Use of different statistical approaches to study genetic variability of OAR6 in sheep breeds farmed in Italy.
Poster
Data di Pubblicazione:
2012
Citazione:
Use of different statistical approaches to study genetic variability of OAR6 in sheep breeds farmed in Italy / R. Steri, A. Criscione, E. Ciani, B. Moioli, P. Crepaldi, L. Nicoloso, D. Marletta, E.L. Nicolazzi, A. Passero, G. Catillo, F. Pilla, N.P.P. Macciotta. - In: JOURNAL OF ANIMAL SCIENCE. - ISSN 0021-8812. - 90:Suppl. 2(2012), pp. W73.526-W73.526. (Intervento presentato al convegno Joint Annual Meeting tenutosi a Phoenix, Arizona nel 2012).
Abstract:
Dense marker maps allow for the investigation of genomic regions that
differentiate between breeds. In this work, 496 sheep belonging to 20
Italian sheep breeds were genotyped with the Illumina OvineSNP50
BeadChip. After data editing, 2,180 SNP located on chromosome 6 were
analyzed with 4 different approaches. I) Fst Outlier Detection (FOD),
implemented in the LOSITAN software, based on the comparison
between Fst calculated on actual data and expected heterozygosity (He)
and Fst under an island model. II) Composite Log-likelihood (CLL),
based on calculation of CLL of the observed allelic frequencies across
overlapping windows of 9 markers. III) Correspondence analysis (CA).
VI) Canonical Discriminant Analysis (CDA). The different approaches
were able to identify regions at OAR6 that expressed variation between
breeds. Highest values for all statistics were found for a region spanning
between 35 and 41 Mb known to harbour BMPR1b and ABCG2
loci. SNPs with a relevant discriminating power between breeds were
also found at 76, 96 and 107 Mb, near to KIT, IL8 and SCD5 genes
respectively. FOD detected 227 not neutral markers (17 under positive
and 210 under balanced selection) using a confidence interval of 0.95.
A total of 62 windows out of 242 were significant for CLL (P < 0.01).
Several 85 and 135 SNPs exceeded empirical threshold for CA and CDA,
respectively. The discriminating power was high for all methods and
in general, they revealed a geographical pattern of variation between
breeds. Moreover, each method provided specific information. FOD
supplied a relatively low number of markers in divergent selection
but it was able to identify loci under balanced selection. CA and CDA
allowed a decomposition of total variability in different and uncorrelated
variables that could be useful for the identification of genes influencing complex traits. The use of different statistical methods to study genetic
variability between ethnic groups could provide indications about the
adaptation to local conditions as well as the effect of selection.
Tipologia IRIS:
01 - Articolo su periodico
Keywords:
sheep breeds ; SNP ; statistical approaches
Elenco autori:
R. Steri, A. Criscione, E. Ciani, B. Moioli, P. Crepaldi, L. Nicoloso, D. Marletta, E.L. Nicolazzi, A. Passero, G. Catillo, F. Pilla, N.P.P. Macciotta
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