基于全基因组选择信号和转录组鉴定28日龄乳鸽胸肌率相关关键基因

doi:10.11843/j.issn.0366-6964.2025.11.015

Abstract

Abstract:

The study aimed to identify the candidate genes associated with breast muscle rate in 28-day-old squabs by the analysis of the genome-wide SNPs and breast muscle transcriptomic data from two populations of pigeons. Ten pigeons from each of the M and B lines were selected for whole genome sequencing. Selective signature analysis was performed based on genomic wide SNPs with extracting and filtering. Ten 28-day-old squabs were selected from two populations with significant differences in breast muscle rate. The transcriptomic data were collected from breast muscles. The expression levels of genes and identification of differentially expressed genes (DEGs) were performed in the pectoral muscle. The key genes associated with breast muscle rate in 28-day-old squabs were identified and screened by combining selection signal analysis. The expression levels of 9 DEGs associated with muscle development were analyzed using real-time fluorescent quantitative PCR (RT-qPCR) and compared with transcriptome data for validation. M-line and B-line squabs were distinctly clustering into separate groups through principal component analysis (PCA) of 11 577 846 SNPs. Twenty-nine genes associated with muscle development were identified through sliding window Fst and pFst analysis. In the breast muscle of 28-day-old squabs, 192 DEGs were identified through transcriptome analysis, including 68 up-regulated and 124 down-regulated genes. The DEGs were mainly enriched in the nuclear component, apoptosis pathway, Foxo signaling pathway, and PI3K-Akt signaling pathway. Four genes were identified with the integrated analysis of whole-genome and transcriptome data. Among these genes, LTBP1, DPP4, and TNFSF10 are associated with muscle development. The data foundation was provided for deciphering the differences in the breast muscle rate among squabs. The expression levels of 9 DEGs validated by RT-qPCR showed a correlation coefficient of 0.50-0.95 with transcriptomic data, indicating that the two datasets were highly consistent. In this study, genes associated with breast muscle rate differences in squabs were revealed by analyzing genome-wide combined with transcriptome data, providing a new perspective on the molecular mechanism of breast muscle development in pigeons.

Key words: pigeon, breast muscle, genome-wide, transcriptome, selection signal, SNPs

CLC Number:

S836.2

ZHANG Yiran, MAO Nannan, WANG Yunlong, ZHOU Rongyan, ZANG Sumin, XIE Hui, WANG Wenjun, ZHANG Weiya. Identification of Key Genes Associated with Breast Muscle Rate in 28-day-old Squabs Based on Genome-wide Selection Signal and Transcriptome[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(11): 5531-5544.

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品系 Species	活体重/g Body weight	胸肌重/g Breast muscle weight	胸肌率/% Breast muscle rate
M系M line	575.48±41.74^a	120.91±9.12^A	33.11±2.11^A
B系B line	489.24±41.82^b	83.46±11.61^B	19.22±0.99^B

基因 Gene	引物序列(5′→3′) Primer sequence	目的基因长度/bp Products size	退火温度/℃ Annealing temperature
MCL1	F: GGCTTAGACCCACGAGGATT R: TCTCGCCTTCTGCTCTGAAA	198	60
SIK1	F: CATTTGAGCTGGCCTTTGCT R: TAGAAGGTGAGCTGCTGAGG	95	60
SLC16A10	F: TGACTCGTTCTCCTTTGGCT R: GGGCTGTGGCTATTGAAAGG	186	60
TRIB2	F: GCTGTACATCTGCACAGTGG R: AACTCCTGGTAGCAGCCAAT	68	60
PIK3R3	F: CTTCACAAAGCCAGGCAACT R: AACCAAGAGCCTCCTCCTTC	97	60
IGF2BP3	F: GTAAAGTGGAGCTGCATGGG R: TACAACTGCAGTCTCCGTGT	191	60
LTBP1	F: GTGCCAGATCCTACCCTCTC R: TGCTGAGCTGAACAGACAGA	127	60
DPP4	F: TCTGCAGTGGCTGAGAAGAA R: CGTTGTCAGGTGCAAAGTGA	170	60
TNFSF10	F: AGTAAAGTGGCACCTGGGAA R: TTGCTGTTGCCTGTCAGATG	168	60
β-actin	F: CTACAGCTTCACCACCACAGCC R: GCTGTGGCCATCTCCTGCTCAA	99	60

染色体 Chromosome	基因ID Gene ID	基因 Gene	功能 Function
1	A306_00003116	ZIC2	肌肉分化^[20]
2	A306_00001266	ANGPT1	骨骼肌卫星细胞增殖^[21]
2	A306_00001269	OXR1	产肉量^[22]
2	A306_00001475	NSMAF	胴体性状^[23]
2	A306_00001476	SDCBP	胴体重量^[23]
2	A306_00001478	UBXN2B	胴体性状^[24]
2	A306_00001489	LYN	胴体性状^[23]
2	A306_00001490	TGS1	胴体产量^[25]
2	A306_00001491	TMEM68	生长性状^[26]
2	A306_00001493	XKR4	胴体产量^[25]
2	A306_00001503	ST18	肌肉发育^[27]
2	A306_00001717	GRB10	肌肉生长和发育^[28]
2	A306_00001726	UPP1	生长性状^[29]
3	A306_00000998	KLHL31	肌肉生长和发育^[30]
3	A306_00000999	GCLC	生长性状^[31]
3	A306_00001095	APOB	肌肉发育^[32]
3	A306_00010435	LTBP1	生长性状^[33-35]
4	A306_00003396	EVC2	肉质^[36]
4	A306_00003397	STK32B	肉质^[37-38]
4	A306_00003399	MSX1	成肌细胞分化^[39-42]
4	A306_00006969	EDNRA	肌肉生长^[43]
6	A306_00003890	ITGB6	骨骼肌卫星细胞增殖^[44]
6	A306_00003896	DPP4	成肌细胞分化^[45]
8	A306_00004220	ROR1	骨骼肌卫星细胞增殖^[46]
8	A306_00004246	MYSM1	肌肉生成^[47]
9	A306_00007726	GHSR	生长性状^[48]
9	A306_00007727	TNFSF10	肌肉萎缩^[49]
10	A306_00006896	PRTG	日增重^[50]
Z	A306_00011946	SMAD2	成肌细胞增殖分化^[51]

样品 Sample	质控后reads/M Clean reads	质控后测序量/G Clean data	Q30/%	GC含量/% GC content	比对率/% Mapped reads rate
B1	87.89	13.18	93.65	49.62	61.49
B2	72.82	10.92	93.94	49.19	59.22
B3	77.07	11.56	94.78	48.31	66.40
B4	80.79	12.12	94.70	49.43	62.99
B5	85.46	12.82	94.43	48.59	60.32
M1	111.22	16.68	95.98	49.62	60.37
M2	90.73	13.61	94.77	49.19	60.20
M3	67.07	10.06	95.35	48.31	38.80
M4	109.00	16.35	95.44	49.43	66.04
M5	82.10	12.32	94.34	48.59	54.74

基因ID Gene ID	基因 Gene	功能 Function
A306_00011622	MCL1	肌肉生长^[52-53]
A306_00004203	GADD45A	肌肉萎缩^[54]
A306_00013720	GADD45B	肌源性分化^[55]
A306_00009707	SIK1	肌肉生长^[56-57]
A306_00001065	TRIB2	肌生成^[58]
A306_00002651	IGF2BP3	成肌细胞增殖和分化^[59-60]；生长性状^[61]
A306_00004566	TIMP3	肌生成^[62]
A306_00010314	PIK3R3	骨骼肌生长发育^[63]
A306_00006126	PIK3CD	成肌细胞增殖^[64]
A306_00013901	CTSK	肌肉损伤或坏死^[65]

Identification of Key Genes Associated with Breast Muscle Rate in 28-day-old Squabs Based on Genome-wide Selection Signal and Transcriptome

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