zhang L, Zhang X, La Y, Xiao F, Jia J, Jin J. Polymorphisms in BMPRIB gene affect litter size in Chinese indigenous sheep breed. Anim Biotechnol 2021:1-8. [PMID: 34570690 DOI: 10.1080/10495398.2021.1980400] [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: 10/20/2022]
Abstract
The BMPRIB gene belongs to the TGF-β superfamily and is considered to be a regulator of sheep reproductive performance. Single nucleotide polymorphisms (SNPs) of BMPRIB gene in the Small Tail Han, Hu, Mongolian, Oula, Gansu Alpine Fine-wool, Dorper and Australian White sheep were detected by Sanger sequencing. Five SNPs (rs427897187 G > A, rs418841713 A > G, rs159952533 T > C, rs429416173 C > A and rs403555643 A > G) of BMPRIB gene were identified. For rs427897187 G > A, further analysis revealed that genotype GG and GA had 0.26 (p < 0.05) and 0.33 (p < 0.05) litter size less than those with genotype AA in Oula sheep. For rs403555643 A > G, further analysis revealed that genotype GG and AG had 0.65 (p < 0.05) and 0.38 (p < 0.05) litter size more than those with genotype AA in Oula sheep, and genotype GG had 0.56 (p < 0.05) litter size more than those with genotype AA in Mongolian sheep. The results showed that rs427897187 G > A and rs403555643 A > G are potential molecular markers wich could improve litter size of Chinese indigenous sheep and be used in Chinese indigenous sheep breeding.
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Affiliation(s)
- Futao Mo
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gansu Grassland Technical Extension Station, Lanzhou, China
| | - Weibo Sun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liping Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoyan Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongfu La
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Fan Xiao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianlei Jia
- Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Jipeng Jin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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