1
|
Shangguan A, Xiang C, Deng Z, Zhang N, Yu M, Zhang F, Suo X, Chen M, Chen C, Tao H, Xiong Q. Genome-wide association study of growth and reproductive traits based on low-coverage whole-genome sequencing in a Chubao black-head goat population. Gene 2024; 931:148891. [PMID: 39187139 DOI: 10.1016/j.gene.2024.148891] [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: 05/27/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 08/28/2024]
Abstract
The Chubao black-head goat is a novel hybrid breed that combines the advantages of Macheng black goats, such as good reproductive performance, strong adaptability, and resistance to rough feeding, with the superior growth and meat characteristics of Boer goats. Given the substantial economic importance of growth (such as birth weight, body height, body length, and chest circumference across different growth stages) and reproductive traits (particularly average litter size after first parity), the aim of this study was to identify significant SNPs and candidate genes associated with these traits in Chubao black-head goats. Through whole-genome sequencing (with 34 goats at approximately 15× coverage and 466 goats at approximately 1× coverage), genotype imputation, and quality control, 22,665,331 SNPs were identified and subsequently used for genetic analyses. Heritability estimates indicated that growth traits exhibit moderate to high heritability (ranging from 0.297 ± 0.071 to 0.535 ± 0.118), while reproductive traits demonstrated low to moderate heritability (with a value of 0.220 ± 0.108). By performing FarmCPU-based genome-wide association studies, we identified 48 potentially significant SNPs associated with growth traits and 7 with reproductive traits. Additionally, 85 candidate genes (such as COL14A1, ZNF148, and TTC39C) linked to growth traits were identified and enriched in pathways associated with fundamental molecular biological activities such as protein deubiquitination, regulation of mRNA stability, and the MAPK signaling pathway. Furthermore, 10 candidate genes (such as SOHLH2, CCNA2, and SOX7) associated with reproductive traits were identified and enriched in pathways related to specific reproductive processes such as oocyte differentiation, endoderm formation, and progesterone-mediated oocyte maturation. Overall, these findings provide valuable preliminary insights into the molecular mechanisms underlying growth and reproductive traits in Chubao black-head goats. However, further functional validation is needed to effectively use these potential SNPs and candidate genes in improving the breeding of these traits in this breed.
Collapse
Affiliation(s)
- Aishao Shangguan
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Chong Xiang
- Institute of Data Information, Changjiang Polytechnic, Wuhan 430074, China
| | - Zhao Deng
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Nian Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Min Yu
- Human Resources Department, Changjiang Polytechnic, Wuhan 430074, China
| | - Feng Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xiaojun Suo
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Mingxin Chen
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Can Chen
- Institute of Data Information, Changjiang Polytechnic, Wuhan 430074, China
| | - Hu Tao
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Qi Xiong
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| |
Collapse
|
2
|
Zhou A, Ding Y, Zhang X, Zhou Y, Liu Y, Li T, Xiao L. Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya. Anim Biotechnol 2024; 35:2258166. [PMID: 37729465 DOI: 10.1080/10495398.2023.2258166] [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: 09/22/2023]
Abstract
In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by FST method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, ITGAV, LRP4, CDH23, TPRN, RYR2 and CELSR1 genes, involved in embryonic morphogenesis, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (ITGAV: c.38C > T; TPRN: c.133A > T, c.1192A > G, c.1250A > C; CELSR1: c.7640T > C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.
Collapse
Affiliation(s)
- Aimin Zhou
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yi Ding
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiaohui Zhang
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Yugang Zhou
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Yadong Liu
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Tingjian Li
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Long Xiao
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| |
Collapse
|
3
|
Yao M, Chang L, Xu S, Zhang J, Li P, Tian B, Luo L, Yang D, Long Q, Zou X. Comparison of production performance and meat quality characteristics between Guizhou Black goats and F4 generation hybrids of South African Kalahari Goats. Sci Rep 2024; 14:18608. [PMID: 39127724 PMCID: PMC11316849 DOI: 10.1038/s41598-024-69174-0] [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: 05/30/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
This study spanned 6 years and 4 generations, involving the progressive crossbreeding of South African Kalahari Goat (SK) and Guizhou Black Goat (GB) over three generations, followed by cross fixation F3 with F1 in the fourth generation, accompanied by the use of molecular markers technology to select a high fertility population, resulting in the creation of a hybrid goat, BKF4 (11/16 SK lineage and 5/16 GB lineage). A comparative evaluation of the BKF4 hybrid breed and its parental breeds was conducted. Reproductive and production parameters of GB, SK, and BKF4 goat groups were monitored, including lambing rate (LR), survival rate (SR), daily weight gain at 3 months of age (DWG), and adult body weight (ABW) (n = 110, 106, 112 per group). In addition, dressing percentage (DP) (n = 12 per group) and analyses of amino acids (n = 8, 6, 10 per group) and fatty acids (n = 6 per group) were conducted to evaluate meat quality indicators. Results: (1) Reproductive and production performance: The index of LR reached 199%, significantly higher than GB and SK (p ≤ 0.001), with a SR of 95.0%, markedly higher than SK (p ≤ 0.001); DWG was 276.5 g, ABW reached 56.6 kg and with a dressing percentage (DP) of 54.5%, they are significantly surpassing GB (p ≤ 0.001). (2) Regarding meat quality: pH45-value and crude protein content (CP) increased, while intramuscular fat content increased compared to GB and ash content decreased. The amino acid composition was similar to GB, but the taste was more similar to SK. However, there were some negative impacts on fatty acid composition and functionality. (3) PCA analysis revealed that: BKF4 exhibited superior meat quality compared to GB and SK, influenced by two key factors contributing 83.49% and 16.51% to the explained variance, respectively. The key factors affecting meat quality include intramuscular fat (IMF), nutrient index (NI), PUFAs/MUFAs, n-6FAs, and drip loss (DL).
Collapse
Affiliation(s)
- Min Yao
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
- Guizhou Testing Center for Livestock and Poultry Germplasm, Guiyang, 550018, Guizhou Province, China
| | - Lingle Chang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences and College of Animal Science, Guizhou University, Guiyang, 500025, Guizhou Province, China
| | - Suyun Xu
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Jing Zhang
- Institute of Animal Husbandry and Veterinary Sciences, Guiyang, 550005, Guizhou Province, China
| | - Ping Li
- Guizhou Testing Center for Livestock and Poultry Germplasm, Guiyang, 550018, Guizhou Province, China
| | - Bing Tian
- Guizhou Testing Center for Livestock and Poultry Germplasm, Guiyang, 550018, Guizhou Province, China
| | - Li Luo
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Danpin Yang
- Guizhou Kalahari Goat Breeding Company, Qianxinan, 562400, Guizhou Province, China
| | - Qingmeng Long
- Guizhou Testing Center for Livestock and Poultry Germplasm, Guiyang, 550018, Guizhou Province, China.
| | - Xiao Zou
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| |
Collapse
|
4
|
Xiao Z, Li Y, Yang L, Cui M, Wang Z, Sun W, Wang J, Chen S, Lai S, Jia X. Genome-Wide Association Studies of Growth Trait Heterosis in Crossbred Meat Rabbits. Animals (Basel) 2024; 14:2096. [PMID: 39061558 PMCID: PMC11273820 DOI: 10.3390/ani14142096] [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: 06/07/2024] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
The application of heterosis can not only effectively improve the disease resistance and meat quality of livestock, but also significantly enhance the reproduction and growth of livestock and poultry. We conducted genome-wide association studies using data from F2 crossbred meat rabbits to screen out candidate genes with significant dominant effects associated with economic trait variation. High-throughput sequencing technology was used to obtain SNPs covering the whole genome to evaluate the homozygosity of the population genome, and analyze the number, length, frequency, and distribution of ROHs in the population. Candidate genes related to economic traits of meat rabbits were searched based on high-frequency ROH regions. After quality control filtering of genotype data, 380 F2 crossbred rabbits were identified with 78,579 SNPs and 42,018 ROHs on the autosomes. The fitting of the Logistic growth curve model showed that 49-day-old rabbits were a growth inflection point. Then, through genome-wide association studies, 10 SNP loci and seven growth trait candidate genes were found to be significantly related to body weight in meat rabbits at 84 days of age. In addition, we revealed the functional roles and locations of 20 candidate genes in the high-frequency ROH region associated with economic traits in meat rabbits. This study identified potential genes associated with growth and development in the high-frequency ROH region of meat rabbits. In this study, the identified candidate genes can be used as molecular markers for assisted selection in meat rabbits. At the same time, the inbreeding situation based on ROH assessment can provide reference for breeding and breeding preservation of meat rabbits.
Collapse
Affiliation(s)
- Zhanjun Xiao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Yuchao Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (Y.L.); (L.Y.); (J.W.)
| | - Li Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (Y.L.); (L.Y.); (J.W.)
| | - Mingyan Cui
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Zicheng Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Wenqiang Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Jie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (Y.L.); (L.Y.); (J.W.)
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Z.X.); (M.C.); (Z.W.); (W.S.); (S.C.); (S.L.)
| |
Collapse
|
5
|
Zhao Q, Huang C, Chen Q, Su Y, Zhang Y, Wang R, Su R, Xu H, Liu S, Ma Y, Zhao Q, Ye S. Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat. Animals (Basel) 2024; 14:1246. [PMID: 38672394 PMCID: PMC11047310 DOI: 10.3390/ani14081246] [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: 03/26/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
Collapse
Affiliation(s)
- Qian Zhao
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Chang Huang
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yingxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Huijuan Xu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Shucai Liu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
| |
Collapse
|
6
|
Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X, Chai W, Khan MZ, Wang C. Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits. Front Vet Sci 2024; 10:1334434. [PMID: 38274664 PMCID: PMC10808162 DOI: 10.3389/fvets.2023.1334434] [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: 11/07/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
| |
Collapse
|
7
|
Mao S, Dong S, Hou B, Li Y, Sun B, Guo Y, Deng M, Liu D, Liu G. Transcriptome analysis reveals pituitary lncRNA, circRNA and mRNA affecting fertility in high- and low-yielding goats. Front Genet 2023; 14:1303031. [PMID: 38152654 PMCID: PMC10751935 DOI: 10.3389/fgene.2023.1303031] [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: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 12/29/2023] Open
Abstract
The pituitary gland serves as the central endocrine regulator of growth, reproduction, and metabolism and plays a crucial role in the reproductive process of female animals. Transcriptome analysis was conducted using pituitary gland samples from Leizhou goats with varying levels of fecundity to investigate the effects of long noncoding RNA (lncRNA), circular RNA (circRNA), and mRNA regulation on pituitary hormone secretion and its association with goat fecundity. The analysis aimed to identify lncRNAs, circRNAs, and mRNAs that influence the fertility of Leizhou goats. GO and KEGG enrichment analyses were performed on differentially expressed lncRNAs, circRNAs, and mRNAs and revealed considerable enrichment in pathways, such as regulation of hormone secretion, germ cell development, and gonadotropin-releasing hormone secretion. The pituitary lncRNAs (ENSCHIT00000010293, ENSCHIT00000010304, ENSCHIT00000010306, ENSCHIT00000010290, ENSCHIT00000010298, ENSCHIT00000006769, ENSCHIT00000006767, ENSCHIT00000006921, and ENSCHIT00000001330) and circRNAs (chicirc_029285, chicirc_026618, chicirc_129655, chicirc_018248, chicirc_122554, chicirc_087101, and chicirc_078945) identified as differentially expressed regulated hormone secretion in the pituitary through their respective host genes. Additionally, differential mRNAs (GABBR2, SYCP1, HNF4A, CBLN1, and CDKN1A) influenced goat fecundity by affecting hormone secretion in the pituitary gland. These findings contribute to the understanding of the molecular mechanisms underlying pituitary regulation of fecundity in Leizhou goats.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China
| |
Collapse
|
8
|
Yan Z, Song K, Wang P, Gun S, Long X. Evaluation of the Genetic Diversity and Population Structure of Four Native Pig Populations in Gansu Province. Int J Mol Sci 2023; 24:17154. [PMID: 38138983 PMCID: PMC10743271 DOI: 10.3390/ijms242417154] [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: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Indigenous pig populations, including Bamei pigs (BM), Hezuo pigs (HZ), Huixian Qingni Black pigs (HX), and Minxian Black pigs (MX) in Gansu Province, live in a particular climate and a relatively closed geographical environment. These local pig breeds are characterized by excellent characteristics (e.g., cold tolerance, robust disease resistance, and superior meat quality). In the past few years, pig populations in Gansu Province have decreased significantly because of their poor lean meat percentage, high fat content, and slow growth rate. Maintaining the diversity of these four breeds can act as a source of new alleles to be incorporated into commercial breeds which are more susceptible to disease and less adaptable to changing conditions because of inbreeding. Genomic data analysis is adequate for determining the genetic diversity and livestock breeding population structure, even in local pig populations. However, the genetic diversity and population structure of the four native pig populations in Gansu Province are still unknown. Thus, we used "Zhongxin-I" porcine chip for the SNP detection of 102 individuals living on four pig conservation farms. A total of 57,466 SNPs were identified among the four pig breeds. The linkage disequilibrium (LD) plot showed that MX had the highest level of LD, followed by BM, HZ, and HX. The observed heterozygosity (Ho) in all four populations was higher than the expected heterozygosity (He). A principal component analysis (PCA) demonstrated that the four local pig populations were isolated. The identity displayed by the state matrix and G matrix heat map results indicated that small numbers of individuals among the four pig breeds had a high genetic distance and weak genetic relationships. The results of the population genetic structure of BM, HZ, HX, and MX pigs showed a slight genetic diversity loss. Our findings enabled us to better understand the genome characteristics of these four indigenous pig populations, which will provide novel insights for the future germplasm conservation and utilization of these indigenous pig populations.
Collapse
Affiliation(s)
- Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.Y.); (K.S.); (P.W.)
| | - Kelin Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.Y.); (K.S.); (P.W.)
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.Y.); (K.S.); (P.W.)
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.Y.); (K.S.); (P.W.)
| | - Xi Long
- Chongqing Academy of Animal Sciences, Chongqing 402460, China
| |
Collapse
|