Comparative genome analysis with the human genome reveals chicken genes associated with fatness and body weight.

The selection of meat-type chickens (broilers) for rapid growth has been accompanied by excessive fat deposition. In this study, we analysed 53 candidate genes that are associated with obesity and obesity-related traits in humans, for which we found chicken orthologues by BLAST searches. We have identified single nucleotide polymorphisms (SNPs) with significant differences in allele frequencies between broilers and layers in each of the following six candidate genes: adrenergic, beta-2-, receptor, surface (ADRB2); melanocortin 5 receptor (MC5R); leptin receptor (LEPR), McKusick-Kaufman syndrome (MKKS), milk fat globule-EGF factor 8 protein (MFGE8) and adenylate kinase 1 (AK1).

QTLs detected in a multigenerational resource chicken population.

The genetic structure of resource populations affects the power of tests to detect associations between DNA markers and complex traits. Following a chicken interline cross (White Plymouth Rock background), we produced a multigenerational resource population based on 4 pedigreed generations. In this large sibship, 265 parents have been genotyped, and their 3317 progenies have been phenotyped for BW21, BW42, breast meat weight, fat pad weight, and egg production.

Detection of agriculturally important QTLs in chickens and analysis of the factors affecting genotyping strategy.

Three single cross populations were generated in order to analyze factors affecting the ability to detect true linkage with minimum false positive or false negative associations, and to detect associations between markers and quantitative traits. The three populations are: (1) a broiler x broiler cross of a single sire and 34 dams, resulting in 266 progeny; (2) a broiler x broiler cross of a single sire and 41 dams resulting in 360 progeny; and (3) a broiler x layer cross of a single sire with 56 dams resulting in 1180 progeny. Based on these three resource populations we show that: a) gradient selective genotyping was more effective than the random selective genotyping; b) selective genotyping was significant at a selected proportion less than 62% of the cumulative truncation point; c) as few as 10% of selected individuals (5% of each of the two tails) were sufficient to show significant association between markers and phenotypes; d) a gradient slices approach was more powerful than using replicates of the extreme groups; and e) in resource populations resulting from crosses between lines of different backgrounds, most of the microsatellite markers used are polymorphic.

Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions.

Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data.

Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L.

Genetic relationships among eight populations of domesticated carp (Cyprinus carpio L.), a species with a partially duplicated genome, were studied using 12 microsatellites and 505 AFLP bands. The populations included three aquacultured carp strains and five ornamental carp (koi) variants.