Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Abstract

Background The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great potential in meeting demands of local food producers, commercial farmers and biotechnology sector of specific pathogen-free (SPF) eggs, the former valuing the breed for its egg weight (EW), EL, age at first egg (AFE), body weight (BW), and the latter for its yield of extraembryonic fluid (YEF) in 12.5-day embryos, ratio of extraembryonic fluid to egg weight, and embryo mass. Moreover, its cold tolerance has been presumably associated with day-old chick down colour (DOCDC) – white rather than yellow, the genetic basis of these traits being however poorly understood. Results We undertook genome-wide association studies (GWASs) for eight performance traits using single nucleotide polymorphism (SNP) genotyping of 146 birds and an Illumina 60KBeadChip. Several suggestive associations ( p < 5.16*10 − 5 ) were found for YEF, AFE, BW and EW. Moreover, on chromosome 2, an association with the white DOCDC was found where there is an linkage disequilibrium block of SNPs including genes that are responsible not for colour, but for immune resistance. Conclusions The obtained GWAS data can be used to explore the genetics of immunity and carry out selection for increasing YEF for SPF eggs production. Electronic supplementary material The online version of this article (10.1186/s12864-019-5605-5) contains supplementary material, which is available to authorized users.

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

“…123,202,074 bp), which could reflect the long-term selection of RW chickens for cold tolerance at the earlier stage of breed development [11][12][13]. Moreover, this region contains a causal SNP associated with day-old chick down color in RW chickens [15].…”

“…Adult individuals were kept in winter at a temperature below 0 • C, while safeguarding the laying performance at a high level [13]. As a result of the long-term selection for critically low temperatures, the RS phenotypes were characterized by exceptional cold tolerance of neonatal chicks; their snowy-white down at day-old presumably caused by a recessive mutant gene, sw, for snow-white down [14,15]; and elevated resistance to a few neoplastic diseases, such as Marek's disease, leukemia, and carcinomas [11]. The current RG population was more recently derived from the RS as a result of a one-time telic crossing with White Leghorns in 2006 not selected further for cold tolerance and subjected to random mating in 2000-2013 [12,[16][17][18].…”

“…Its examination for the effects of indels in the PRL (prolactin) and DRD2 (dopamine receptor D2) genes on YEF showed significant associations of the PRL insertion variant with greater YEF and egg weight (EW) [16]. In a genome-wide association study (GWAS) using the Illumina Chicken 60K SNP iSelect BeadChip, several suggestive SNP loci and candidate genes were detected for YEF as well as EW, egg number, age at first egg, body weight, and day-old chick down color [15]. The RW demographic history was explored at the genomic level using the same Illumina BeadChip.…”

Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity

“…Assessment of the genome-wide diversity plays a significant role in conserving local and imported genetic resources and maintaining an effective program for breeding commercial populations (e.g., [ 1 , 2 , 3 ]). Previously, in the framework of a poultry germplasm conservation and utilization research project, we assessed a broad spectrum of the world’s chicken germplasm populations for genetic variation at economically important loci [ 4 , 5 ] and multiple single nucleotide polymorphisms (SNP) loci [ 6 , 7 , 8 , 9 ].…”

Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review

“…GWAS is a powerful approach with which to identify candidate genes, genomic regions, and polymorphisms related to specific phenotypic features. Its application has become increasingly widespread because it is useful for more accurate breeding programs for chickens and other animals [ 50 , 51 ].…”