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.

1. Ovarian transcriptomic profiling between birds showing high egg number (HEN) and birds of low egg number (LEN) in Longyan Shan-ma ducks at 71 weeks of age was carried out using Illumina Hiseq 2500 technology. 2. A total of 343 differentially expressed genes (DEGs, 269 upregulated and 74 downregulated) were identified between HEN and LEN ovaries. These DEGs were enriched in 30 Gene Ontology terms. Pathway functional analysis found that the DEGs were enriched in 10 metabolic pathways (P < 0.05), one of which was regulation of the actin cytoskeleton pathway (Q < 0.05). 3. Three integrin family genes, ITGB2, ITGB5 and ITGA8 were differentially expressed in the RNA-seq and qPCR experiments. 4. The DEGs and signalling pathways identified in ovarian tissue in this study provide new insights into high egg production in Longyan Shan-ma duck.

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.

Bacillus coagulans LYBC06 strain with lactate-producing capacity was isolated from mucosal tissue of the digestive tract of a fattening pig. The resequencing of the LYBC06 strain revealed that the overall genome was less variable, with a genome-wide heterozygous ratio of 0.042 %, total SNP locus variants 0.4273% of the entire genome, total InDel mutations 0.0182%, total increased and decreased CNV copies 0.0031% and total SV annotated variants 0.0083% of the entire genome. The mutated genes were mainly involved in the growth of the strain, regulation of energy metabolism, and production of proteases and lactate. The whole genome of LYBC06 strain was sequenced with the length of 3385106 bp, GC content of 46.86% and 4092 coding genes (85.96% of coding). Functional annotation of the proteins encoding genes showed that the growth process of LYBC06 strain involved several metabolic pathway transformation processes of various substances, and many encoding genes were involved in the resistance to macrolides, polypeptides and tetracyclines. The basic characteristics of the genome of LYBC06 strain were relatively similar to those of other Bacillus coagulans, and the collinearity between several Bacillus coagulans strains was relatively good. Bacterial growth, gene expression of lactate dehydrogenase and lactate production in LYBC06 strain were largely synchronized, and the maximum amount of lactate could be produced up to 92 g/L at 16 h culture during the logarithmic growth phase, in which the LdhL1 gene played an important role in the production of lactate in LYBC06 strain.