College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
Genes (Basel). 2024 Mar 12;15(3):353. doi: 10.3390/genes15030353.
DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, : chr26_27046601_27046800, . chr2_79720201_79720400, : chr1_40088601_40088800, : chr17_59385801_59386000, : chr2_117418601_117418800 and : chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size.
DNA 甲基化（DNAm）与生殖系统有关。然而，DNAm 调节基因表达从而影响山羊产仔数的遗传机制尚不清楚。因此，在本研究中，通过 WGBS 全面分析了 HP 和 LP 济宁青山羊卵巢组织的全基因组 DNAm 图谱，并结合 RNA-Seq 数据鉴定了与济宁青山羊产仔数性状相关的候选基因。最后，使用 BSP 和 RT-qPCR 验证了关键基因的测序结果。值得注意的是，HP 组中 DNMT 基因的表达水平下调。两组的甲基化水平相当。本研究共鉴定出 976 个差异甲基化区域（DMRs）（973 个 CG DMRs 和 3 个 CHG DMRs）和 310 个差异甲基化基因（DMGs）。通过 WGBS 和 RNA-Seq 数据的整合，我们鉴定出 59 个差异甲基化和差异表达基因（DEGs），最终筛选出 8 个与济宁青山羊产仔数性状相关的关键 DMGs（9 个 DMRS）：（chr24_62258801_62259000）、NDRG4（chr18_27599201_27599400）、（chr26_27046601_27046800）、（chr2_79720201_79720400）、（chr1_40088601_40088800）、（chr40_40088601_40088800）、（chr17_59385801_59386000）、（chr2_117418601_117418800）和（chr10_16913801_16914000）以及 chr10_16916401_16916600）。总之，本研究全面分析了 HP 和 LP 济宁青山羊卵巢组织的全基因组 DNAm 图谱。研究结果表明，山羊卵巢中的 DNAm 可能在决定产仔数方面发挥重要作用。
