Genome-wide association study for body weight and feed consumption traits in Japanese quail using Bayesian approaches

The aim of this study was to perform a genome-wide association study (GWAS) based on Bayes A and Bayes B statistical methods to identify genomic loci and candidate genes associated with body weight gain, feed intake, and feed conversion ratio in Japanese quail. For this purpose, genomic data obtained from Illumina iSelect 4K quail SNP chip were utilized. After implementing various quality control steps, genotype data from a total of 875 birds for 2,015 SNP markers were used for subsequent analyses. The Bayesian analyses were performed using hibayes package in R (version 4.3.1) and Gibbs sampling algorithm. The results of the analyses showed that Bayes A accounted for 11.43, 11.65, and 11.39% of the phenotypic variance for body weight gain, feed intake, and feed conversion ratio, respectively, while the variance explained by Bayes B was 7.02, 8.61, and 6.48%, respectively. Therefore, in the current study, results obtained from Bayes A were used for further analyses. In order to perform the gene enrichment analysis and to identify the functional pathways and classes of genes that are over-represented in a large set of genes associated with each trait, all markers that accounted for more than 0.1% of the phenotypic variance for each trait were used. The results of this analysis revealed a total of 23, 38, and 14 SNP markers associated with body weight gain, feed intake, and feed conversion ratio in Japanese quail, respectively. The results of the gene enrichment analysis led to the identification of biological pathways (and candidate genes) related to lipid phosphorylation (TTC7A gene) and cell junction (FGFR4 and FLRT2 genes) associated with body weight gain, calcium signaling pathway (ADCY2 and CAMK1D genes) associated with feed intake, and glycerolipid metabolic process (LIPC gene), lipid metabolic process (ADGRF5 and ESR1 genes), and glutathione transferase (GSTK1 gene) associated with feed conversion ratio. Overall, the findings of this study can provide valuable insights into the genetic architecture of growth and feed consumption traits in Japanese quail.

A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes

Background

Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (F_ST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken.

Results

Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1).

Conclusions

Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00664-9.

Sequence variations in estrogen receptor 1 and 2 genes and their association with egg production traits in Chinese Dagu chickens

Estrogen receptors α (ESR1) and β (ESR2) play central roles in folliculogenesis and therefore in reproductive biology. In the present study, two single nucleotide polymorphisms (SNPs) were identified in the ESR1 and ESR2 genes using PCR-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing. One of the identified SNPs, a T1101C transition located within exon 4 of the ESR1 gene, was significantly associated with hen-housed egg production (HHEP) at 30, 43, 57 and 66 weeks of age (P<0.05), and egg weight (EW) at 30 weeks (P<0.05). Another SNP, a G1755A transition leading to a non-synonymous substitution (valine 459-to-isoleucine) located within exon 8 of the ESR2 gene, was also markedly correlated with the HHEP at 30, 43, 57 and 66 weeks of age (P<0.05), and EW at 30 weeks (P<0.05). A greater proportion of the additive variance was explained by the SNPs for most of the associated egg production traits (>1%). Furthermore, the results of the combined genotype-based association analysis supported the finding that the two SNPs were associated with the traits under a study. Taken together, our findings suggest that the two sequence variations in the ESR1 and ESR2 genes may provide promising genetic markers for the early selection and prediction of advantageous phenotypes in chicken breeding.