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Yang Q, Zhang S, Liu L, Lei C, Qi X, Lin F, Qu W, Qi X, Liu J, Wang R, Chen H, Lan X. The evaluation of 23-bp and 12-bp insertion/deletion within the PRNP gene and their effects on growth traits in healthy Chinese native cattle breeds. JOURNAL OF APPLIED ANIMAL RESEARCH 2017. [DOI: 10.1080/09712119.2017.1348950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| | - Liangliang Liu
- School of Business Information, Shanghai University of International Business and Economics, Shanghai, People’s Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| | - Xinglei Qi
- Xia'nan cattle Technology Development Company, Biyang, People’s Republic of China
- Bureau of Animal Husbandry, Biyang, People’s Republic of China
| | - Fengpeng Lin
- Xia'nan cattle Technology Development Company, Biyang, People’s Republic of China
- Bureau of Animal Husbandry, Biyang, People’s Republic of China
| | - Weidong Qu
- Bureau of Animal Husbandry, Biyang, People’s Republic of China
| | - Xingshan Qi
- Bureau of Animal Husbandry, Biyang, People’s Republic of China
| | - Jiming Liu
- Animal Husbandry Technology Promotion Station of Jiangxi, Nanchang, People’s Republic of China
| | - Rongmin Wang
- Animal Husbandry Technology Promotion Station of Jiangxi, Nanchang, People’s Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, People’s Republic of China
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Sorbolini S, Gaspa G, Steri R, Dimauro C, Cellesi M, Stella A, Marras G, Marsan PA, Valentini A, Macciotta NPP. Use of canonical discriminant analysis to study signatures of selection in cattle. Genet Sel Evol 2016; 48:58. [PMID: 27521154 PMCID: PMC4983034 DOI: 10.1186/s12711-016-0236-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/01/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Cattle include a large number of breeds that are characterized by marked phenotypic differences and thus constitute a valuable model to study genome evolution in response to processes such as selection and domestication. Detection of "signatures of selection" is a useful approach to study the evolutionary pressures experienced throughout history. In the present study, signatures of selection were investigated in five cattle breeds farmed in Italy using a multivariate approach. METHODS A total of 4094 bulls from five breeds with different production aptitudes (two dairy breeds: Italian Holstein and Italian Brown Swiss; two beef breeds: Piemontese and Marchigiana; and one dual purpose breed: Italian Simmental) were genotyped using the Illumina BovineSNP50 v.1 beadchip. Canonical discriminant analysis was carried out on the matrix of single nucleotide polymorphisms (SNP) genotyping data, separately for each chromosome. Scores for each canonical variable were calculated and then plotted in the canonical space to quantify the distance between breeds. SNPs for which the correlation with the canonical variable was in the 99th percentile for a specific chromosome were considered to be significantly associated with that variable. Results were compared with those obtained using an FST-based approach. RESULTS Based on the results of the canonical discriminant analysis, a large number of signatures of selection were detected, among which several had strong signals in genomic regions that harbour genes known to have an impact on production and morphological bovine traits, including MSTN, LCT, GHR, SCD, NCAPG, KIT, and ASIP. Moreover, new putative candidate genes were identified, such as GCK, B3GALNT1, MGAT1, GALNTL1, PRNP, and PRND. Similar results were obtained with the FST-based approach. CONCLUSIONS The use of canonical discriminant analysis on 50 K SNP genotypes allowed the extraction of new variables that maximize the separation between breeds. This approach is quite straightforward, it can compare more than two groups simultaneously, and relative distances between breeds can be visualized. The genes that were highlighted in the canonical discriminant analysis were in concordance with those obtained using the FST index.
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Affiliation(s)
- Silvia Sorbolini
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Giustino Gaspa
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Roberto Steri
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, via Salaria 31, 00015, Monterotondo, Italy
| | - Corrado Dimauro
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Massimo Cellesi
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | | | | | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Alessio Valentini
- Dipartimento per l'Innovazione dei Sistemi Biologici Agroalimentari e Forestali DIBAF, Università della Tuscia, Viterbo, Italy
| | - Nicolò Pietro Paolo Macciotta
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy.
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