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Helal M, Sameh J, Gharib S, Merghany RM, Bozhilova-Sakova M, Ragab M. Candidate genes associated with reproductive traits in rabbits. Trop Anim Health Prod 2024; 56:94. [PMID: 38441694 PMCID: PMC10914644 DOI: 10.1007/s11250-024-03938-8] [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: 12/11/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
In the era of scientific advances and genetic progress, opportunities in the livestock sector are constantly growing. The application of molecular-based methods and approaches in farm animal breeding would accelerate and improve the expected results. The current work aims to comprehensively review the most important causative mutations in candidate genes that affect prolificacy traits in rabbits. Rabbits are a source of excellent-tasting meat that is high in protein and low in fat. Their early maturity and intensive growth are highly valued all over the world. However, improving reproductive traits and prolificacy in rabbits could be very tricky with traditional selection. Therefore, traditional breeding programs need new methods based on contemporary discoveries in molecular biology and genetics because of the complexity of the selection process. The study and implementation of genetic markers related to production in rabbits will help to create populations with specific productive traits that will produce the desired results in an extremely short time. Many studies worldwide showed an association between different genes and productive traits in rabbits. The study of these polymorphisms and their effects could be useful for molecular-oriented breeding, particularly marker-assisted selection programs in rabbit breeding.
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Affiliation(s)
- Mostafa Helal
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Jana Sameh
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Sama Gharib
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Rana M Merghany
- Department of Pharmacognosy, National Research Centre, Giza, 12622, Egypt
| | | | - Mohamed Ragab
- Poultry Production Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
- Animal Breeding and Genetics Department, National Institute for Agricultural and Food Research and Technology (INIA), Madrid, 28040, Spain
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Bian Z, Li K, Chen S, Man C, Wang F, Li L. Association between INHA gene polymorphisms and litter size in Hainan black goats. PeerJ 2023; 11:e15381. [PMID: 37187517 PMCID: PMC10178212 DOI: 10.7717/peerj.15381] [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: 11/29/2022] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Background The inhibin alpha (INHA) gene is one of the important genes affecting the reproductive traits of animals. Hainan black goats are the main goat breed in Hainan Island (China), whose development is limited by low reproductive performance. However, the relationship between INHA gene and the reproductive performance of Hainan black goats is still unclear. Therefore, the purpose of this work was to explore the effect of INHA gene polymorphisms on the litter size of Hainan black goats. Methods Single nucleotide polymorphisms (SNPs) of INHA were detected, and the genetic parameters and haplotype frequency of these SNPs were calculated and association analysis was performed for these SNPs with the litter size. Finally, the SNP with significant correlations to litter size was analyzed by Bioinformatics tools. Results The results showed that the litter size of individuals with the AC genotype at loci g.28317663A>C of INHA gene was significantly higher than those with the AA genotype. This SNP changed the amino acid sequence, which may affect the function of INHA protein by affecting its structure. Our results suggest that g.28317663A>C loci may serve as a potential molecular marker for improving the reproductive traits in Hainan black goats.
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Blaj I, Tetens J, Bennewitz J, Thaller G, Falker-Gieske C. Structural variants and tandem repeats in the founder individuals of four F 2 pig crosses and implications to F 2 GWAS results. BMC Genomics 2022; 23:631. [PMID: 36057580 PMCID: PMC9440560 DOI: 10.1186/s12864-022-08716-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/23/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Structural variants and tandem repeats are relevant sources of genomic variation that are not routinely analyzed in genome wide association studies mainly due to challenging identification and genotyping. Here, we profiled these variants via state-of-the-art strategies in the founder animals of four F2 pig crosses using whole-genome sequence data (20x coverage). The variants were compared at a founder level with the commonly screened SNPs and small indels. At the F2 level, we carried out an association study using imputed structural variants and tandem repeats with four growth and carcass traits followed by a comparison with a previously conducted SNPs and small indels based association study. RESULTS A total of 13,201 high confidence structural variants and 103,730 polymorphic tandem repeats (with a repeat length of 2-20 bp) were profiled in the founders. We observed a moderate to high (r from 0.48 to 0.57) level of co-localization between SNPs or small indels and structural variants or tandem repeats. In the association step 56.56% of the significant variants were not in high LD with significantly associated SNPs and small indels identified for the same traits in the earlier study and thus presumably not tagged in case of a standard association study. For the four growth and carcass traits investigated, many of the already proposed candidate genes in our previous studies were confirmed and additional ones were identified. Interestingly, a common pattern on how structural variants or tandem repeats regulate the phenotypic traits emerged. Many of the significant variants were embedded or nearby long non-coding RNAs drawing attention to their functional importance. Through which specific mechanisms the identified long non-coding RNAs and their associated structural variants or tandem repeats contribute to quantitative trait variation will need further investigation. CONCLUSIONS The current study provides insights into the characteristics of structural variants and tandem repeats and their role in association studies. A systematic incorporation of these variants into genome wide association studies is advised. While not of immediate interest for genomic prediction purposes, this will be particularly beneficial for elucidating biological mechanisms driving the complex trait variation.
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Affiliation(s)
- Iulia Blaj
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany.
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | - Jörn Bennewitz
- Institute of Animal Husbandry and Breeding, University of Hohenheim, Stuttgart, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany
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Wang SZ, E GX, Zeng Y, Han YG, Huang YF, Na RS. Three SNPs within exons of INHA and ACVR2B genes are significantly associated with litter size in Dazu black goats. Reprod Domest Anim 2021; 56:936-941. [PMID: 33720451 DOI: 10.1111/rda.13927] [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: 07/30/2020] [Accepted: 03/12/2021] [Indexed: 11/26/2022]
Abstract
The aim of this study was to analyse the association between single-nucleotide polymorphisms within INHA and ACVR2B and litter size in Dazu black goats. In total, twenty-two SNPs were genotyped in 190 individuals by SNaPshot and resequencing. The results showed that three SNPs (SNP_1, SNP_12 and SNP_13 in this study) were detected to have significant additive genetic effect on the recorded goat litter size (p < .05). The SNP_1 (NC_030809.1), a non-synonymous substitution of G for T at chr2-g. 28314990 in the exon 2 of INHA gene (NM_001285606.1), resulted in homozygote 2 (HOM2) contributed 0.25 and heterozygote (HET) contributed 0.12 larger litter than homozygote 1 (HOM1). Meanwhile, SNP_12 (Chr22-g. 11721225 A > T) and SNP_13 (Chr22-g. 11721227 A > C) (NC_030829.1) simultaneously mutated at the first and third position of a triplet AAA (lysine, K) in the exon 4 of ACVR2B gene (XM_018066623.1) had estimated genetic effects of HOM1 (0.00) and HOM2 (0.03) larger than HET (-0.12). In conclusion, one SNPs (chr2-g. 28314990 T > G) within the exon 2 of INHA and two SNPs (Chr22-g. 11721225 A > T and Chr22-g. 11721227 A > C) in the exon 4 of ACVR2B gene were highly recommended as candidate markers of litter size in Dazu black goats. A large-scale association study to assess the impact of these variants on litter size is still necessary.
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Affiliation(s)
- Shi-Zhi Wang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Guang-Xin E
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan-Guo Han
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yong-Fu Huang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Ri-Su Na
- College of Animal Science and Technology, Southwest University, Chongqing, China
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Lu H, Zhao C, Zhu B, Zhang Z, Ge W. Loss of Inhibin Advances Follicle Activation and Female Puberty Onset but Blocks Oocyte Maturation in Zebrafish. Endocrinology 2020; 161:5921142. [PMID: 33045050 DOI: 10.1210/endocr/bqaa184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/06/2020] [Indexed: 02/01/2023]
Abstract
Inhibin was first characterized in mammals as a gonadal dimeric protein that inhibited pituitary follicle-stimulating hormone (FSH) secretion. As in mammals, the inhibin-specific α subunit (INHA/Inha/inha) has also been characterized in teleosts; however, its functions and physiological importance in fish reproduction remain unknown. Using CRISPR/Cas9 method, we generated an inha-deficient zebrafish line and analyzed its reproductive performance. As expected, pituitary expression of fshb increased significantly in both the young and the adult inha mutant. The expression of lhb also increased in the mutant, but only in sexually mature adults. Interestingly, the expression of activin βA (inhbaa) increased significantly in both the ovary and the testis of inha mutant, and the expression of ovarian aromatase (cyp19a1a) also increased dramatically in the mutant ovary. The juvenile female mutant showed clear signs of early follicle activation or precocious puberty onset. However, the adult female mutant was infertile with follicles arrested at the full-grown stage without final oocyte maturation and ovulation. Although follicle growth was normal overall in the mutant, the size and distribution of yolk granules in oocytes were distinct and some follicles showed granulosa cell hypertrophy. In contrast to females, inha-null males showed normal spermatogenesis and fertility. As reported in mammals, we also found sporadic tumor formation in inha mutants. Taken together, our study not only confirmed some conserved roles of inhibin across vertebrates, such as inhibition of FSH biosynthesis and tumor formation, but also revealed novel aspects of inhibin functions such as disruption of folliculogenesis and female infertility but no obvious involvement in spermatogenesis in fish.
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Affiliation(s)
- Huijie Lu
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Cheng Zhao
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Bo Zhu
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Zhiwei Zhang
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau, China
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Xu H, Khan A, Zhao S, Wang H, Zou H, Pang Y, Zhu H. Effects of Inhibin A on Apoptosis and Proliferation of Bovine Granulosa Cells. Animals (Basel) 2020; 10:ani10020367. [PMID: 32102430 PMCID: PMC7071129 DOI: 10.3390/ani10020367] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022] Open
Abstract
Inhibin A is well known for its inhibitory properties against follicle-stimulating hormone (FSH), released through a pituitary-gonadal negative feedback loop to regulate follicular development. Ovarian folliculogenesis, hormonal biosynthesis, and gametogenesis are dependent on inhibins, playing vital roles in promoting or inhibiting cell proliferation. The present study explored the physiological and molecular response of bovine granulosa cells (GCs) to different concentrations of inhibin A in vitro. We treated the primary GCs isolated from ovarian follicles (3-6 mm) with different levels of inhibin A (20, 50, and 100 ng/mL) along with the control (0 ng/mL) for 24 h. To evaluate the impact of inhibin A on GCs, several in vitro cellular parameters, including cell apoptosis, viability, cell cycle, and mitochondrial membrane potential (MMP) were detected. Besides, the transcriptional regulation of pro-apoptotic (BAX, Caspase-3) and cell proliferation (PCNA, CyclinB1) genes were also quantified. The results indicated a significant (p < 0.05) increase in the cell viability in a dose-dependent manner of inhibin A. Likewise, MMP was significantly (p < 0.05) enhanced when GCs were treated with high doses (50, 100 ng/mL) of inhibin A. Furthermore, inhibin A dose (100 ng/mL) markedly improved the progression of the G1 phase of the cell cycle and increased the cell number in the S phase, which was supported by the up-regulation of the proliferating cell nuclear antigen PCNA (20, 50, and 100ng/mL) and CyclinB (100 ng/mL) genes. In addition, higher doses of inhibin A (50 and 100 ng/mL) significantly (p < 0.05) decreased the apoptotic rate in GCs, which was manifested by down regulating BAX and Caspase-3 genes. Conclusively, our study presented a worthy strategy for the first time to characterize the cellular adaptation of bovine GCs under different concentrations of inhibin A. Our results conclude that inhibin A is a broad regulatory marker in GCs by regulating apoptosis and cellular progression.
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Affiliation(s)
- Huitao Xu
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.X.); (S.Z.); (H.W.); (H.Z.); (Y.P.)
| | - Adnan Khan
- Key Laboratory of Animal Genetics, Breeding, and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Shanjiang Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.X.); (S.Z.); (H.W.); (H.Z.); (Y.P.)
| | - Huan Wang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.X.); (S.Z.); (H.W.); (H.Z.); (Y.P.)
| | - Huiying Zou
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.X.); (S.Z.); (H.W.); (H.Z.); (Y.P.)
| | - Yunwei Pang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.X.); (S.Z.); (H.W.); (H.Z.); (Y.P.)
| | - Huabin Zhu
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.X.); (S.Z.); (H.W.); (H.Z.); (Y.P.)
- Correspondence: ; Tel.: +86-010-62895971
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Analysis of Expression and Single Nucleotide Polymorphisms of INHA Gene Associated with Reproductive Traits in Chickens. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8572837. [PMID: 31485447 PMCID: PMC6702802 DOI: 10.1155/2019/8572837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/02/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Abstract
Inhibin α (INHA) is a candidate gene controlling ovulation in poultry. As the functional center of inhibin, INHA is a molecular marker associated with egg-laying performance. The objective of the current study was to analyze the expression differences of INHA in reproductive system and single nucleotide polymorphisms (SNPs) associations with reproductive traits in chickens. A total of 260 LuHua chickens (barred-feather chicken) were adopted. Twelve SNPs were detected in INHA gene. Among the exonic SNPs, three (g. 22177991A>G, g. 22178249G>C, and g. 22178414G>A) were missense mutations, resulting in the amino acid substitutions Val→Ala, Ala→Gly, and Ala→Gly, respectively. Four SNPs in the 3' untranslated region of INHA were predicted to either disturb or create microRNA-target interactions. Five SNPs (g. 22176870T>C, g. 22177100T>C, g. 22177149T>C, g. 22177991A>G, and g. 22178975G>A) were significantly associated with the number of eggs at 300 d of age (EN) (P < 0.05). Birds carrying GA genotype exhibited more EN than those with AA genotype (P < 0.01). In addition, quantitative real-time PCR revealed that INHA is mainly expressed in follicles on d 300 in chickens. Firstly, INHA expression increased and then decreased. The highest INHA mRNA abundance was found in the fifth largest preovulatory follicle (F5) (P < 0.01). In the prehierarchical follicles, INHA mRNA expression increased dramatically in small yellow follicles (SYF) (P < 0.01). Western blotting analysis showed that the INHA protein expression profile in the follicle was similar to its mRNA counterpart with greater expression in F5 and SYF follicles and lowest expression in F1 follicles (P < 0.05). These results suggest that INHA is a potential candidate gene improving reproductive traits in chickens.
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Li W, Li C, Chen S, Sun L, Li H, Chen L, Zhou X. Effect of inhibin A on proliferation of porcine granulosa cells in vitro. Theriogenology 2018; 114:136-142. [DOI: 10.1016/j.theriogenology.2018.03.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 03/20/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
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Insertion of 275-bp SINE into first intron of PDIA4 gene is associated with litter size in Xiang pigs. Anim Reprod Sci 2018; 195:16-23. [PMID: 29728275 DOI: 10.1016/j.anireprosci.2018.04.079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/14/2018] [Accepted: 04/25/2018] [Indexed: 11/20/2022]
Abstract
The aim of the study was to investigate the SINE polymorphism in Xiang, Kele, Qianbei black, Jiangkouluobo, Large White, and Duroc pig breeds. The PCR based detection method was conducted to identify the short interspersed nuclear element (SINE) polymorphism in the PDIA4 gene. There were greater frequencies of the SINE-/- genotypes in Xiang pigs (55.9%) as compared with other pig breed groups. There was an association between this 275 bp SINE polymorphism and litter size (P = 0.003). The homozygous SINE+/+ genotype of the PDIA4 gene had a 1.45-piglets larger litter sizes compared to those with the homozygous SINE-/- genotype. Furthermore, there were assessments of mRNA and protein abundances as a result of PDIA4 gene expression in the ovaries of Xiang pigs for the three different SINE genotypes, and the results indicated that relative abundances of PDIA4 mRNA and protein was greater for the SINE-/- and SINE-/+ genotypes compared with the SINE+/+ genotype (P < 0.05). These findings suggested that the 275 bp SINE polymorphism might change the expression of the PDIA4 gene and could be used as a candidate DNA marker for the selection for litter size in Xiang pigs.
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Liu C, Ran X, Yu C, Xu Q, Niu X, Zhao P, Wang J. Whole-genome analysis of structural variations between Xiang pigs with larger litter sizes and those with smaller litter sizes. Genomics 2018; 111:310-319. [PMID: 29481841 DOI: 10.1016/j.ygeno.2018.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 02/08/2018] [Accepted: 02/11/2018] [Indexed: 11/30/2022]
Abstract
To gain a better knowledge of structural variations (SVs) in Xiang pig, we used next-generation sequencing to analyze the Xiang pigs with larger (XL) or smaller litter sizes (XS). Our analysis yielded 28,040 putative SVs in the Xiang pig. These SVs distributed throughout all of chromosomes. Some functional regions including exons and untranslated regions were less varied than introns and intergenic regions. We detected 4637 and 4119 specific SVs, which contained 1697 and 1582 genes in XL and XS group, respectively. These genes were mainly enriched in the well-known pathways involved in development and reproduction processes. Population validation was carried out on 50 SVs candidates using PCR method in 144 Xiang pig crowds. All of 50 SVs were confirmed by PCR method and 14 SVs were associated with the litter size of Xiang pigs. These results may be helpful for the elucidation of growth and reproduction regulation in Xiang pig.
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Affiliation(s)
- Chang Liu
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China.
| | - Changyan Yu
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Qian Xu
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Xi Niu
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Pengju Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing 100083, China
| | - Jiafu Wang
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China; Tongren University, Tongren 554300, China.
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