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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling

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Author(s):
Rosario, M. F. [1] ; Margarido, G. R. A. [1] ; Boschiero, C. [2] ; Moura, A. S. A. M. T. [2] ; Ledur, M. C. [3] ; Coutinho, L. L. [4] ; Garcia, A. A. F. [1]
Total Authors: 7
Affiliation:
[1] Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, Piracicaba, SP - Brazil
[2] Univ Estadual Sao Paulo, Dept Anim Prod, Fac Med Vet & Zootecnia, Botucatu, SP - Brazil
[3] EMBRAPA, Ctr Nacl Pesquisa Suinos & Aves, Concordia, SC - Brazil
[4] Univ Sao Paulo, Dept Zootecnia, Escola Super Agr Luiz de Queiroz, Piracicaba, SP - Brazil
Total Affiliations: 4
Document type: Journal article
Source: Genetics and Molecular Research; v. 9, n. 3, p. 1357-1376, 2010.
Web of Science Citations: 3
Abstract

Some factors complicate comparisons between linkage maps from different studies. This problem can be resolved if measures of precision, such as confidence intervals and frequency distributions, are associated with markers. We examined the precision of distances and ordering of microsatellite markers in the consensus linkage maps of chromosomes 1, 3 and 4 from two F 2 reciprocal Brazilian chicken populations, using bootstrap sampling. Single and consensus maps were constructed. The consensus map was compared with the International Consensus Linkage Map and with the whole genome sequence. Some loci showed segregation distortion and missing data, but this did not affect the analyses negatively. Several inversions and position shifts were detected, based on 95% confidence intervals and frequency distributions of loci. Some discrepancies in distances between loci and in ordering were due to chance, whereas others could be attributed to other effects, including reciprocal crosses, sampling error of the founder animals from the two populations, F(2) population structure, number of and distance between microsatellite markers, number of informative meioses, loci segregation patterns, and sex. In the Brazilian consensus GGA1, locus LEI1038 was in a position closer to the true genome sequence than in the International Consensus Map, whereas for GGA3 and GGA4, no such differences were found. Extending these analyses to the remaining chromosomes should facilitate comparisons and the integration of several available genetic maps, allowing meta-analyses for map construction and quantitative trait loci (QTL) mapping. The precision of the estimates of QTL positions and their effects would be increased with such information. (AU)