GWAS 和转录组分析的整合揭示了青春期开始时鸭性腺发育的候选基因。

Integration of GWAS and transcriptomic analyses reveal candidate genes for duck gonadal development during puberty onset.

机构信息

Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, P.R. China.

出版信息

BMC Genomics. 2024 Nov 29;25(1):1151. doi: 10.1186/s12864-024-11079-3.

DOI:10.1186/s12864-024-11079-3

PMID:39614145

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11605953/

Abstract

BACKGROUND

Puberty onset signifies the beginning of sexual maturation and reproductive phase in poultry indeed, and plays an essential role in genetics and breeding. Studying gonadal development is one of the important approaches to exploring the genetic mechanism of puberty onset.

RESULT

In our study, the phenotype data of the testes and ovaries of the 120-day-old Nonghua duck showed a large coefficient of variation, indicating that their gonads were in different developmental states. The CNV-based GWAS results for 358 Nonghua ducks showed two deleted-type CNVRs were associated with testicular weight (TW) and testicular percentage (TP), namely CNVR492 (Chr2: 59473501-59478500 bp) and CNVR494 (Chr2: 59514001-59517000 bp). Additionally, two both-type CNVRs were associated with ovarian weight (OW) and ovarian percentage (OP), namely CNVR557 (Chr2: 99951001-99956500 bp) and CNVR891 (Chr7: 39115001-39122500 bp). RNA-seq analysis showed 6228 and 1070 differentially expressed genes (DEGs) related to the TW and OW. These DEGs were mainly enriched in the MAPK signaling pathway, cytokine-cytokine receptor interaction, and focal adhesion, which were reported to affect gonadal development. Further, by joint analysis of CNV-based GWAS and RNA-seq data, 3 genes, including LOC106019197, CDH19 (LOC101793040), and TYW5 were identified as potential candidate genes for TW and OW. LOC106019197 and CDH19 were down-regulated in the heavier-testes group (> 5 g), while TYW5 was also down-regulated in the heavier-ovaries group (> 3 g). The qRT-PCR revealed that LOC106019197 and CDH19 exhibited higher expression levels in the wild/CN0 and CN0/CN0 genotypes compared to the wild/wild genotype. TYW5 showed the highest expression level in the wild/CN0 genotype and the lowest in the CN2/CN2 genotype. In addition, the expression levels of LOC106019197 and CDH19 were significantly higher at 0w than at 8w and 24w.

CONCLUSION

Our results revealed that LOC106019197 and CDH19 may act as inhibitors of duck testicular development. TYW5 may play a role in delaying ovarian development. These findings provide new insights into the mechanism of puberty onset in ducks.

摘要

背景

性成熟和生殖阶段的开始标志着禽类青春期的开始，在遗传和育种中起着重要作用。研究性腺发育是探索青春期开始遗传机制的重要途径之一。

结果

我们的研究中，120 日龄瘤头鸭睾丸和卵巢的表型数据显示出较大的变异系数，表明它们的性腺处于不同的发育状态。对 358 只瘤头鸭的基于 CNV 的 GWAS 结果显示，两个缺失型 CNVR 与睾丸重量（TW）和睾丸百分比（TP）有关，即 CNVR492（Chr2:59473501-59478500 bp）和 CNVR494（Chr2:59514001-59517000 bp）。此外，两个均有型 CNVR 与卵巢重量（OW）和卵巢百分比（OP）有关，即 CNVR557（Chr2:99951001-99956500 bp）和 CNVR891（Chr7:39115001-39122500 bp）。RNA-seq 分析显示，与 TW 和 OW 相关的差异表达基因（DEGs）有 6228 个和 1070 个。这些 DEGs 主要富集在 MAPK 信号通路、细胞因子-细胞因子受体相互作用和粘着斑中，这些通路被报道会影响性腺发育。进一步，通过基于 CNV 的 GWAS 和 RNA-seq 数据的联合分析，鉴定出 3 个基因，包括 LOC106019197、CDH19（LOC101793040）和 TYW5，它们可能是 TW 和 OW 的潜在候选基因。LOC106019197 和 CDH19 在睾丸较重（>5 g）的组中下调，而 TYW5 在卵巢较重（>3 g）的组中也下调。qRT-PCR 显示，与野生型/CN0 和 CN0/CN0 基因型相比，LOC106019197 和 CDH19 在野生型/CN0 基因型中的表达水平更高。TYW5 在野生型/CN0 基因型中的表达水平最高，在 CN2/CN2 基因型中的表达水平最低。此外，LOC106019197 和 CDH19 的表达水平在 0w 时明显高于 8w 和 24w。