| 摘要: |
| 为解析南阳黑猪种群中脂肪表型极端差异个体之间的遗传变异基础，本研究以南阳黑猪种群中体重相近但脂肪表型差异明显的6月龄全同胞或半同胞个体为研究对象，分别对其进行胴体性状和肉质性状统计分析，采用高通量测序技术对高脂肪组和低脂肪组的样品进行全基因组重测序，整合课题组前期转录组数据分析南阳黑猪脂肪沉积相关的遗传位点和功能基因。结果表明:1)高脂肪组肌内脂肪含量((4.96±0.62)%)显著高于低脂肪组((3.61±0.11)%)(P<0.05)，高脂肪组平均背膘厚((43.74±2.33)mm)极显著高于低脂肪组((28.36±4.17)mm)(P<0.01)，与肌内脂肪含量相关的性状(剪切力、pH45 min、蒸煮损失和48 h滴水损失)在两组之间均存在显著差异，其余各项性状指标在两组之间无显著差异；2)本次测序共得到208.00 Gb有效序列数据，测序覆盖度达98.68%以上。在高-低脂肪组共检测到25 827 091个单核苷酸多态性(Single nucleotide polymorphism，SNP)、5 802 822个小片段插入和缺失(Insertion-deletion，InDel)、56 358个染色体结构变异(Structural variation，SV)及1 898个拷贝数变异(Copy number variation，CNV)。通过对SNP非同义突变和InDel移码突变进行功能注释，发现所鉴定到的209个组间差异基因主要参与到mTOR信号通路、甲状腺信号通路以及ABC 转运蛋白信号通路等与脂肪沉积相关的通路中；3)与课题组前期转录组数据联合分析后筛选到2个与脂肪分化相关的关键基因(PLP1和ITGA6)，这些基因的多态性变化可能是影响南阳黑猪肌内脂肪沉积出现差异的关键。综上，本研究从全基因组水平上筛选到了南阳黑猪群体内影响脂肪沉积相关的基因和位点，为进一步研究猪脂肪沉积调控机制及品种选育奠定基础。 |
| 关键词: 南阳黑猪 重测序 脂肪沉积 候选基因 |
| DOI：10.11841/j.issn.1007-4333.2023.08.13 |
| 投稿时间：2022-12-06 |
| 基金项目:国家自然科学基金项目(32102515,32060736) |
|
| Screening of candidate genes related to fat deposition in Nanyang black pigs based on whole genome resequencing |
|
LI Pan1,PUBU Zhandui1,ZHANG Hao1,LU Yunfeng2,ZHANG Bo1*
|
| (1.College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;2. College of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China) |
| Abstract: |
| To explore the basis of genetic variation among individuals with extreme differences in adipose phenotype in Nanyang black pig population, in this study, the whole siblings or half siblings of Nanyang black pig population with similar body weight but significant differences in adipose phenotypes at 6 months of age were used as test subjects, and statistical analysis of carcass traits and meat quality traits were performed respectively. High-throughput sequencing technology was used to re-sequence the whole genome of samples from High-fat and Low-fat groups, and the transcriptome data of the previous group were integrated to mine genetic loci and functional genes related to fat deposition of Nanyang black pig. The results showed that: 1)Intramuscular fat content was significantly higher in the High-fat group((4. 96±0. 62)%)than that in the Low-fat group((3. 61±0. 11)%)(P<0. 05), the mean backfat thickness was extremely significantly higher in the High-fat group((43. 74±2. 33)mm)than that in the Low-fat group((28. 36±4. 17)mm)(P<0. 01). There were significant differences between the two groups in the traits related to intramuscular fat content(shear force, pH45 min, steaming loss and 48 h drip loss). There was no significant difference between the two groups in other traits; 2)A total of 208. 00 Gb of effective sequence data was obtained, and the sequencing coverage reached more than 98. 68%. A total of 25 827 091 single nucleotide polymorphisms(SNPs)were detected in the High-Low fat group, and 5 802 822 small fragment insertions and deletion(InDels)were detected 56 358 chromosome structural variation(SVs)and 1 898 copy number Variation(CNVs)were detected in the High-Low fat group. Through functional annotation of SNP non-synonymous mutations and InDel frameshift mutations, it was found that 209 intergroup differential genes were mainly involved in the mTOR signaling pathway, thyroid signaling pathway, ABC transporter signaling pathway and other pathways related to fat deposition; 3)Two key genes related to adipose differentiation(PLP1 and ITGA6)were screened after joint analysis with the transcriptome data of our research group, and the polymorphisms of these genes may be the key to the difference of intramuscular adipose deposition in Nanyang black pig. In conclusion, the study screened the genes and sites related to fat deposition in Nanyang black pig population from the whole genome level, which laid a foundation for further research on the regulation mechanism of pig fat deposition and breed breeding. |
| Key words: Nanyang black pig resequencing fat deposition candidate genes |
