畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (1): 147-158.doi: 10.11843/j.issn.0366-6964.2025.01.014
吴平先1,2(), 王俊戈1, 刁淑琪1,2, 柴捷1,2, 查琳4, 郭宗义1,2, 陈红跃3, 龙熙1,2,*(
)
收稿日期:
2024-08-09
出版日期:
2025-01-23
发布日期:
2025-01-18
通讯作者:
龙熙
E-mail:wupingxianxian@163.com;981568078@qq.com
作者简介:
吴平先(1993-),男,四川雅安人,副研究员,博士,主要从事猪遗传育种研究,E-mail: wupingxianxian@163.com
基金资助:
WU Pingxian1,2(), WANG Junge1, DIAO Shuqi1,2, CHAI Jie1,2, ZHA Lin4, GUO Zongyi1,2, CHEN Hongyue3, LONG Xi1,2,*(
)
Received:
2024-08-09
Online:
2025-01-23
Published:
2025-01-18
Contact:
LONG Xi
E-mail:wupingxianxian@163.com;981568078@qq.com
摘要:
旨在基于填充序列数据,通过选择信号分析挖掘荣昌猪重要经济性状相关的候选基因,探究其在人工和自然选择过程中的受选择情况。本研究选取591头荣昌猪进行猪50K基因分型,随机选取其中120头进行全基因组测序,以全基因组重测序数据为填充参考模板对50K基因数据进行填充,基于填充序列数据开展遗传结构、Tajima’D和CLR分析。基因型填充后,基因型填充正确率为0.942,质控后保留了8 823 367个高质量SNPs(填充正确率为1.00)。遗传结构分析显示,荣昌猪群体不存在明显的群体分层,且绝大部分个体间遗传距离>0.1,分子亲缘系数 < 0.1。CLR检验筛选到226个潜在受选择区域,基因注释发现与繁殖、生长、胴体等性状相关的候选基因(CDK9、SLC2A8、IGF1R、GSK3B等基因)。利用Tajima’D检验检测到225个潜在受选择区域,基因注释发现与毛长度(CFAP299)、毛色或耳聋(MITF、ZNF532)、脂肪沉积(GSK3B)、繁殖(FOXP1)等性状相关的基因。进一步整合不同方法分析结果,发现11个相同的潜在受选择区域和123个候选基因,包括MITF、ZNF532、GSK3B等与耳聋和白化病、繁殖等经济性状相关的基因,并且发现1条显著的GO条目和KEGG通路(P < 0.05)与黑色素生成、视觉发育等通路相关。本研究根据富集分析结果和基因分子生物学功能,筛选出MITF、ZNF532、GSK3B、FOXP1、SLC2A8、CDK9、IGF1R、TBC1D4等8个重要候选基因可能参与调控荣昌猪毛色、耳聋、脂肪沉积、繁殖性能、生长性能等经济性状相关。该结果从全基因组水平探究了荣昌猪的遗传结构和选择信号特征,筛选出的重要候选基因为后续荣昌猪保种育种和特色性状的遗传机制解析提供了重要的理论参考。
中图分类号:
吴平先, 王俊戈, 刁淑琪, 柴捷, 查琳, 郭宗义, 陈红跃, 龙熙. 基于填充测序数据的荣昌猪群体遗传结构和选择信号分析[J]. 畜牧兽医学报, 2025, 56(1): 147-158.
WU Pingxian, WANG Junge, DIAO Shuqi, CHAI Jie, ZHA Lin, GUO Zongyi, CHEN Hongyue, LONG Xi. Analysis of Genetic Architecture Characteristics and Selection Signature by Imputed Whole Genome Sequencing Data in Rongchang Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(1): 147-158.
表 1
共享候选区域和基因"
染色体 Chromosome | 候选区域/Mb Region | 基因 Gene |
1 | 107.68~108.42 | CSNK1G1、PPIB、SNX22、SNX1、CIAO2A、DAPK2、HERC1、FBXL22、USP3 |
1 | 159.7~162.25 | CDH20、MC4R、PMAIP1、CCBE1、LMAN1、CPLX4、RAX、GRP、SEC11C、ZNF532、MALT1、ALPK2 |
4 | 80.05~80.31 | SPIDR |
6 | 37.25~40.23 | NETO2、DNAJA2、GPT2、C16orf87、MYLK3、ORC6、VPS35、SHCBP1、UQCRFS1、VSTM2B、POP4、PLEKHF1、C19orf12、URI1 |
11 | 46.28~48.45 | TBC1D4、UCHL3、LMO7 |
11 | 49.03~49.85 | KCTD12、ACOD1、CLN5、FBXL3、MYCBP2、SCEL、SLAIN1 |
13 | 34.25~34.97 | TWF2、PPM1M、WDR82、MIRLET7G、GLYCTK、MIR135A1、DNAH1、BAP1、PHF7等 |
13 | 46.11~54.30 | MITF、GSK3B、FOXP1、ADAMTS9、MAGI1、SLC25A26、LRIG1、KBTBD8、SUCLG2、ARL6IP5、LMOD3、FRMD4B等 |
13 | 139.98~141.27 | GPR156、NR1I2、CFAP91、COX17、POPDC2、PLA1A、ADPRH、CD80等 |
15 | 51.75~51.96 | — |
15 | 89.48~90.07 | ZNF804A |
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