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United States Department of Agriculture

Agricultural Research Service


item Ben-avraham, D
item Blum, S
item Granevitze, Z
item Weigend, S
item Cheng, Hans
item Hillel, J

Submitted to: Animal Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/20/2005
Publication Date: 3/20/2006
Citation: Ben-Avraham, D., Blum, S., Granevitze, Z., Weigend, S., Cheng, H.H., Hillel, J. 2006. W-specific microsatellite loci detected by in silico analysis, map to chromosome Z of the chicken genome. Animal Genetics. 37:179-188.

Interpretive Summary: It has been widely stated that future advances in poultry breeding and health will come through biotechnology and genomic resources. One key resource released in 2004 was the generation of the draft genome sequence of the chicken genome. By having the “blueprint” of the chicken, it was envisioned that it would be much easier to identify genes of agricultural importance. In this study, we find that the chromosome W assembly had errors. This is not a surprising result as this has been the case for other organisms with genome sequences, which is why multiple assemblies and continuous improvements are required. However, our results suggest that other errors are also probably in other chicken chromosomes. Consequently, scientists and companies that wish to take advantage of the chicken genome assembly need to be aware of the current limitations of the current release.

Technical Abstract: Unlike mammals, avian females are the heterogametic gender (ZW) and males are the homogametic (ZZ). The non-recombining, female-specific regions are maternally inherited. As such, they have a special value for matrilineal phylogenetic analysis of chicken populations and possibly for avian species in general. This approach, using Y-specific microsatellites, has been shown to be reliable for human populations. Discovering W-specific regions may also be important for other applications; among them would be studies on the evolution of sex chromosomes and gender identification. The aim of this study was to detect microsatellite loci in the W-specific regions of the chicken genome that do not have homologues at any other chromosome, including chromosome Z. Our results indicate that the draft assembly of the W-specific regions is erroneous. Specifically, as the majority of our mapped microsatellites were located within the 5 large supercontigs that spanned from 721,718 to 4,842,841 bp of chromosome W sequence, we can conclude that the majority of chromosome W is incorrectly placed.

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