A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep
文献类型： 外文期刊
作者： Zhao, Bingru 1 ; Luo, Hanpeng 2 ; Fu, Xuefeng 3 ; Zhang, Guoming 1 ; Clark, Emily L. 5 ; Wang, Feng 1 ; Dalrymple, Brian Paul 6 ; Oddy, V. Hutton 9 ; Vercoe, Philip E. 7 ; Wu, Cuiling 10 ; Liu, George E. 11 ; Li, Cong-jun 11 ; Xiang, Ruidong 6 ; Tian, Kechuan 15 ; Zhang, Yanli 1 ; Fang, Lingzhao 16 ;
作者机构： 1.Nanjing Agr Univ, Coll Anim Sci & Technol, Jiangsu Livestock Embryo Engn Lab, Nanjing 210095, Peoples R China
2.Capital Med Univ, Sch Basic Med Sci, Dept Immunol, Beijing 100069, Peoples R China
3.Xinjiang Acad Anim Sci, Inst Anim Sci, Key Lab Genet Breeding & Reprod Xinjiang Wool shee, Urumqi 830011, Peoples R China
4.Nanjing Agr Univ, Coll Vet Med, Nanjing 210095, Peoples R China
5.Univ Edinburgh, Roslin Inst, Edinburgh EH25, Midlothian, Scotland
6.CSIRO Agr, St Lucia, Qld 4067, Australia
7.Univ Western Australia, Sch Agr & Environm, Perth, WA 6009, Australia
8.Univ Western Australia, Inst Agr, Perth, WA 6009, Australia
9.Univ New England, Livestock Ind Ctr, NSW Dept Primary Ind, Armidale, NSW 2351, Australia
10.Xinjiang Normal Univ, Coll Life Sci, Int Ctr Collaborat Management Cross border Pest Ce, Sch Life Sci,Key Lab Special Environm Biodivers Ap, Urumqi 830053, Peoples R China
11.Agr Res Serv, USDA, Henry A Wallace Beltsville Agr Res Ctr, Anim Genom & Improvement Lab, Beltsville, MD 20705 USA
12.Univ Melbourne, Fac Vet & Agr Sci, Parkville, Vic 3052, Australia
13.Ctr AgriBiosciences, Agr Victoria, AgriBio, Bundoora, Vic 3083, Australia
14.Baker Heart & Diabet Inst, Cambridge Baker Syst Genom Initiat, Melbourne, Vic 3004, Australia
15.Shandong Acad Agr Sci, Inst Anim Sci & Vet Med, Jinan 250032, Peoples R China
16.Aarhus Univ, Ctr Quantitat Genet & Genom QGG, DK-8000 Aarhus, Denmark
关键词： Sheep; Developmental biology; Gene Expression Atlas; Genome-wide association study; Complex trait
期刊名称：GENOMICS PROTEOMICS & BIOINFORMATICS （ 影响因子：7.9； 五年影响因子：9.1 ）
ISSN： 1672-0229
年卷期： 2025 年 23 卷 1 期
页码：
收录情况： SCI
摘要： Sheep (Ovis aries) represent one of the most important livestock species for global animal protein and wool production. However, little is known about the genetic and biological basis of ovine phenotypes, particularly those with high economic value and environmental impact. Here, by integrating 1413 RNA sequencing (RNA-seq) samples from 51 distinct tissues across 14 developmental time points, representing early-prenatal, late-prenatal, neonatal, lamb, juvenile, adult, and elderly stages, we constructed a high-resolution Developmental Gene Expression Atlas (dGEA) in sheep. We observed dynamic patterns of gene expression and regulatory networks across tissues and developmental stages. Leveraging this resource to interpret genetic associations for 48 monogenic and 12 complex traits in sheep, we found that genes upregulated at prenatal developmental stages played more important roles in shaping these phenotypes than those upregulated at postnatal stages. For instance, genetic associations of crimp number, mean staple length (MSL), and individual birthweight were significantly enriched in the prenatal rather than postnatal skin and immune tissues. By comprehensively integrating genome-wide association study (GWAS) fine-mapping results with the sheep dGEA, we identified several candidate genes for complex traits in sheep, such as SOX9 for MSL, GNRHR for litter size at birth, and PRKDC for live weight. These results provide novel insights into the developmental and molecular architecture of ovine phenotypes. The dGEA (https://sheepdgea.njau.edu.cn/) will serve as an invaluable resource for sheep developmental biology, genetics, genomics, and selective breeding. Highlights 1) A high-resolution developmental Gene Expression Atlas (dGEA) in sheep.2) Dynamic gene expression patterns and regulatory networks across sheep development stages.3) Prenatal gene expression has a stronger influence on sheep traits than postnatal stages.4) Integration of GWAS and dGEA highlights candidate genes for complex traits in sheep.
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