Genome‐wide association study reveals novel variants for growth and egg traits in Dongxiang blue‐shelled and White Leghorn chickens

Abstract

The Dongxiang Blue-shelled chicken is one of the most valuable Chinese indigenous poultry breeds. However, compared to the Italian native White Leghorn, although this Chinese breed possesses numerous favorable characteristics, it also exhibits lower growth performance and fertility. Here, we utilized genotyping sequencing data obtained via genome reduction on a sequencing platform to detect 100,114 single nucleotide polymorphisms and perform further biological analysis and functional annotation. We employed cross-population extended haplotype homozygosity, eigenvector decomposition combined with genome-wide association studies (EigenGWAS), and efficient mixed-model association expedited methods to detect areas of the genome that are potential selected regions (PSR) in both chicken breeds, and performed gene ontology (GO) enrichment and quantitative trait loci (QTL) analyses annotating using the Kyoto Encyclopedia of Genes and Genomes. The results of this study revealed a total of 2424 outlier loci (p-value ,0.01), of which 2144 occur in the White Leghorn breed and 280 occur in the Dongxiang Blue-shelled chicken. These correspond to 327 and 94 PSRs containing 297 and 54 genes, respectively. The most significantly selected genes in Blue-shelled chicken are TMEM141 and CLIC3, while the SLCO1B3 gene, related to eggshell color, was identified via EigenGWAS. We show that the White Leghorn genes JARID2, RBMS3, GPC3, TRIB2, ROBO1, SAMSN1, OSBP2, and IGFALS are involved in immunity, reproduction, and growth, and thus might represent footprints of the selection process. In contrast, we identified six significantly enriched pathways in the Dongxiang Blue-shelled chicken that are related to amino acid and lipid metabolism as well as signal transduction. Our results also reveal the presence of a GO term associated with cell metabolism that occurs mainly in the White Leghorn breed, while the most significant QTL regions mapped to the Chicken QTL Database (GG_4.0) for the Dongxiang Blue-shelled breed are predominantly related to lesions, bone mineral content, and other related traits compared to tibia length and body weight (i.e., at 14, 28, 42, and 70 d) in the White Leghorn. The results of this study highlight differences in growth, immunity, and egg quality traits between the two breeds, and provide a foundation for the exploration of their genetic mechanisms.

Deciphering the mode of action and position of genetic variants impacting on egg number in broiler breeders

“…ELL and ARL8A. Note that the first is among the prioritized candidates (ranked 8th) while the second ARL8A (ADP ribosylation factor like GTPase 8A) has been associated with eggshell thickness and eggshell formation [5] in chickens.…”

“…High-density SNP (single nucleotide polymorphism) genotyping arrays have greatly facilitated the detection of candidate causal variants in genome-wide association studies (GWAS) for various traits related to egg production and egg quality. Most GWAS have, so far, focused on the detection of additive SNPs for egg production [5][6][7] and egg quality traits [5,[7][8][9][10]. It is noted that these studies have been focusing on EN in layer chickens and not broiler breeders.…”

Genome-Wide Association Analysis of Age-Dependent Egg Weights in Chickens

“…It is well-known that EW is a highly heritable quantitative trait (Savegnago et al, 2011 ; Yi et al, 2014 ). Thus, in concert with developments in molecular genetics, research has been carried out to elucidate the genetic basis of EW (Schreiweis et al, 2006 ; Wright et al, 2006 ; Liu et al, 2011 ; Wolc et al, 2012 , 2014 ; Yi et al, 2015 ; Liao et al, 2016 ); a total of 248 quantitative trait loci (QTLs) on 19 different chromosomes (18 autosomes and one sex chromosome) have been reported to be associated with EW and are listed in the AnimalQTLdatabase ( https://www.animalgenome.org/cgi-bin/QTLdb/index ). However, despite a range of studies in this area, wide confidence intervals for the positions of QTL remain that have rarely been replicated.…”

Identification of 19 loci for reproductive traits in a local Chinese chicken by genome-wide study

“…Yuan et al (2015) detected nine genome-wide loci that significantly affected egg number during the laying phases of 21-26, 27-36, and 37-72 weeks using GWAS technology. Liao et al (2016) found a genome-wide significant locus (ss1985401199) located on the sex chromosome Z, which was associated with egg number in hens at 25-45 weeks. In the present study, six SNPs were significantly associated with ENA300 (4) and EN462 (2).…”

“…Tuiskula-Haavisto et al (2002) found that a region related to egg weight at 40 weeks was located on chromosome 4. Liao et al (2016) discovered an SNP (ss1985401190) located on GGA4, which was significantly associated with EW. In the present study, six SNPs were significantly associated with FEW (1), EW300 (3), and EW462 (2), two of which were mapped to chromosome 4.…”