Molecular phylogenetic analysis of Chinese indigenous blue-shelled chickens inferred from whole genomic region of the SLCO1B3 gene

Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology

Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.

An EAV-HP insertion in the promoter region of SLCO1B3 has pleiotropic effects on chicken liver metabolism based on the transcriptome and proteome analysis

Solute carrier organic anion transporter 1B3 (SLCO1B3) is an important liver primarily highly expressed gene, its encoded protein (OATP1B3) involved in the transport of multi-specific endogenous and exogenous substances. We previously reported that an EAV-HP inserted mutation (IM+) in the 5' flanking region of SLCO1B3 was the causative mutation of chicken blue eggs, and a further research showed that IM+ significantly reduced the expression of SLCO1B3 in liver. Herein, we confirmed a cholate response element (IR-1) played an important role in activating SLCO1B3 and in vitro experiments showed that the activation of IR-1 can be significantly reduced by the EAV-HP IM+ . We performed transcriptome and proteomic analysis using the same set of IM+ and IM- liver tissues from Yimeng hens (a Chinese indigenous breed) to study the effect of SLCO1B3 and OATP1B3 expression reduction on chicken liver function. The results showed that common differential expression pathways were screened out from both transcriptome and proteome, in which fatty acid metabolism and drug metabolism-cytochrome P450 were significantly enriched in the KEGG analysis. The lipid-related metabolism was weakened in IM+ group, which was validated by serum biochemical assay. We unexpectedly found that EAV-HP fragment was highly expressed in the liver of the IM+ chickens. We cloned the EAV-HP full-length transcript and obtained the complete open reading frame. It is worth noting that there was some immune related differential expressed genes, such as NFKBIZ, NFKBIA, and IL1RL1, which were higher expressed in the IM+ group, which may due to the high expression of EAV-HP. Our study showed that EAV-HP IM+ reduced the expression of SLCO1B3 in liver, resulting in the decrease of fatty metabolism and exogenous substance transport capacity. The mutation itself also expressed in the liver and may be involved in the immune process. The mechanism needs further study.

A selection method of chickens with blue-eggshell and dwarf traits by molecular marker-assisted selection

The blue-eggshell and dwarf traits have an important economic value in poultry production. Using a genetic aggregation-based strategy, the molecular marker-assisted selection technology was jointly used to provide a rapid breeding method for pure strain chickens simultaneously with hens exhibiting the blue-eggshell and dwarf traits. Overall, 80 male dwarf chickens and 1,000 hybrid blue-eggshell hens (F0) were used for the hybridization experiment. Subsequently, the crossing of F1 or F2 chicks was performed in succession. The F1 and F2 chicks were respectively detected by the joint molecular markers of the solute carrier organic anion transporter family, namely, 1B3 (SLCO1B3) and the growth hormone receptor (GHR) genes, which relate to blue-eggshell and dwarf traits. Meanwhile, the selection of blue-eggshell and dwarf phenotypes was used to validate the data obtained by the molecular markers. The results showed that F1 chicks included the heterozygous and wild-type of SLCO1B3, as well as the homozygous (hens) and heterozygous (roosters) of GHR. However, F2 chicks included 3 different genotypes of both SLCO1B3 and GHR. Ultimately, 196 F1 roosters (concurrently with heterozygous genotype of SLCO1B3 and GHR) and 1,073 F1 hens (concurrently with heterozygous genotype of SLCO1B3 and homozygous genotype of GHR) were obtained from the initial 10,040 F1 chicks. Further, 27 F2 roosters and 345 F2 hens, which simultaneously carried the homozygous genotype of SLCO1B3 and GHR, were screened from the initial 6,000 F2 chicks. Data obtained on the blue-eggshell and dwarf phenotypes were consistent with the results by molecular markers. Similarly, the purity verification of the strain obtained through 2 crossing experiments (F0♂ × F2♀ and F2♂ × F2♀) revealed that all chickens had the blue-eggshell and dwarf traits, supporting that the obtained F2 strain was pure. In summary, for the first time, we successfully bred a pure strain chicken with blue-eggshell and dwarf traits by jointly using the molecular markers of the SLCO1B3 and GHR genes. Our study provides a new method for the rapid cultivation of new chicken strains.