Gene hunting: molecular analysis of the chicken genome

This dissertation describes the development of molecular tools to identify genes that are involved in production and health traits in poultry. To unravel the chicken genome, fluorescent molecular markers (microsatellite markers) were developed and optimized to perform high throughput screening of resource populations. The markers can be divided in markers located within chicken genes or ESTs (type I markers) and random markers (type II). The microsatellite markers (430) were subsequently used for the development of a highly informative comprehensive linkage map of the chicken genome. The type I markers provide the necessary links to create a comparative map between chicken and human. A further step in the analysis of the chicken genome is the construction of a physical map and the improvement of the chicken-human comparative map.Therefore a chicken Bacterial Artificial Chromosome (BAC) library was constructed with a 5.5x genome coverage and an average insert size of the BAC clones of 134 kb. Physical mapping was performed by building a BAC contig of chromosome 10 by chromosome walking. Using a bi-directional approach that utilizes the information from the chicken as well as the human genome, a detailed comparative map was obtained for chicken chromosome10 and human chromosome 15. This approach involved sample sequencing of BAC clones as well as FISH mapping. The STS markers developed for chromosome walking are currently used for the development of SNP markers, which will subsequently be used in the advanced intercross lines of the Wageningen resource population to narrow down the chromosomal regions containing the QTL. This information together with a very detailed comparative map will allow the identification of candidate genes for these particular QTL.</p

The gene order on Human Chromosome 15 and Chicken Chromosome 10 reveal multiple inter- and intrachromosomal rearrangements

Comparative mapping between the human and chicken genomes has revealed a striking conservation of synteny between the genomes of these two species, but the results have been based on low-resolution comparative maps. To address this conserved synteny in much more detail, a high-resolution human-chicken comparative map was constructed from human chromosome 15. Mapping, sequencing, and ordering of specific chicken bacterial artificial chromosomes has improved the comparative map of chromosome 15 (Hsa15) and the homologous regions in chicken with almost 100 new genes and/or expressed sequence tags. A comparison of Hsa15 with chicken identified seven conserved chromosomal segments between the two species. In chicken, these were on chromosome 1 (Gga1; two segments), Gga5 (two segments), and Gga10 (three segments). Although four conserved segments were also observed between Hsa15 and mouse, only one of the underlying rearrangement breakpoints was located at the same position as in chicken, indicating that the rearrangements generating the other three breakpoints occurred after the divergence of the rodent and the primate lineages. A high-resolution comparison of Gga10 with Hsa15 identified 19 conserved blocks, indicating the presence of at least 16 intrachromosomal rearrangement breakpoints in the bird lineage after the separation of birds and mammals. These results improve our knowledge of the evolution and dynamics of the vertebrate genomes and will aid in the clarification of the mechanisms that underlie the differentiation between the vertebrate species

Whole genome QTL mapping for growth, meat quality and breast meat yield traits in turkey

Background The turkey (Meleagris gallopavo) is an important agricultural species and is the second largest contributor to the world's poultry meat production. Demand of turkey meat is increasing very rapidly. Genetic markers linked to genes affecting quantitative traits can increase the selection response of animal breeding programs. The use of these molecular markers for the identification of quantitative trait loci, and subsequently fine-mapping of quantitative trait loci regions, allows for pinpointing of genes that underlie such economically important traits. Results The quantitative trait loci analyses of the growth curve, body weight, breast yield and the meat quality traits showed putative quantitative trait loci on 21 of the 27 turkey chromosomes covered by the linkage map. Forty-five quantitative trait loci were detected across all traits and these were found in 29 different regions on 21 chromosomes. Out of the 45 quantitative trait loci, twelve showed significant (p <0.01) evidence of linkage while the remaining 33 showed suggestive evidence (p <0.05) of linkage with different growth, growth curve, meat quality and breast yield traits. Conclusion A large number of quantitative trait loci were detected across the turkey genome, which affected growth, breast yield and meat quality traits. Pleiotropic effects or close linkages between quantitative trait loci were suggested for several of the chromosomal regions. The comparative analysis regarding the location of quantitative trait loci on different turkey, and on the syntenic chicken chromosomes, along with their phenotypic associations, revealed signs of functional conservation between these specie

Quantitative trait loci associated with pre-weaning growth in South African Angora goats

This study aimed to identify chromosomal regions associated with genetic variation in preweaning growth traits in Angora goats. A genome-wide scan was performed by genotyping 1042 offspring from 12 half-sib families using 88 microsatellite caprine markers covering 1368cM. Phenotypes were recorded at birth (BW) and weaning (WW) and analysed using GridQTL software. A total of six putative QTL were detected on six different chromosomes, all at chromosome-wide significance level. Four QTL were identified for BW on CHI 4, 8, 17 and 27 and two QTL for WW on CHI 16 and 19. QTL effects ranged from −0.32 to 0.25 in units of residual standard deviation in different families. Some of these QTL correspond to chromosomes where QTL associated with growth have been identified in other species. These chromosomal segments hold potential to influence weight gain in young goats.http://www. elsevier.com/locate/smallrumreshb201