Characterization analysis of Rongchang pig population based on the Zhongxin-1 Porcine Breeding Array PLUS
3
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
Objective: To carry out a comprehensive production planning of the existing Rongchang pig population from both environmental and genetic aspects, and to establish a closed population with stable genetic diversity and strict pathogen control, it is necessary to fully understand the genetic background of the population. Methods: We genotyped 54 specific pathogen free (SPF) Rongchang pigs using the Zhongxin-1 Porcine Breeding Array PLUS, calculated their genetic diversity parameters and constructed their families. In addition, we also counted the runs of homozygosity (ROH) of each individual and calculated the value of inbreeding coefficient based on ROH for each individual. Results: Firstly, the results of genetic diversity analysis showed that the effective population size (Ne) of this population was 3.2, proportion of polymorphic markers (PN) was 0.515, desired heterozygosity (He) and observed heterozygosity (Ho) were 0.315 and 0.335. Ho was higher than He, indicating that the heterozygosity of all the selected loci was high. Secondly, combining the results of genomic relatedness analysis and cluster analysis, it was found that the existing Rongchang pig population could be divided into four families. Finally, we also counted the ROH of each individual and calculated the inbreeding coefficient value accordingly, whose mean value was 0.09. Conclusion: Due to the limitation of population size and other factors, the genetic diversity of this Rongchang pig population is low. The results of this study can provide basic data to support the development of Rongchang pig breeding program, the establishment of SPF Rongchang pig closed herd and its experimental utilization.
Abstract
Objective: To carry out a comprehensive production planning of the existing Rongchang pig population from both environmental and genetic aspects, and to establish a closed population with stable genetic diversity and strict pathogen control, it is necessary to fully understand the genetic background of the population. Methods: We genotyped 54 specific pathogen free (SPF) Rongchang pigs using the Zhongxin-1 Porcine Breeding Array PLUS, calculated their genetic diversity parameters and constructed their families. In addition, we also counted the runs of homozygosity (ROH) of each individual and calculated the value of inbreeding coefficient based on ROH for each individual. Results: Firstly, the results of genetic diversity analysis showed that the effective population size (Ne) of this population was 3.2, proportion of polymorphic markers (PN) was 0.515, desired heterozygosity (He) and observed heterozygosity (Ho) were 0.315 and 0.335. Ho was higher than He, indicating that the heterozygosity of all the selected loci was high. Secondly, combining the results of genomic relatedness analysis and cluster analysis, it was found that the existing Rongchang pig population could be divided into four families. Finally, we also counted the ROH of each individual and calculated the inbreeding coefficient value accordingly, whose mean value was 0.09. Conclusion: Due to the limitation of population size and other factors, the genetic diversity of this Rongchang pig population is low. The results of this study can provide basic data to support the development of Rongchang pig breeding program, the establishment of SPF Rongchang pig closed herd and its experimental utilization.
참고문헌 (39)
- Ma X, "BMP15 regulates FSHR through TGF-β receptor II and SMAD4 signaling in prepubertal ovary of Rongchang pigs", Res Vet Sci, 143, pp.66~73 (2022)[DOI]
- Chen X, "Deciphering the miRNA transcriptome of Rongchang pig longissimus dorsi at weaning and slaughter time points", J Anim Physiol Anim Nutr(Berl), 104, pp.954~964 (2020)[DOI]
- Gan L, "Transcriptomic analysis of Rongchang pig brains and livers", Gene, 560, pp.96~106 (2015)[DOI]
- Liu H, "Microbial and metabolic alterations in gut microbiota of sows during pregnancy and lactation", FASEB J, 33, pp.4490~4501 (2019)[DOI]
- Gerdts V, "Large animal models for vaccine development and testing", ILAR J, 56, pp.53~62 (2015)[DOI]
- Qi R, "The intestinal microbiota contributes to the growth and physiological state of muscle tissue in piglets", Sci Rep, 11, pp.11237~ (2021)[DOI]
- Chen L, "A de novo silencer causes elimination of MITF-M expression and profound hearing loss in pigs", BMC Biol, 14, pp.52~ (2016)[DOI]
- Gao X, "Establishment of porcine and human expanded potential stem cells", Nat Cell Biol, 21, pp.687~699 (2019)[DOI]
- Oldenbroek JK, "The use of genomic information for the conservation of animal genetic diversity", Animals(Basel), 11, pp.3208~ (2021)[DOI]
- Oldenbroek JK, "Advances in breeding of dairy cattle" (2019), Burleigh Dodds Science Publishing Limited
- Denman A, "Molecular cloning : a laboratory manual", Immunology, 49, pp.411~ (1983)
- Li H, "A fully integrated continuous-time 50-Hz notch filter with center frequency tunability", 2011Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp.3558~3562 (2011)
- Purcell S, "PLINK : a tool set for whole-genome association and population-based linkage analyses", Am J Hum Genet, 81, pp.559~575 (2007)[DOI]
- Barbato M, "SNeP : a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data", Front Genet, 6, pp.109~ (2015)[DOI]
- Sun H, "Genomic signatures reveal selection of characteristics within and between Meishan pig populations", Anim Genet, 49, pp.119~126 (2018)[DOI]
- Herrero-Medrano JM, "Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula", BMC Genet, 14, pp.106~ (2013)[DOI]
- Sved JA, "Linkage disequilibrium and homozygosity of chromosome segments in finite populatio ns", Theor Popul Biol, 2, pp.125~141 (1971)[DOI]
- VanRaden PM, "Efficient methods to compute genomic predictions", J Dairy Sci, 91, pp.4414~4423 (2008)[DOI]
- Gu Z, "Complex heatmap visualization", iMeta, 1, pp.e43~ (2022)[DOI]
- Kumar S, "MEGA X : Molecular evolutionary genetics analysis across computing platforms", Mol Biol Evol, 35, pp.1547~1549 (2018)[DOI]
- Silio L, "Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics", J Anim Breed Genet, 130, pp.349~360 (2013)[DOI]
- McQuillan R, "Runs of homozygosity in European populations", Am J Hum Genet, 83, pp.359~372 (2008)[DOI]
- Welsh CS, "Pedigree analysis of 5 swine breeds in the United States and the implications for genetic conservation", J Anim Sci, 88, pp.1610~1618 (2010)[DOI]
- G.Q. Tang, "Inbreeding and Genetic Diversity in Three Imported Swine Breeds in China Using Pedigree Data", Animal Bioscience, 26(6), pp.755~765 (2013), 아세아·태평양축산학회[DOI]
- Melka M, "Analysis of genetic diversity in four Canadian swine breeds using pedigree data", Can J Anim Sci, 90, pp.331~340 (2010)[DOI]
- Meuwissen TH, "Effective sizes of livestock populations to prevent a decline in fitness", Theor Appl Genet, 89, pp.1019~1026 (1994)[DOI]
- Liu B, "Revealing genetic diversity and population structure of endangered altay white-headed cattle population using 100 k SNP markers", Animals(Basel), 12, pp.3214~ (2022)[DOI]
- Liu Bin, "Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population", Animal Bioscience, 34(7), pp.1105~1115 (2021), 아세아·태평양축산학회[DOI]
- Huang M, "Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs", Animal, 15, pp.100354~ (2021)[DOI]
- Krupa E, "Assessment of the Genetic diversity of a local pig breed using pedigree and SNP data", Genes(Basel), 12, pp.1972~ (2021)[DOI]
- Dobrzański J, "Conservation of goose genetic resources in Poland-past and present status", World's Poult Sci J, 75, pp.387~400 (2019)[DOI]
- de Araujo Neto FR, "Population structure of Simmental beef cattle using pedigree analysis", Trop Anim Health Prod, 52, pp.1513~1517 (2020)[DOI]
- Jarnecka O, "Pedigree analysis in the Polish Red cattle population", Animal, 15, pp.100238~ (2021)[DOI]
- Wang J, "Pedigrees or markers : Which are better in estimating relatedness and inbreeding coefficient?", Theor Popul Biol, 107, pp.4~13 (2016)[DOI]
- Medugorac I, "Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size", Mol Ecol, 18, pp.3394~3410 (2009)[DOI]
- Zanella R, "Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data", Genet Sel Evol, 48, pp.24~ (2016)[DOI]
- Purfield DC, "Runs of homozygosity and population history in cattle", BMC Genet, 13, pp.70~ (2012)[DOI]
- Wang Yanping, "High-density single nucleotide polymorphism chip-based conservation genetic analysis of indigenous pig breeds from Shandong Province, China", Animal Bioscience, 34(7), pp.1123~1133 (2021), 아세아·태평양축산학회[DOI]
- Peripolli E, "Runs of homozygosity : current knowledge and applications in livestock", Anim Genet, 48, pp.255~271 (2017)[DOI]
