Use of canonical discriminant analysis to study signatures of selection in cattle

Genetics Selection Evolution

Research Article

Gabriele Marras¹  Alessandra Stella¹  Roberto Steri²  Silvia Sorbolini³  Massimo Cellesi³  Corrado Dimauro³  Nicolò Pietro Paolo Macciotta³  Giustino Gaspa³  Alessio Valentini⁴  Paolo Ajmone Marsan⁵ 

[1] Consiglio Nazionale delle Ricerche - IBBA, Lodi, Italy;Consiglio per la Ricerca e la Sperimentazione in Agricoltura, via Salaria 31, 00015, Monterotondo, Italy;Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy;Dipartimento per l’Innovazione dei Sistemi Biologici Agroalimentari e Forestali DIBAF, Università della Tuscia, Viterbo, Italy;Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy;

关键词: Single Nucleotide Polymorphism;    Canonical Variable;    Bovine Spongiform Encephalopathy;    Growth Hormone Receptor;    Significant SNPs;   

DOI  :  10.1186/s12711-016-0236-7

 received in 2016-01-26, accepted in 2016-08-01,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundCattle 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.MethodsA 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.ResultsBased 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s) 2016

【 图 表 】

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