鹅豁眼与深浅黄羽性状的遗传标记筛选及分子基础初探

doi:10.11843/j.issn.0366-6964.2025.11.014

Abstract

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

CLC Number:

S835.2

ZHU Gongquan, ZHANG Yuehong, WANG Jun, LI Xiaoming, GE Jing, MU Xiaohui, ZHAO Hongchang, ZHAO Minmeng, LIU Long, GONG Daoqing, WANG Jian, GENG Tuoyu. Screening of Genetic Markers and Preliminary Exploration of Molecular Basis for the Traits of the Eyelid-Colobomus and the Dark/Light Yellow Feathers in Goose[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(11): 5512-5530.

Figures/Tables 19

Table 1

Information of the PCR primers"

基因 Gene	引物 Primer	序列(5′→3′) Sequence	产物大小/bp Products size	备注 Note
FREM1	F R	GTTGCCACTGCTGTCCATTC ATCTGAACAGGGAGCCAAGC	828	扩增CDS片段1
FREM1	F R	TCAAATTCCCAAACCTGCTC CAGGATCATCTGTCCCTCGT	742	扩增CDS片段2
FREM1	F R	TTACCAAACCACCACAGGCT TCACCTTCGCTCATGGGAAC	826	扩增CDS片段3
FREM1	F R	GTGGACACAAAACAGGAGCA AGCCCATCGGTGACATAAAG	977	扩增CDS片段4
FREM1	F R	AAATGGAGCCAACGACAGAC TGTCTCCCTTTTCCATGTCC	846	扩增CDS片段5
FREM1	F R	TGTGGGATGGGTACAACAGA CAGAACAGCAGTGGAGGTGA	801	扩增CDS片段6
FREM1	F R	TCACCTCCACTGCTGTTCTG ACTCTCAGCCTGGTCCTTGA	885	扩增CDS片段7
FREM1	F R	CTTCACAGTGACTCCCTCCA TGCCTTATCAGCTTGTGGGA	720	扩增CDS片段8
FREM1	F R	AACCAAGCACAAACGCAGAT GTTCCGTTTGACCTTCCTGC	603	扩增CDS片段9
FREM1	F R	AGTTCCCAAAGCAAGGAGGT CTTTGGGCAGAGTTCAAAGC	633	扩增CDS片段10
FREM1	F R	CATGAAGTCTGAAGCTGCCC TGCACTTTCACAGGGATCCT	554	扩增含SNP6的基因组序列
FREM1	F R	GCAGTATCACCACAGGCAAG TTTCCAGGCTCTGTTTGCAC	847	扩增含SNP10的基因组序列
FREM1	F R	CTTCACAGTGACTCCCTCCA TGCCTTATCAGCTTGTGGGA	628	扩增含SNP14的基因组序列
FREM1	F R	AACCAAGCACAAACGCAGAT GTTCCGTTTGACCTTCCTGC	603	扩增含SNP15的基因组序列
PTPRM	F R	GAGAGGGACGAGAAGGAGAG TCCTGCTGCCCCATCTAAAA	867	扩增CDS片段1
PTPRM	F R	AGCCCTCCTCAGATCAATGG TACAGTCCAGTCAGCTTCCC	851	扩增CDS片段2
PTPRM	F R	TGCGGAACTGATAGTCAAAGG TTCTTCAGTGGAGAGAGCCA	985	扩增CDS片段3
PTPRM	F R	TGGAGGACAAGAGCAAGTGA ACACCATACATTCGCATCGC	945	扩增CDS片段4
PTPRM	F R	TGCAGAGTTTCCAGCCAATG TGAAGGCGAAACAAGCTCTG	983	扩增CDS片段5
PTPRM	F R	ACCGTGGGATTCAGCTAAGA GCCTGCCTTTCCTCATAACG	964	扩增CDS片段6
PTPRM	F R	TGAAGGCGAAACAAGCTCTG TCTCAATGTTACGCTTCTACTGC	926	扩增CDS片段7
PTPRM	F R	CGCAGCTTAGTACCAAATGC ACTTCTCACTCCTCACCCTG	745	扩增含SNP5的基因组序列
SLC45A2	F R	AGTTCCCAAAGCAAGGAGGT CTTTGGGCAGAGTTCAAAGC	633	扩增CDS片段1
SLC45A2	F R	CATGCCATCCCACTATCGCT AAGCACCAGTGCTACTGACC	715	扩增CDS片段2
SLC45A2	F R	GTGGATTTGGTCTGCACTGG AGTTTATCGAGGGTGGCACA	515	扩增含SNP2的基因组序列
TYRP1	F R	GAGAGAAGAGAGGGAGCTGG ACACGCCACTGAGAGAAGAT	962	扩增CDS片段1
TYRP1	F R	CATGAGGGACCAGCTTTTGT GCTTGGTGTTGCTATGCCAT	957	扩增CDS片段2
TYRP1	F R	TGGAAGGGGCAGATTGAAGG GCAGAACTTCATTGTAAATGCACCT	603	扩增含SNP1的基因组序列
TYRP1	F R	GGATTACACATGCTAGGGACA TTCTCACCCCACTGACATCC	600	扩增含SNP2的基因组序列
PRLR	F R	CAAGCTCAACCACTCTGTTATCAA TGGAGTTTCTCTTCAGCCCTA	557	扩增含插入/缺失突变位点的的基因组序列

Table 1

Table 2

Table 3

Table 4

Table 5

Table 6

Table 7

Table 8

Table 9

Table 10

Table 11

Table 12

Table 13

Table 14

Fig. 1

Fig. 2

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Fig. 4

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基因 Gene	引物 Primer	序列(5′→3′) Sequence	产物大小/bp Products size	登录号 Accession number
DUSP12	F R	GGCGCTCTCTATTCCGTAGT CACAAGAACACTGCTCACCC	255	XM_066990420
ACTC1	F R	TGTGACAACAGCTGAACGTG CGTTGTTAGCGTACAGGTCC	246	XM_048058696
MC3R	F R	GGCACCTTTCTTCCTTCACC CCACACTCATGCCGTAACAG	203	XM_048072592
GRM8	F R	GGGATCCACAGACTAGAGGC GTGAAAATAGGTGGGTCGCC	212	XM_048080808
NPSR1	F R	GAGCAGCTGGTGACTCTTTG GACCACCTGTAAGTAGCGGA	240	XM_066991189
FZD10	F R	CCAGCCCATAGAAATCCCCA CGGTGTAGAAACTTGCTCCG	205	XM_013173432
WNT3	F R	TTTCAAGCCACCAACAGAGC ACTCACATAGCAGCACCAGT	229	XM_013201438
CACNA1I	F R	CATCATCTGCCTCAACGTGG TCTTCCAGTGTGATGCCCAT	225	XM_048069774
MRPS10	F R	TCAGAGGAGCCAGAAACACT ACTCCAAGTACACTGCAGCA	283	XM_048057518
ANO2	F R	CATTCCCAAGGACATCAGCG ACGCTGCCTTTCTGACTTTG	201	XM_048046752
OBSCN	F R	TCATTGTGTGGGAAGGAGCT CTGAATCTTCCCGTTCGTGC	231	XM_066991378
ODF2L	F R	TTGGCAAGCACAGTAGAAGC GCAGCTTTTCGTTTCTGGGA	221	XM_048059125
TTN	F R	TCCGCTGTGCAAAAGATCAC GCCTTCTTTCTGCAACACCA	219	XM_066999168
PDCD1	F R	AGTACCTGCTCTCCAACCAC CCTGTAGGTGACGATGCAGT	296	XM_048076630
SLITRK4	F R	CTCCGAGCTGACACTTTCCT TTCCAGGGGTTGTCTTCCAG	284	XM_067004832
COL9A1	F R	TCTCCAGGTGTGAAAGGCAT TGAACCCCTGTCACCCTTAC	273	XM_066994732
VIT	F R	GAGATCAGACATCGCCGGTA AGTGCCCCTGAATGCTGTAT	296	XM_013170623
UBAP1L	F R	CCATCCTCACCCTCCAGAAG TCTCTCTGGTTCCCGCAAAG	244	XM_048076334
PROCR	F R	CATCAACTACACGCAGAGCC GGTGTTGAGGAAATGCTGCA	235	XM_048077345
FHAD1	F R	GACCACAACCTCAGGCAATG GCCATCGCTGCAATTTTGTC	204	XM_066982271

位点 Locus	位置 Location	侧翼序列 Flanking sequence	突变类型 Mutation type
SNP1	c.246T>C	TGCCA(C/T)TTCCT	同义突变
SNP2	c.272C>G	ATATA(C/G)TCACA	同义突变
SNP3	c.273T>C	TATAC(C/T)CACAA	同义突变
SNP4	c.305T>A	AGACA(A/T)GGTCA	同义突变
SNP5	c.1976A>C	TGCTC(A/C)CCTCA	错义突变
SNP6	c.2502T>C	GAAGG(C/T)GACAG	同义突变
SNP7	c.2823G>T	AAAGC(G/T)GGCGT	错义突变
SNP8	c.3822G>T	GATGA(G/T)AAACC	错义突变
SNP9	c.4304C>T	AACTT(C/T)CCCAC	错义突变
SNP10	c.4514T>C	CCAAG(C/T)TTTGC	错义突变
SNP11	c.5049T>C	GAAAA(C/T)GTAAC	同义突变
SNP12	c.5566A>G	AGTGC(A/G)GCTCT	错义突变
SNP13	c.5567G>C	GTGCA(G/C)CTCTT	错义突变
SNP14	c.6330C>T	GACTT(C/T)AGTGG	同义突变
SNP15	c.6348T>C	GGACA(C/T)TGGGA	同义突变

位点 Locus	表型 Phenotype	样本数 Sample size	等位基因频率 Allele frequency		P值 P-value	基因型频率 Genotype frequency			P值 P-value
位点 Locus	表型 Phenotype	样本数 Sample size	C	T	P值 P-value	CC	CT	TT	P值 P-value
SNP6	豁眼	56	0.16	0.84	0.240 0	0.09	0.14	0.77	2.87
	正常	19	0.21	0.79		0.05	0.32	0.63
SNP10	豁眼	72	0.75	0.25	0.007 3	0.69	0.11	0.19	0.022
	正常	19	0.53	0.47		0.37	0.32	0.32
SNP14	豁眼	69	0.29	0.71	0.007 2	0.19	0.20	0.61	0.043
	正常	18	0.53	0.47		0.33	0.39	0.28
SNP15	豁眼	67	0.79	0.21	0.000 48	0.72	0.15	0.13	0.009 0
	正常	18	0.50	0.50		0.33	0.33	0.33

位点 Locus	位置 Location	侧翼序列 Flanking sequence	突变类型 Mutation type
SNP1	c.1131G>A	GATCC(A/G)ATGCG	同义突变
SNP2	c.1200G>T	GAACC(G/T)TTTGG	同义突变
SNP3	c.2174G>T	CACTC(G/T)AAAAC	错义突变
SNP4	c.2202G>C	AAGCA(C/G)ACCGA	错义突变
SNP5	c.2625C>T	AGCAG(C/T)CTGGT	同义突变
SNP6	c.2997T>A	GAGAC(A/T)ATATA	同义突变
SNP7	c.3351T>C	TGCAG(C/T)GCTGG	同义突变

表型Phenotype	样本数 Sample size	等位基因频率 Allele frequency	P值 P-value	基因型频率 Genotype frequency	P值 P-value
豁眼Eyelid-colobomus	70	C: T=0.54:0.46	0.039	CC: CT: TT=0.30:0.49:0.21	0.11
正常Normal	20	C: T=0.72:0.28		CC: CT: TT=0.55:0.35:0.10

Screening of Genetic Markers and Preliminary Exploration of Molecular Basis for the Traits of the Eyelid-Colobomus and the Dark/Light Yellow Feathers in Goose

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位点 Locus	位置 Location	插入/缺失碱基 Insertion/Deletion bases	突变类型 Mutation type
INS1	G.126358→G.126359	AACT	插入
INS2	G.126568→G.126569	TA	插入
DEL	G.126611→G.126621	TAAGAATTTGT	缺失

位点 Locus	羽色 Feather color	样本数 Sample size	等位基因频率 Allele frequency	P值 P-value	基因型频率 Genotype frequency	P值 P-value
SNP1	深羽	27	G: A=0.74:0.26	0.050	GG: GA: AA=0.67:0.15:0.19	0.081
	浅羽	68	G: A=0.86:0.14		GG: GA: AA=0.77:0.19:0.04
SNP2	深羽	27	A: G=0.74:0.26	0.050	AA: AG: GG=0.67:0.15:0.19	0.081
	浅羽	68	A: G=0.86:0.14		AA: AG: GG=0.77:0.19:0.04

基因 Gene	豁眼 Eyelid colobomus	正常 Normal	倍数的对数 log₂fold change	P值 P-value
上调Up-regulation
LOC106044829	46.9	177.7	1.92	4.72×10^-5
LOC106029457	14.6	143.3	3.29	3.51×10^-4
ODF2L	98.1	309.7	1.66	5.07×10^-4
LOC106029573	137.3	544.7	1.99	5.75×10^-4
FHAD1	116.2	406.6	1.81	5.97×10^-4
LOC106033930	24.4	73.7	1.60	7.43×10^-4
ZNFX1	1155.9	3510.1	1.60	9.49×10^-4
LOC106030924	3.4	42.9	3.65	1.23×10^-3
APOBEC1	23.8	149.8	2.65	1.49×10^-3
LOC106041921	89.9	346.3	1.95	1.69×10^-3
下调Down-regulation
MYOC	141.0	17.9	-2.98	5.62×10^-9
LOC106029652	81.0	0.0	-8.66	1.60×10^-8
MRAP	322.7	108.4	-1.57	5.01×10^-8
STEAP2	518.1	181.4	-1.52	1.54×10^-7
MEGF10	246.2	87.1	-1.50	9.79×10^-6
RPL38	307.4	86.3	-1.83	1.44×10^-5
COL6A6	542.9	141.6	-1.94	2.75×10^-4
CDH13	398.6	133.1	-1.58	5.78×10^-4
RAB3C	72.6	21.7	-1.74	6.90×10^-4
LOC106045060	498.9	157.1	-1.67	6.93×10^-4

基因 Gene	深羽 Dark yellow feathers	浅羽 Light yellow feathers	倍数的对数 log₂fold change	P值 P-value
上调Up-regulation
ACTC1	1 166.8	377.5	1.63	8.20×10^-5
HGD	41.7	0.0	7.83	5.94×10^-4
UBB	1 192.9	377.8	1.66	8.25×10^-4
TM4SF4	35.2	0.0	7.58	8.67×10^-4
HMGCS2	246.0	27.5	3.16	9.76×10^-4
GC	335.5	38.3	3.13	1.09×10^-3
KNG1	133.6	17.3	2.95	2.29×10^-4
APOH	266.8	30.1	3.15	2.37×10^-3
DUSP12	176.6	39.0	2.18	2.74×10^-3
LOC106037939	207.2	27.1	2.94	2.83×10^-3
下调Down-regulation
LOC106040172	3.9	245.5	-5.90	2.92×10^-12
LOC106030726	2.9	292.9	-6.83	5.46×10^-12
VWA3B	0.0	276.5	-10.59	1.15×10^-10
B3GNT7	0.0	225.1	-10.29	1.99×10^-10
LOC106033866	0.0	200.2	-10.12	3.02×10^-9
MC3R	0.0	174.5	-9.93	6.36×10^-9
LOC106041797	0.0	173.5	-9.92	8.65×10^-9
MYT1	0.0	143.3	-9.64	1.32×10^-8
PKHD1	0.0	150.6	-9.71	1.34×10^-8
COL9A1	0.0	150.7	-9.71	2.09×10^-8

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