ABSTRACT
Background: To reveal candidate genes and the molecular genetic mechanism underlying primary feather color trait in ducks, a genome-wide association study (GWAS) for the primary feather color trait was performed based on the genotyping-by-sequencing (GBS) technology for a native Chinese female duck, Longyan Shan-ma ducks. Methods: Blood genomic DNA from 314 female Longyan Shan-ma duck were genotyped using GBS technology. A GWAS for the primary feather color trait with genome variations was performed using an univariate linear mixed model based on all SNPs in autosomes. Results: Seven genome-wide significant single nucleotide polymorphisms (SNPs, Bonferroni-adjusted p-value <8.03 × 10-7) within the introns of the genes STARD9, ZNF106, SLC7A5, and BANP genes were associated with the primary feather color trait. Twenty-two genome-wide suggestive SNPs (Bonferroni-adjusted p-value <1.61 × 10-5) of 17 genes (besides ZNF106 and SLC7A5) were also identified. Seven SNPs were located at one 0.22 Mb region (38.65-38.87 Mb) on chromosome 5, and six SNPs were located at one 0.31 Mb region (19.53-19.84 Mb) on chromosome 11. The functions of STARD9, SLC7A5, BANP, LOC101798015, and IPMK were involved pigmentation and follicle development, especially, STARD9 upregulated expression in black feather (haplotype-CCCC) bulb tissue compared with in pockmarked feather (haplotype-TGTT) bulb tissue, implicating these genes as candidate genes for primary feather color trait. Conclusion: The preliminarily findings suggested candidate genes and regions, and the genetic basis of primary feather color trait in a female duck.
ABSTRACT
Egg production traits are economically important in laying ducks. Genetic molecular mechanisms and candidate genes underlying these traits remain unclear. In this study, whole genome variants were identified through whole-genome resequencing using three high-egg producing (HEN) and three low-egg producing (LEN) laying ducks. The gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genome (KEGG) pathways for the genes of common differential variants between HEN and LEN ducks were determined. Frizzled class receptor 6 (FZD6) was further genotyped using the Sequenom MassARRAY iPLEX platform. The association of FZD6 gene polymorphisms with 73 egg production and weight traits in 329 female ducks were estimated. A total of 65,535 single nucleotide polymorphisms (SNPs) and 4,702 indels were identified across the genome. Fourteen GO terms and 14 KEGG pathways were determined for the genes of common differential variants, including MAPK signaling, Wnt signaling, melanogenesis and calcium signaling pathways, which are key functional pathways for poultry egg production reported in previous reports. Further analysis showed that 27 SNPs of FZD6 were associated with three early egg production of duck and egg weight traits, including egg production at 17 weeks (EP17), 18 weeks (EP18) and 19 weeks (EP19) and egg weight at 59 weeks (EW59). The FZD6 should be considered a novel candidate gene for egg production traits in laying ducks.
Subject(s)
Ducks , Genome , Animals , Female , Ducks/genetics , Genotype , Phenotype , Polymorphism, Single NucleotideABSTRACT
OBJECTIVE: To assess the differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production, and to obtain new transcriptomic data of these egg-producing ducks. METHODS: The Illumina HiSeq 2000 system was used for high throughput sequencing of ovarian transcriptomes from Shan Ma ducks at their peak or late stages of egg production. RESULTS: Greater than 93% of the sequencing data had a base quality score (Q score) that was not less than 20 (Q20). From ducks at their peak stage of egg production, 42,782,676 reads were obtained, with 4,307,499,083 bp sequenced. From ducks at their late stage of egg production, 45,316,166 reads were obtained, with 4,562,063,363 bp sequenced. A comparison of the two datasets identified 2,002 differentially expressed genes, with 790 upregulated and 1,212 downregulated. Further analysis showed that 1,645 of the 2,002 differentially expressed genes were annotated in the non-redundant (NR) database, with 646 upregulated and 999 downregulated. Among the differentially expressed genes with annotations in the NR database, 696 genes were functionally annotated in the clusters of orthologous groups of proteins database, involving 25 functional categories. One thousand two hundred four of the differentially expressed genes with annotations in the NR database were functionally annotated in the gene ontology (GO) database, and could be divided into three domains and 56 categories. The three domains were cellular component, molecular function, and biological process. Among the genes identified in the GO database, 451 are involved in development and reproduction. Analysis of the differentially expressed genes with annotations in the NR database against the Kyoto encyclopedia of genes and genomes database revealed that 446 of the genes could be assigned to 175 metabolic pathways, of which the peroxisome proliferator-activated receptor signaling pathway, insulin signaling pathway, fructose and mannose metabolic pathways, gonadotropin releasing hormone signaling pathway and transforming growth factor beta signaling pathway were significantly enriched. CONCLUSION: The differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production were elucidated, which greatly enriched the ovarian transcriptomic information of egg-producing ducks.
ABSTRACT
Variations of pigment content in the microscopic conchocelis stage of four Alaskan Porphyra species were investigated in response to environmental variables. Conchocelis filaments were cultured under varying conditions of irradiance and nutrient concentrations for up to 60 d at 11°C and 30 psu salinity. Results indicate that conchocelis filaments contain relatively high concentrations of phycobilins under optimal culture conditions. Phycobilin pigment production was significantly affected by irradiance, nutrient concentration, and culture duration. For Porphyra abbottiae V. Krishnam., Porphyra sp., and Porphyra torta V. Krishnam., maximal phycoerythrin (63.2-95.1 mg · g dwt(-1) ) and phycocyanin (28.8-64.8 mg · g dwt(-1) ) content generally occurred at 10 µmol photons · m(-2) · s(-1) , f/4-f/2 nutrient concentration after 10-20 d of culture. Whereas for Porphyra hiberna S. C. Lindstrom et K. M. Cole, the highest phycoerythrin (73.3 mg · g dwt(-1) ) and phycocyanin (70.2 mg · g dwt(-1) ) content occurred at 10 µmol photons · m(-2) · s(-1) , f nutrient concentration after 60 d in culture. Under similar conditions, the different species showed significant differences in pigment content. P. abbottiae had higher phycoerythrin content than the other three species, and P. hiberna had the highest phycocyanin content. P. torta had the lowest phycobilin content.
ABSTRACT
Photosynthesis and respiration of three Alaskan Porphyra species, P. abbottiae V. Krishnam., P. pseudolinearis Ueda species complex (identified as P. "pseudolinearis" below), and P. torta V. Krishnam., were investigated under a range of environmental parameters. Photosynthesis versus irradiance (P-I) curves revealed that maximal photosynthesis (Pmax ), irradiance at maximal photosynthesis (Imax ), and compensation irradiance (Ic ) varied with salinity, temperature, and species. The Pmax of Porphyra abbottiae conchocelis varied between 83 and 240 µmol O2 â·âg dwt(-1) â·âh(-1) (where dwt indicates dry weight) at 30-140 µmol photonsâ·âm(-2) â·âs(-1) (Imax ) depending on temperature. Higher irradiances resulted in photoinhibition. Maximal photosynthesis of the conchocelis of P. abbottiae occurred at 11°C, 60 µmol photonsâ·âm(-2) ·s(-1) , and 30 psu (practical salinity units). The conchocelis of P. "pseudolinearis" and P. torta had similar Pmax values but higher Imax values than those of P. abbottiae. The Pmax of P. "pseudolinearis" conchocelis was 200-240 µmol O2 â·âg dwt(-1) â·âh(-1) and for P. torta was 90-240 µmol O2 â·âg dwt(-1) â·âh(-1) . Maximal photosynthesis for P. "pseudolinearis" occurred at 7°C and 250 µmol photonsâ·âm(-2) â·âs(-1) at 30 psu, but Pmax did not change much with temperature. Maximal photosynthesis for P. torta occurred at 15°C, 200 µmol photonsâ·âm(-2) â·âs(-1) , and 30 psu. Photosynthesis rates for all species declined at salinities <25 or >35 psu. Estimated compensation irradiances (Ic ) were relatively low (3-5 µmolâ·âphotonsâ·âm(-2) â·âs(-1) ) for intertidal macrophytes. Porphyra conchocelis had lower respiration rates at 7°C than at 11°C or 15°C. All three species exhibited minimal respiration rates at salinities between 25 and 35 psu.
