关键词: 鹅, 伴性性状, 豁眼, 羽色, 单核苷酸多态性, 差异表达基因

Abstract:

To screen for molecular markers of the eyelid-colobomus trait and the dark/light yellow feather trait in geese, in this study, the nucleotide polymorphic loci in the coding sequences (CDS) of candidate genes (FREM1, SLC45A2, TYRP1, and PTPRM) were detected using the skin samples of different phenotypic individuals (n=10, totally 40, regardless of genders) in 1-day-old goslings. The genomic DNA of 95 goslings was used to detect the key polymorphic loci identified on the CDS, and the association of the loci with the traits was analyzed. This study also carried out a similar analysis on the intron sequence of the candidate gene PRLR gene. In addition, to explore the molecular basis underlying the formation of the traits, this study screened out differentially expressed genes (DEGs) and their enriched pathways through transcriptome sequencing analysis of skin samples. The results showed that a total of 15 single nucleotide polymorphisms (SNPs) loci (SNP1-SNP15) were identified over the CDS of FREM1 gene, of which 7 were missense mutations and 8 were synonymous mutations, and SNP10, SNP14 and SNP15 loci were significantly associated with the eyelid-colobomus trait. A total of 7 SNPs loci (SNP1-SNP7) were identified over the CDS of PTPRM gene, of which 2 were missense mutations and 5 were synonymous mutations, and SNP5 was significantly associated with the eyelid-colobomus trait at the allele level. A total of 11 SNP loci (SNP1-SNP11) were identified over the CDS of SLC45A2 gene, of which 10 were missense mutations and 1 was synonymous mutation, and no locus was significantly associated with the dark/light yellow feather trait. A total of 2 SNPs loci (SNP1 and SNP2) were identified over the CDS of TYRP1 gene, both of which were synonymous mutations, and their association with the dark/light yellow feather trait was close to the significant level at the allele level. Deletion or insertion mutation (INDEL), namely insertion mutation 1 (INS1), insertion mutation 2 (INS2) and deletion mutation (DEL), were identified over the intron of PRLR gene, and were significantly associated with the dark/light yellow feather trait. In addition, a total of 131 DEGs (62 up-regulated and 69 down-regulated) related to the eyelid-colobomus trait were identified by transcriptome sequencing analysis. These genes were mainly enriched in the ECM-receptor interaction pathway and the cell adhesion molecules pathway. A total of 1 280 DEGs (92 up-regulated and 1 188 down-regulated) related to the feather color trait were identified. These genes were mainly enriched in the neuroactive ligand-receptor interaction pathway, the tyrosine metabolism pathway, the phenylalanine metabolism pathway and the calcium signaling pathway. In summary, the results of association analysis have not only identified some molecular markers significantly correlated with the eyelid-colobomus trait and the dark/light yellow feather trait, but also provided more scientific evidence that FREM1, PTPRM, PRLR, and TYRP1 are the causative genes for these traits. In addition, the transcriptomic sequencing analysis suggested that the pathways including ECM-receptor interaction, cell adhesion molecules, neuroactive ligand-receptor interaction and tyrosine metabolism are involved in the formation of these traits.

Key words: goose, sex-linked trait, eyelid colobomus, feather color, single nucleotide polymorphism, differentially expressed gene