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Li S, Liu L, Ahmed Z, Wang F, Lei C, Sun F. Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data. Front Genet 2024; 15:1435793. [PMID: 39119576 PMCID: PMC11306169 DOI: 10.3389/fgene.2024.1435793] [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: 05/21/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors. Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.
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Affiliation(s)
- Shuang Li
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Li Liu
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Kashmir, Pakistan
| | - Fuwen Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fang Sun
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
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2
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Lin R, Li H, Lin W, Yang F, Bao X, Pan C, Lai L, Lin W. Whole-genome selection signature differences between Chaohu and Ji'an red ducks. BMC Genomics 2024; 25:522. [PMID: 38802792 PMCID: PMC11131323 DOI: 10.1186/s12864-024-10339-6] [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: 09/20/2023] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.
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Affiliation(s)
- Ruiyi Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Huihuang Li
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Weilong Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Fan Yang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Xinguo Bao
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Chengfu Pan
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Lianjie Lai
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Weimin Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
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Luo Y, Zhang M, Guo Z, Wijayanti D, Xu H, Jiang F, Lan X. Insertion/Deletion (InDel) Variants within the Sheep Fat-Deposition-Related PDGFD Gene Strongly Affect Morphological Traits. Animals (Basel) 2023; 13:ani13091485. [PMID: 37174523 PMCID: PMC10177341 DOI: 10.3390/ani13091485] [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: 12/30/2022] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Platelet-derived growth factor D (PDGFD) is a member of the PDGF gene family, and it plays an important role in the regulation of adipocyte development in mammals. Furthermore, genome-wide association studies (GWAS) have previously identified it as a candidate gene associated with fleece fiber variation, body size, and the fat-tail phenotype in domestic Chinese sheep. In this study, a total of 1919 indigenous Chinese sheep were genotyped to examine the association between nucleotide sequence variations in PDGFD and body morphology. Our results detected both a 14 bp insertion in intron 2 and a 13 bp deletion in intron 4 of PDGFD. Moreover, these two InDel loci had low to moderate polymorphism. Notably, the 13 bp deletion mutation of PDGFD was found to significantly affect sheep body size. Yearling rams in the Luxi black-headed sheep (LXBH) containing a heterozygous genotype (insertion/deletion, ID) were found to have larger body length, chest depth, and body weight than those with wild genotypes. Furthermore, adult ewes in the Guiqian semi-fine wool sheep (GSFW) containing a homozygous mutation (deletion/deletion, DD) were found to have smaller chest width than their peers. Moreover, yearling ewes in this group with the same homozygous mutation were found to have lower body weight, chest width, and cannon circumference compared to those of other individuals. This study demonstrates that PDGFD InDel polymorphisms have the potential to be effective molecular markers to improve morphological traits in domestic Chinese sheep.
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Affiliation(s)
- Yunyun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Mengyang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhengang Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Bijie Animal Husbandry and Veterinary Science Research Institute, Bijie 551700, China
| | - Dwi Wijayanti
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Fugui Jiang
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, 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 712100, China
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4
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Li S, Lei H, Li J, Sun A, Ahmed Z, Duan H, Chen L, Zhang B, Lei C, Yi K. Analysis of genetic diversity and selection signals in Chaling cattle of southern China using whole-genome scan. Anim Genet 2023; 54:284-294. [PMID: 36864643 DOI: 10.1111/age.13305] [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: 10/12/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 03/04/2023]
Abstract
China has diversified resources of indigenous cattle, which are classified into Northern, Central, and Southern groups according to their geographical distribution. Chaling cattle belong to Southern group. This breed is famous for the production of good quality meat with elite meat grades. To analyze the genetic diversity of Chaling cattle, 20 samples were sequenced using whole-genome resequencing technology, along with 138 published whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, East Asian taurine cattle, Eurasian taurine cattle, and European taurine cattle as control. It was found that Chaling cattle originated from Chinese indicine cattle. The genetic diversity of Chaling cattle is higher than that of Indian indicine cattle, East Asian taurine cattle, Eurasian taurine cattle, and European taurine cattle, but lower than that of Chinese indicine cattle and Xiangxi cattle. Annotating the selection signals obtained by composite likelihood ratio, θπ, FST , π-ratio, and XP-EHH methods, several genes associated with immunity, heat tolerance, reproduction, growth, and meat quality showed strong selection signals. In general, this study provides a theoretical basis for analyzing the genetic mechanism of Chaling cattle with excellent adaptability, rough feeding tolerance, good immune performance, and good meat quality. This work lays a foundation for genetic breeding of Chaling cattle in future.
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Affiliation(s)
- Shuang Li
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Lei
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Jianbo Li
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Ao Sun
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Science, University of Poonch Rawalakot, Azad Kashmir, Pakistan
| | - Hongfeng Duan
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Lin Chen
- Chaling County Agricultural Development Corporation Ltd, Chaling, Hunan, China
| | - Baizhong Zhang
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
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Assessing the Role of Ancestral Fragments and Selection Signatures by Whole-Genome Scanning in Dehong Humped Cattle at the China-Myanmar Border. BIOLOGY 2022; 11:biology11091331. [PMID: 36138810 PMCID: PMC9495559 DOI: 10.3390/biology11091331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/31/2022] [Accepted: 09/04/2022] [Indexed: 12/05/2022]
Abstract
Dehong humped cattle are precious livestock resources of Yunnan Province, China; they have typical zebu traits. Here, we investigated their genetic characteristics using whole-genome resequencing data of Dehong humped animals (n = 18). When comparing our data with the publicly-available data, we found that Dehong humped cattle have high nucleotide diversity. Based on clustering models in a population structure analysis, Dehong humped cattle had a mutual genome ancestor with Chinese and Indian indicine cattle. While using the RFMix method, it is speculated that the body sizes of Dehong humped cattle were influenced by the Chinese indicine segments and that the immune systems of Dehong humped cattle were affected by additional ancestral segments (Indian indicine). Furthermore, we explored the position selection regions harboring genes in the Dehong humped cattle, which were related to heat tolerance (FILIP1L, ABHD6) and immune responses (GZMM, PRKCZ, STOML2, LRBA, PIK3CD). Notably, missense mutations were detected in the candidate gene ABHD6 (c.870C>A p.Asp290Glu; c.987C>A p.Ser329Arg). The missense mutations may have implications for Dehong humped cattle adaptation to hot environments. This study provides valuable genomic resource data at the genome-wide level and paves the way for future genetic breeding work in the Dehong humped cattle.
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Liu Y, Cheng H, Wang S, Luo X, Ma X, Sun L, Chen N, Zhang J, Qu K, Wang M, Liu J, Huang B, Lei C. Genomic Diversity and Selection Signatures for Weining Cattle on the Border of Yunnan-Guizhou. Front Genet 2022; 13:848951. [PMID: 35873486 PMCID: PMC9301131 DOI: 10.3389/fgene.2022.848951] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Weining cattle is a Chinese indigenous breed influenced by complex breeding and geographical background. The multi-ethnic breeding culture makes Weining cattle require more attention as livestock resources for its genetic diversity. Here, we used 10 Weining cattle (five newly sequenced and five downloaded) and downloaded another 48 genome data to understand the aspects of Weining cattle: genetic diversity, population structure, and cold-adapted performance. In the current study, a high level of genetic diversity was found in Weining cattle, and its breed comprised two potential ancestries, which were Bos taurus and Bos indicus. The positive selective sweep analysis in Weining cattle was analyzed using composite likelihood ratio (CLR) and nucleotide diversity (θπ), resulting in 203 overlapped genes. In addition, we studied the cold adaptation of Weining cattle by comparing with other Chinese cattle (Wannan and Wenshan cattle) by three methods (FST, θπ-ratio, and XP-EHH). Of the top 1% gene list, UBE3D and ZNF668 were analyzed, and these genes may be associated with fat metabolism and blood pressure regulation in cold adaptation. Our findings have provided invaluable information for the development and conservation of cattle genetic resources, especially in southwest China.
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Affiliation(s)
- Yangkai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyv Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohui Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Mingjin Wang
- Bijie Animal Husbandry and Veterinary Science Institute, Bijie, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
- *Correspondence: Bizhi Huang, ; Chuzhao Lei,
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- *Correspondence: Bizhi Huang, ; Chuzhao Lei,
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Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages. Animals (Basel) 2022; 12:ani12111356. [PMID: 35681821 PMCID: PMC9204547 DOI: 10.3390/ani12111356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/07/2022] [Accepted: 05/23/2022] [Indexed: 12/16/2022] Open
Abstract
Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats.
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Jin L, Qu K, Hanif Q, Zhang J, Liu J, Chen N, Suolang Q, Lei C, Huang B. Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures. Front Genet 2022; 13:833475. [PMID: 35422847 PMCID: PMC9001881 DOI: 10.3389/fgene.2022.833475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/04/2022] [Indexed: 12/14/2022] Open
Abstract
Dengchuan cattle are the only dairy yellow cattle and endangered cattle among Yunnan native cattle breeds. However, its genetic background remains unclear. Here, we performed whole-genome sequencing of ten Dengchuan cattle. Integrating our data with the publicly available data, Dengchuan cattle were observed to be highly interbred than other cattle in the dataset. Furthermore, the positive selective signals were mainly manifested in candidate genes and pathways related to milk production, disease resistance, growth and development, and heat tolerance. Notably, five genes (KRT39, PGR, KRT40, ESR2, and PRKACB) were significantly enriched in the estrogen signaling pathway. Moreover, the missense mutation in the PGR gene (c.190T > C, p.Ser64Pro) showed a homozygous mutation pattern with higher frequency (83.3%) in Dengchuan cattle. In addition, a large number of strong candidate regions matched genes and QTLs related to milk yield and composition. Our research provides a theoretical basis for analyzing the genetic mechanism underlying Dengchuan cattle with excellent lactation and adaptability, crude feed tolerance, good immune performance, and small body size and also laid a foundation for genetic breeding research of Dengchuan cattle in the future.
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Affiliation(s)
- Liangliang Jin
- Yunnan Academy of Grassland and Animal Science, Kunming, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quji Suolang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
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