Comparative transcriptomic analysis reveals candidate genes for seasonal breeding in the male Lion-Head goose

Figures & data

Table 1. Primers used for quantitative real-time PCR.

Gene name	Forward primer sequence(5’-3’)	Reverse primer sequence(5’-3’)	PCR product (bp)
β-actin	GCACCCAGCACGATGAAAAT	GACAATGGAGGGTCCGGATT	150
SLC24A4	ATGTTGCTGGGGCTACATTCA	GGTGAGACAAACCACCTGTC	173
WIPF3	ATTCAGTCTGCTGTGCCGTC	AGGGAGGAGAAAGAAAAACAGTCC	104
LRRTM2	CAATGTACTCAAAAGAATGGGCTT	CAGCGACATTTTGGTGGACA	135
TH	ATGCCAACCCCCAACATCTC	CGATGAACCGTGGAGACATGA	106
PCK1	AGCATTCCCTAGTGCCTGTG	TTGCCCTTAAGTGGCCTTGT	131
HOXB4	CATGTAAGCACGGTAAACCCC	TGCGTCTCCGGGTGAGATA	130
HOXA5	AACTGCACATAAGTCATGACAACA	CAATCCTTCTTCTGCGGGTC	135
HOXB5	CTACCCAAATGGCCCCGACT	CCATCCCATTGTAGTTGTAG	122
HOXA7	TGGATGAGGTCTTCAGGTCCA	CGCCGAGTCAGATAGCGATT	110
HOXD8	TGGATGAGACCACAAGCAGCG	TCTCGGTGAGTCCTAGTGCG	154

Figure 1. Global patterns of 8864 1:1 orthologous gene expressions among poultry. (a) The visualisation of the gene expression pattern of all RNA-seq samples using the t-SNE. (b) The heatmap of gene expressions among all RNA-seq samples. (c) The gene expression phylogenies for the hypothalamus.

Figure 2. The overall analysis of differentially expressed genes (DEGs). (a) The number of DEGs including up-regulated and down-regulated genes for male Lion-Head geese within breeding and non-breeding periods. (b) The number of overlapping DEGs between geese within the non-breeding period (goose.R) and chickens, ducks or pigeons within the breeding period in the hypothalamus. (c) Top 10 pathways in the KEGG enrichment of 119 DEGs for the pituitary. (d) Top 10 pathways in the KEGG enrichment of 302 DEGs for the testis.

Figure 3. The survey of key differentially expressed genes (DEGs). (a) Venn diagrams of two kinds of DEGs for the hypothalamus, the pituitary and the testis. A: The number of DEGs shared in geese within the non-breeding period (goose.R) and chickens, ducks and pigeons, B: The number of DEGs for male Lion-Head geese within breeding and non-breeding periods. (b) The distribution of expression of 40 DEGs across poultry in the testis. (c) The protein-protein interaction network for 4 DEGs of the hypothalamus. (d) qPCR verification of 4 DEGs in the hypothalamus of male Lion-Head geese. (d) qPCR verification of 5 HOX DEGs in the testis of male Lion-Head geese. L: male Lion-Head geese within the breeding period, R: male Lion-Head geese within the non-breeding period.

Data availability statement

The RNA-seq datasets of hypothalamus, pituitary and testis from geese are available in the Sequence Read Archive of the National Center for Biotechnology Information (accession number: PRJNA885911).