1
|
Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:ijms24055061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [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: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
Collapse
|
2
|
Jiang H, Chai ZX, Cao HW, Zhang CF, Zhu Y, Zhang Q, Xin JW. Genome-wide identification of SNPs associated with body weight in yak. BMC Genomics 2022; 23:833. [PMID: 36522700 PMCID: PMC9756674 DOI: 10.1186/s12864-022-09077-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The yak is the most important livestock in the Qinghai-Tibet Plateau, and body weight directly affects the economic values of yak. Up to date, the genome-wide profiling of single-nucleotide polymorphisms (SNPs) associating with body weight has not been reported in yak. In the present study, the SNPs in 480 yaks from three breeds were analyzed using the commercial high-density (600 K) yak SNP chips. RESULTS The results identified 12 and 4 SNPs potentially associated with body weight in male and female yaks, respectively. Among them, 9 and 2 SNPs showed significant difference in yak body weight between different genotypes at each locus in male and female yaks, respectively. Further exploration found 33 coding genes within the 100 kbp upstream or downstream to the SNP loci, which might be potentially affected by the variation of SNPs. Among them, G protein-coupled receptor kinase 4 (GRK4) might be potentially affected by the SNP AX-174555047, which has been reported to affect the functioning of two body-weight associated hormones (parathyroid hormone, PTH, and adrenomedullin, ADM). Determination of PTH and ADM levels in yak revealed positive relationship between PTH level and body weight, negative relationship between ADM level and body weight along with the variation of AX-174555047 mutation. CONCLUSIONS These results suggested that the SNP AX-174555047 might potentially affect body weight through mediating GRK4 expression and then PTH and ADM functioning. Thus, the SNP AX-174555047 might be used as a biomarker for molecular breeding of yak. More investigations are required to validate this point.
Collapse
Affiliation(s)
- Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Zhi-Xin Chai
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041 Sichuan China
| | - Han-Wen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Cheng-Fu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| | - Jin-Wei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850000 Tibet China ,grid.464485.f0000 0004 1777 7975Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary (TAAAS), Lhasa, 850009 Tibet China
| |
Collapse
|
3
|
Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
Collapse
Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| |
Collapse
|
4
|
Asma B, Zhao F, Cai X, Luo X. Mining and Polymorphic Analysis of Di-Nucleotide Microsatellites from Yak Genome. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
6
|
Ma Z. Genome-wide characterization of perfect microsatellites in yak (Bos grunniens). Genetica 2015; 143:515-20. [PMID: 26071092 DOI: 10.1007/s10709-015-9849-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 06/05/2015] [Indexed: 11/25/2022]
Abstract
Microsatellites or simple sequence repeats (SSRs) constitute a significant portion of genomes and play an important role in gene function and genome organization. The availability of a complete genome sequence for yak (Bos grunniens) has made it possible to carry out genome-wide analysis of microsatellites in this species. We analyzed the abundance and density of perfect SSRs in the yak genome. We found a total of 723,172 SSRs with 1-6 bp nucleotide motifs, indicating that about 0.47 % of the yak whole genome sequence (2.66 Gb) comprises perfect SSRs, the average length of which was 17.34 bp/Mb. The average frequency and density of perfect SSRs was 272.18 loci/Mb and 4719.25 bp/Mb, respectively. The proportion of the six classes of perfect SSRs was not evenly distributed in the yak genome. Mononucleotide repeats (44.04 %) with a total number of 318,435 and a average length of 14.71 bp appeared to be the most abundant SSRs class, while the percentages of dinucleotide, trinucleotide, pentanucleotide, tetranucleotide and hexanucleotide repeats was 24.11 %, 15.80 %, 9.50 %, 6.40 % and 0.15 %, respectively. Different repeat classes of SSRs varied in their repeat number with the highest being 1206. Our results suggest that 15 motifs comprised the predominant categories with a frequency above 1 loci/Mb: A, AC, AT, AG, AGC, AAC, AAT, ACC, ATTT, GTTT, AATG, CTTT, ATGG, AACTG and ATCTG.
Collapse
Affiliation(s)
- Zhijie Ma
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, No. 1 Weier Road, Bio-Science Industrial District, Xining, 810016, Qinghai, People's Republic of China,
| |
Collapse
|