Three indel variants in chicken LPIN1 exon 6/flanking region are associated with performance and carcass traits

The Novel Structural Variation in the GHR Gene Is Associated with Growth Traits in Yaks (Bos grunniens)

The growth hormone receptor (GHR) is a member of the cytokine/hematopoietic factor receptor superfamily, which plays an important role in the growth and development, immunity, and metabolism of animals. This study identified a 246 bp deletion variant in the intronic region of the GHR gene, and three genotypes, including type II, type ID, and type DD, were observed. Genotype analysis of structural variation (SV) was performed on 585 individuals from 14 yak breeds, and it was found that 246 bp deletion was present in each breed. The II genotype was dominant in all yak breeds except for SB yak. The association analysis of gene polymorphisms and growth traits in the ASD yak population showed that the 246 bp SV was significantly associated with body length at 6 months (p < 0.05). GHR messenger RNA (mRNA) was expressed in all the tested tissues, with significantly higher levels in the liver, muscle, and fat than in other organs. The results of transcription activity showed that the luciferase activity of the pGL4.10-DD vector was significantly higher than that of the pGL4.10-II vector (p < 0.05). Additionally, the transcription-factor binding prediction results showed that the SV in the runt-related transcription factor 1 (Runx1) transcription-factor binding site may affect the transcriptional activity of the GHR gene, regulating yak growth and development. This study showed that the novel SV of the GHR gene could be used as a candidate molecular marker for the selection of the early growth trait in ASD yak.

Association of PRKCA expression and polymorphisms with layer duck eggshell quality

1. Eggshell quality is important for the poultry industry. Calcium is deposited during eggshell formation, and protein kinase C alpha (PRKCA) is involved in transmembrane transport of calcium ions in cells. However, the biological function of PRKCA in poultry is still not understood. Therefore, the aim of this study was to explore the association of mRNA expression and single nucleotide polymorphisms (SNPs) of the PRKCA gene with eggshell quality in laying ducks. 2. The mRNA expression and SNPs of the PRKCA gene were detected by real-time fluorescence quantitative PCR (qRT-PCR) and sequencing of PCR products in 45-week-old female Sansui ducks, which is a high production layer duck breed in China. The association of mRNA expression and SNPs in the PRKCA gene with layer duck eggshell traits was analysed using SPSS (v18.0) software. 3. The results demonstrated that PRKCA mRNA was widely expressed in all examined tissues, and expression was highest in kidney and lowest in the gizzard. Furthermore, the PRKCA mRNA level in uterus was significantly positively correlated with eggshell strength and eggshell weight (P < 0.05). Three novel SNPs, the synonymous mutations of g.9571770 T > C in exon 5, g.9583222 C > T and g.9583227 G > A in exon 7, were found in the PRKCA gene, giving four haplotypes and 10 diplotypes, which affected the mRNA secondary structure and free energy. The g.9583222 C > T and g.9583227 G > A mutations were significantly associated with eggshell strength (P < 0.05). Diplotype H1H1 was advantageous for increasing the strength and thickness of an eggshell. 4. In conclusion, the study showed that the mRNA transcription and genetic variation in the PRKCA gene could significantly affect the strength of duck eggshell and that the PRKCA gene is an important candidate gene for improving eggshell quality in poultry.

Variation in the Lipin 1 Gene Is Associated with Birth Weight and Selected Carcass Traits in New Zealand Romney Sheep

Lipin 1 plays an important role in lipid metabolism. In this study; we searched for variation in the ovine lipin 1 gene (LPIN1) in three gene regions (a 5' non-coding region; a region containing an alternatively spliced exon in intron 4; and a region containing coding exon 6) using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. The greatest amount of alleles was found in coding exon 6; with five sequences being detected. The effect of variation in this exon was investigated in 242 New Zealand Romney lambs derived from 12 sire-lines. The presence of variant E₃ was associated with a decrease in birth weight (p = 0.005) and the proportion of leg yield (p = 0.045), but with an increase in hot carcass weight (p = 0.032) and the proportion of loin yield (p = 0.014). The presence of variant B₃ was associated with an increased pre-weaning growth rate (p = 0.041), whereas the presence of variant C₃ was associated with an increase in shoulder yield (p < 0.001). These results suggest that ovine LPIN1 variation may have value as a genetic marker for improving meat production and carcass traits.

Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

Background

Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection.

Results

A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development.

Conclusions

In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4444-0) contains supplementary material, which is available to authorized users.