Overview on the use of molecular markers to characterize genetic diversity in chickens

Abstract: Decisions on conservation of genetic resources have to rely upon a range of information including the degree of endangerment, adaptation to a specific environment, possession of specific traits, and breed cultural or historical value. Suggesting that the more distant a breed or population is from others the more likely it might carry unique genetic features, the assessment of genetic distances by means of molecular marker information may provide useful information for initial evaluation of chicken genetic resources. Various types of molecular techniques and markers such as RFLP, endogenous avian virus loci, DFP, RAPD, AFLP and mtDNA markers have been employed to study genetic diversity in chickens. The most extensively used class of highly polymorphic molecular markers are the variable number of tandem repeat (VNTR) loci, in particular microsatellites, that show extensive allelic differences in length based mainly on variation in the number of repeats and partly on polymorphism of adjacent regions. Genetic diversity measures using VNTR markers yield reliable information for the study of genetic relationships between chicken populations. In an European project on chicken biodiversity (AVIANDIV) a large number of diverse chicken breeds were typed at 22 microsatellite loci using population DNA pools. Results showed that jungle fowl populations and traditional unselected breeds are widely heterogeneous populations that may include a large portion of the genetic diversity of the tested breeds. Within commercial chickens, broiler lines were slightly more polymorphic than layers. Single nucleotide polymorphism (SNP) is a new and very promising molecular marker system. It offers assessment of genetic diversity in farm animal species in a different way by investigating the mode and extent of sequence changes in both coding and non-coding regions of the genome. SNPs are either analysed as single loci or in combination as haplotypes. They have a lower mutation rate than microsatellites and can be quite stable over evolutionary time scale. In chicken biodiversity studies, high bootstrap values of phylogenetic trees and correct affiliation of individuals to their original populations were found with SNPs. On the other hand, due to higher mutation rate and degree of polymorphism microsatellites may be better suited than SNPs for differentiating between more recently separated populations. Further research is necessary to evaluate the specific suitability and genetic features of these molecular markers for assessing genetic diversity and phylogenetic issues in chickens.