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Use of locally weighted scatterplot smoothing (LOWESS) regression to study selection signatures in Piedmontese and Italian Brown cattle breeds

Pintus, Elia and Sorbolini, Silvia and Albera, Andrea and Gaspa, Giustino and Dimauro, Corrado and Steri, Roberto and Marras, Gabriele and Macciotta, Nicolò Pietro Paolo (2014) Use of locally weighted scatterplot smoothing (LOWESS) regression to study selection signatures in Piedmontese and Italian Brown cattle breeds. Animal Genetics, Vol. 45 (1), p. 1-11. ISSN 0268-9146. eISSN 1365-2052. Article.

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DOI: 10.1111/age.12076

Abstract

Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50 years, cattle breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index (Fst) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach were used to investigate selection signatures in two cattle breeds with different production aptitudes (dairy and beef). Fst was calculated for 42 514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of Fst values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA2 in the region where the myostatin gene is located and for BTA6 in the region harbouring the ABCG2 locus. Moreover, several loci not previously reported in cattle studies were detected.

Item Type:Article
ID Code:10252
Status:Published
Refereed:Yes
Uncontrolled Keywords:Cattle genome, fixation index, SNPs
Subjects:Area 07 - Scienze agrarie e veterinarie > AGR/17 Zootecnica generale e miglioramento genetico
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Agraria
Publisher:Blackwell / Wiley
ISSN:0268-9146
eISSN:1365-2052
Deposited On:31 Oct 2014 12:20

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