Please wait a minute...
Journal of Integrative Agriculture
Advanced Online Publication | Current Issue | Archive | Adv Search
Integrating genome-wide association and transcriptome analysis to provide molecular insights into growth rates in sheep

Liming Zhao1, Fadi Li1, Xiaoxue Zhang2, Lvfeng Yuan3, Huibin Tian1, Dan Xu1, Deyin Zhang1, Yukun Zhang1, Yuan Zhao1, Kai Huang1, Xiaolong Li1, Jiangbo Cheng1, Zongwu Ma2, Quanzhong Xu1, Xiaobin Yang1, Kunchao Han1, Xiuxiu Weng1, Weimin Wang1,#

1 State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China

2 College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China

3 Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
摘要  

利用综合多组学分析方法研究与绵羊生长速度相关的关键基因和遗传标记可以为养羊业提供有价值的见解。在本研究中,基于平均日增重(ADG),我们选择快生长型(Ncase=70)和慢生长型(Ncontrol=70)湖羊用于全基因组关联分析(GWAS);并选择10只湖羊(快生长型,n = 5;慢生长型,n = 5)和10只杜泊羊(快生长型,n = 5;慢生长型,n = 5)用于比较转录组分析(RNA-Seq)。分别利用加权基因共表达网络分析(WGCNA)和来自10种组织的转录组测序数据鉴定了核心基因(Hub genes)和组织特异性基因(TSGs)。研究结果表明,GWAS分析共鉴定到10个与绵羊生长速度显著关联的基因(LOC106990525, BRINP3, DSCAML1, CEP164, TOX, BMP1, PHYHIP, SFTPC, LGI3, REEP4);基于比较转录组分析,在HF vs. HS 与DF vs. DS比较对中分别鉴定出501441个差异表达基因(DEGs)。功能富集分析显示,一些重要的信号通路与脂肪代谢和能量代谢相关,如“脂肪细胞中脂肪分解的调节(regulation of lipolysis in adipocytes)”、“氧化磷酸化(Oxidative phosphorylation)”、“产热(Thermogenesis)”;一些与脂肪沉积(如ADRB3, PDE3B, FABP4, SERPINE1, PLIN1, FOXO6)和肌肉发育(如MYL3)相关的DEGs也被鉴定到。使用WGCNA分析鉴定到了15个被认为是与绵羊平均日增重(ADG)相关的核心基因(INPP5K, ZNF692, MAN2C1, PPP1R12C, SLC27A5, LRP3, PPP6R1, BRF1, EN1, AMBRA1, LITAF, PARVA, TGFBR3, YWHAQ, DCN)。联合GWASRNA-Seq数据表明,BRINP3PENK基因可能通过调节绵羊的摄食行为而进一步影响其生长速度。进一步在1071只湖羊群体中进行关联分析,结果显示,BRINP3 g.16903465 T>CPENK g.39289926 T>C突变位点均与湖羊生长性状显著相关(P < 0.05)。因此,BRINP3PENK基因可能是与绵羊生长速度相关的潜在关键候选基因,我们的研究为理解绵羊生长性状相关的分子机制提供了新的见解。



Abstract  

Investigating genetic markers and key genes associated with sheep growth rate using integrated multi-omics approaches could provide valuable insights for the sheep industry. Based on the average daily gain (ADG), fast-growing (Ncase=70) and slow-growing (Ncontrol=70) Hu sheep were selected for a genome-wide association study (GWAS). Ten Hu sheep (fast-growing, n=5; slow-growing, n=5) and ten Dorper sheep (fast-growing, n=5; slow-growing, n=5) were selected for comparative transcriptome analysis. We identified hub genes and tissue-specific genes (TSGs) using weighted gene co-expression network analysis (WGCNA) and RNA sequencing (RNA-Seq) data from ten tissues, respectively. Ten genes were found within 50 kb distances of the significant single nucleotide polymorphisms (SNPs). Based on a comparative transcriptomic analysis, a total of 501 and 441 differentially expressed genes (DEGs) were identified in the HF vs. HS and DF vs. DS comparisons, respectively. We found some important signaling pathways closely associated with fat metabolism and energy metabolism, such as “regulation of lipolysis in adipocytes”, “Oxidative phosphorylation”, and “Thermogenesis”. Several DEGs play a crucial role in fat deposition (such as ADRB3, PDE3B, FABP4, SERPINE1, PLIN1, and FOXO6) and muscle development (MYL3). Using the WGCNA analysis, 15 genes were considered as hub genes associated with ADG. Integration of GWAS and RNA-Seq data indicates that BRINP3 and PENK may further influence the growth rate by regulating feeding behavior in sheep. Association analysis of 1,071 Hu sheep populations revealed that mutations in the BRINP3 (BRINP3 g.16903465 T>C) and PENK (PENK g.39289926 T>C) genes were significantly related to the growth traits (P<0.05). Our research provides novel insights into understanding the molecular mechanisms underlying growth traits in sheep. BRINP3 and PENK genes may be potential key candidate genes related to sheep growth rate.

Keywords:  Sheep growth rate       GWAS        Transcriptomic        BRINP3        PENK  
Online: 20 August 2024  
Fund: 
This work was supported by the National Key Research and Development Program of China (2021YFD1300901, 2022YFD1302000, and 2023YFF1001000), the Major Science and Technology Projects in Gansu Province, China (22ZD6NC069), and the Key R&D Program of Gansu Province, China (20YF3NA012).
About author:  Liming Zhao, E-mail: zlmfxy1807285865@163.com Correspondence Weimin Wang, Tel: 0931-7631225, E-mail: wangweimin@lzu.edu.cn

Cite this article: 

Liming Zhao, Fadi Li, Xiaoxue Zhang, Lvfeng Yuan, Huibin Tian, Dan Xu, Deyin Zhang, Yukun Zhang, Yuan Zhao, Kai Huang, Xiaolong Li, Jiangbo Cheng, Zongwu Ma, Quanzhong Xu, Xiaobin Yang, Kunchao Han, Xiuxiu Weng, Weimin Wang. 2024. Integrating genome-wide association and transcriptome analysis to provide molecular insights into growth rates in sheep. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2024.08.011

A K J L, B T D S. 2001. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 ΔΔ C T Method. Methods, 25, 402-408.

Abdalla B A, Chen X, Li K, Chen J, Nie Q. 2021. Control of preadipocyte proliferation, apoptosis and early adipogenesis by the forkhead transcription factor FoxO6. Life Sciences, 265, 118858.

An B, Xia J, Chang T, Wang X, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. 2019. Genome-wide association study reveals candidate genes associated with body measurement traits in Chinese Wagyu beef cattle. Animal Genetics, 50, 386-390.

Armstrong E, Ciappesoni G, Iriarte W, Da Silva C, Macedo F, Navajas E, Brito G, San Julián R, Gimeno D, Postiglioni A. 2018. Novel genetic polymorphisms associated with carcass traits in grazing Texel sheep. Meat science, 145, 202-208.

Arora R, Naveen K S, Sudarshan S, Fairoze M N, Manjunatha S S. 2019. Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India. Plos One, 14, e0217461-.

Bai Y-Y, Xu X, Yu X-J, Guo J, Dong X-X, Wang X-Y, Zhao Z-A, Wang J. 2020. Skimmed milk diluent promotes the sperm motility and conception rate of Dorper sheep compared to vitamin B12 diluent. CryoLetters, 41, 358-364.

Ballester M, Puig-Oliveras A, Castelló A, Revilla M, Fernández A, Folch J. 2017. Association of genetic variants and expression levels of porcine FABP4 and FABP5 genes. Animal Genetics, 48, 660-668.

Berkowicz S R, Featherby T J, Whisstock J C, Bird P I. 2016. Mice Lacking Brinp2 or Brinp3, or Both, Exhibit Behaviors Consistent with Neurodevelopmental Disorders. Front Behav Neurosci, 10, 196.

Cardoso T F, Quintanilla R, Castelló A, González-Prendes R, Amills M, Cánovas Á. 2018. Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles. BMC genomics, 19, 145.

Cheng S, Wang X, Wang Q, Yang L, Shi J, Zhang Q. 2020. Comparative analysis of Longissimus dorsi tissue from two sheep groups identifies differentially expressed genes related to growth, development and meat quality. Genomics, 112, 3322-3330.

Chung Y W, Ahmad F, Tang Y, Hockman S C, Kee H J, Berger K, Guirguis E, Choi Y H, Schimel D M, Aponte A M. 2017. White to beige conversion in PDE3B KO adipose tissue through activation of AMPK signaling and mitochondrial function. Scientific Reports, 7, 40445.

Cloney R. 2016. Complex traits: Integrating gene variation and expression to understand complex traits. Nat Rev Genet, 17, 194.

Faucher L, Godé C, Arnaud J F. 2016. Development of Nuclear Microsatellite Loci and Mitochondrial Single Nucleotide Polymorphisms for the Natterjack Toad, Bufo (Epidalea) calamita (Bufonidae), Using Next Generation Sequencing and Competitive Allele Specific PCR (KASPar). J Hered, 107, 660-665.

Feng X, Li F, Wang F, Zhang G, Pang J, Ren C, Zhang T, Yang H, Wang Z, Zhang Y. 2018. Genome-wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep. Bioscience reports, 38.

Fontanesi L, Schiavo G, Galimberti G, Calò D G, Russo V. 2014. A genomewide association study for average daily gain in Italian Large White pigs. Journal of Animal Science, 92, 1385.

Forrest R, Hickford J, Hogan A, Frampton C. 2003. Polymorphism at the ovine β3‐adrenergic receptor locus: associations with birth weight, growth rate, carcass composition and cold survival. Animal genetics, 34, 19-25.

González J R, Armengol L, Solé X, Guinó E, Mercader J M, Estivill X, Moreno V. 2007. SNPassoc: an R package to perform whole genome association studies. Bioinformatics, 23, 654-655.

Goszczynski D, Papaleo-Mazzucco J, Ripoli M, Villarreal E, Rogberg-Muñoz A, Mezzadra C, Melucci L, Giovambattista G. 2017. Genetic variation in FABP4 and evaluation of its effects on beef cattle fat content. Animal biotechnology, 28, 211-219.

He J, Zhao B, Huang X, Fu X, Liu G, Tian Y, Wu C, Mao J, Liu J, Gun S, Tian K. 2022. Gene network analysis reveals candidate genes related with the hair follicle development in sheep. BMC Genomics, 23, 428.

Ikeda H, Ardianto C, Yonemochi N, Yang L, Ohashi T, Ikegami M, Nagase H, Kamei J. 2015. Inhibition of opioid systems in the hypothalamus as well as the mesolimbic area suppresses feeding behavior of mice. Neuroscience, 311, 9-21.

Innes D J, Hudson N J, Anderson S T, Poppi D P, Quigley S P. 2023. Differential voluntary feed intake and whole transcriptome profiling in the hypothalamus of young sheep offered CP and phosphorus-deficient diets. animal, 17, 100973.

Jiang J, Cao Y, Shan H, Wu J, Song X, Jiang Y. 2021. The GWAS analysis of body size and population verification of related SNPs in Hu Sheep. Front Genet, 12, 642552.

Jiang L, Zheng Z, Fang H, Yang J. 2021. A generalized linear mixed model association tool for biobank-scale data. Nat Genet, 53, 1616-1621.

Jiao, S., Maltecca, C., Gray, K., A., Cassady, J., P. 2014. Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Du roc pigs: II. Genomewide association. Journal of Animal Science.

Jiao D, Ji K, Liu H, Wang W, Wu X, Zhou J, Zhang Y, Zhou H, Hickford J G H, Degen A A, Yang G. 2021. Transcriptome analysis reveals genes involved in thermogenesis in two Cold-Exposed Sheep breeds. Genes (Basel), 12.

Kim H A, Baek K J, Yun H-Y. 2021. Integrative proteomic network analyses support depot‑specific roles for leucine rich repeat LGI family member 3 in adipose tissues. Experimental and Therapeutic Medicine, 22, 1-12.

Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559.

Larzul C, Lefaucheur L, Ecolan P, Gogué J, Talmant A, Sellier P, Le Roy P, Monin G. 1997. Phenotypic and genetic parameters for longissimus muscle fiber characteristics in relation to growth, carcass, and meat quality traits in large white pigs. J Anim Sci, 75, 3126-3137.

Lee S H, Lee D, Lee M, Ryoo S H, Choi I. 2020. Analysis of single nucleotide polymorphisms related to heifer fertility in Hanwoo (Korean cattle). Animal Biotechnology, 1-6.

Li B, Weng Q, Dong C, Zhang Z, Li R, Liu J, Jiang A, Li Q, Jia C, Wu W, Liu H. 2018. A Key Gene, PLIN1, Can affect Porcine intramuscular fat content based on transcriptome analysis. Genes, 9.

Li J, Liu J, Liu S, Plastow G, Zhang C, Wang Z, Campanile G, Salzano A, Gasparrini B, Hua G, Liang A, Yang L. 2018. Integrating RNA-seq and GWAS reveals novel genetic mutations for buffalo reproductive traits. Anim Reprod Sci, 197, 290-295.

Li S, Raza S, Zhao C, Cheng G, Zan L. 2020. PLIN1 overexpression of promotes lipid metabolism in bovine adipocytes. Animals : an open access journal from MDPI, 10.

Liufu S, Lan Q, Liu X, Chen B, Xu X, Ai N, Li X, Yu Z, Ma H. 2023. Transcriptome analysis reveals the age-related developmental dynamics pattern of the longissimus Dorsi muscle in Ningxiang pigs. Genes, 14, 1050.

Mahala S, Saini S, Kumar A, Sharma R C, Gowane G R. 2020. Genetic trends for the growth rates and Kleiber ratio in Avikalin sheep. Small Ruminant Research, 189, 106143.

Mine K, Zhao Y, Eleanor W, Dong L, Nuno R, Li C, Griffin J D, Satish P, Marcel V, Glastonbury C A. 2021. Identification of rare loss-of-function genetic variation regulating body fat distribution. The Journal of Clinical Endocrinology & Metabolism.

Mohammadi H, Rafat S A. 2020. Genome-wide association study and gene ontology for growth and wool characteristics in Zandi sheep. Shahid Bahonar University of Kerman and Iranian Society of Animal Science.

Na S W, Park S J, Hong S J, Baik M. 2020. Transcriptome changes associated with fat deposition in the longissimus thoracis of Korean cattle following castration. J Anim Physiol a Anim Nutr.

Osborn D P S, Pond H L, Mazaheri N, Dejardin J, Munn C J, Mushref K, Cauley E S, Moroni I, Pasanisi M B, Sellars E A, Hill R S, Partlow J N, Willaert R K, Bharj J, Malamiri R A, Galehdari H, Shariati G, Maroofian R, Mora M, Swan L E, et al. 2017. Mutations in INPP5K cause a form of congenital muscular dystrophy overlapping marinesco-Sjögren syndrome and dystroglycanopathy. Am J Hum Genet, 100, 537-545.

Ouyang H, Wang Z, Chen X, Yu J, Li Z, Nie Q. 2017. Proteomic analysis of chicken skeletal muscle during embryonic development. Frontiers in physiology, 8, 281.

Park J, Lee J, Kim S, Han J, Kang K, Kim S, Park T. 2018. Muscle differentiation induced up-regulation of calcium-related gene expression in quail myoblasts. Asian-Australasian journal of animal sciences, 31, 1507-1515.

Pasandideh M, Gholizadeh M, Rahimi-Mianji G. 2020. A genome-wide association study revealed five SNPs affecting 8-month weight in sheep. Anim Genet, 51, 973-976.

Pere P, Spiegelman B M. 2003. Peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1 alpha): transcriptional coactivator and metabolic regulator. Endocrine Reviews, 78.

Piórkowska K, Żukowski K, Ropka-Molik K, Tyra M, Gurgul A. 2018. A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits. Genet Mol Biol, 41, 125-136.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A, Bender D, Maller J, Sklar P, de Bakker P I, Daly M J, Sham P C. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet, 81, 559-575.

Qiu C, Han Z, Li W, Ye K, Xie Y, Wang Z. 2018. A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora). Scientific Reports, 8, 17271.

Rakus D, Gizak A, Deshmukh A, Wi?Niewski J R. 2015. Absolute quantitative profiling of the key metabolic pathways in slow and fast skeletal muscle. Journal of proteome research, 14, 1400-1411.

Remignon H, Gardahaut M F, Marche G, Ricard F H. 1995. Selection for rapid growth increases the number and the size of muscle fibres without changing their typing in chickens. J Muscle Res Cell Motil, 16, 95-102.

Ropka-Molik K, ?ukowski K, Eckert R, Gurgul A, Piórkowska K, Oczkowicz M. 2015. Comprehensive analysis of the whole transcriptomes from two different pig breeds using RNA‐Seq method. Animal Genetics, 45, 674-684.

Ruan D, Zhuang Z, Ding R, Qiu Y, Zhou S, Wu J, Xu C, Hong L, Huang S, Zheng E, Cai G, Wu Z, Yang J. 2021. Weighted single-step GWAS identified candidate genes associated with growth traits in a Duroc pig population. Genes (Basel), 12.

Shafey H, Mahrous K, Hassan A, Rushdi H, Ibrahim M. 2020. FABP4 single-nucleotide polymorphisms in gene associated with growth traits in Egyptian sheep. Veterinary world, 13, 1126-1132.

She X, Rohl C, Castle J, Kulkarni A, Johnson J, Chen R. 2009. Definition, conservation and epigenetics of housekeeping and tissue-enriched genes. BMC genomics, 10, 269.

Sohn J, Lee Y, Han J, Jeon Y, Kim J, Choe S, Kim S, Yoo H, Kim J. 2018. Perilipin 1 (Plin1) deficiency promotes inflammatory responses in lean adipose tissue through lipid dysregulation. The Journal of biological chemistry, 293, 13974-13988.

Stickland N C, Widdowson E M, Goldspink G. 1975. Effects of severe energy and protein deficiencies on the fibres and nuclei in skeletal muscle of pigs. Br J Nutr, 34, 421-428.

Tan X, Liu R, Zhao D, He Z, Li W, Zheng M, Li Q, Wang Q, Liu D, Feng F. 2024. Large-scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens. Journal of advanced research, 55, 1-16.

Tao X, Dong H, Zhang H, Xin H. 2011. Sex-based responses of plasma creatine kinase in broilers to thermoneutral constant and cyclic high temperatures. British poultry science, 52, 800-806.

Utsunomiya Y T, Carmo A S D, Carvalheiro R, Neves H H, Matos M C, Zavarez L B, O’Brien A M P, Sölkner J, Mcewan J C, Cole J B. 2013. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genetics,14,1(2013-06-13), 14, 1-12.

Walling G A, Visscher P M, Wilson A D, McTeir B L, Simm G, Bishop S C. 2004. Mapping of quantitative trait loci for growth and carcass traits in commercial sheep populations. J Anim Sci, 82, 2234-2245.

Wang T, Zhou M, Guo J, Guo Y Y, Ding K, Wang P, Wang Z P. 2021. Analysis of selection signatures on the Z chromosome of bidirectional selection broiler lines for the assessment of abdominal fat content. BMC Genom Data, 22, 18.

Wang Z, Shang P, Li Q, Wang L, Cham Ba  Y, Zhang B, Zhang H, Wu C. 2017. iTRAQ-based proteomic analysis reveals key proteins affecting muscle growth and lipid deposition in pigs. Rep, 7, 46717.

Wei C, Zeng H, Zhong Z, Cai X, Teng J, Liu Y, Zhao Y, Wu X, Li J, Zhang Z. 2023. Integration of non-additive genome-wide association study with a multi-tissue transcriptome analysis of growth and carcass traits in Duroc pigs. Animal, 17, 100817.

Wijayanti D, Erdenee S, Akhatayeva Z, Li H, Li J, Cai Y, Jiang F, Xu H, Lan X. 2022. Genetic polymorphisms within the ETAA1 gene associated with growth traits in Chinese sheep breeds. Anim Genet, 53, 460-465.

Wu J, Qiao L, Liu J, Yuan Y, Liu W. 2012. SNP variation in ADRB3 gene reflects the breed difference of sheep populations. Molecular biology reports, 39, 8395-8403.

Würfel M, Breitfeld J, Gebhard C, Scholz M, Baber R, Riedel-Heller S G, Blüher M, Stumvoll M, Kovacs P, Tönjes A. 2022. Interplay between adipose tissue secreted proteins, eating behavior and obesity. European journal of nutrition, 1-15.

Xia J, Qi X, Wu Y, Zhu B, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. 2016. Genome-wide association study identifies loci and candidate genes for meat quality traits in Simmental beef cattle. Mammalian Genome, 27, 246-255.

Yan W, Zhou H, Hu J, Luo Y, Hickford J. 2018. Variation in the FABP4 gene affects carcass and growth traits in sheep. Meat science, 145, 334-339.

Yang J, Lee S H, Goddard M E, Visscher P M. 2011. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet, 88, 76-82.

Yin B, Fang J, Zhang J, Zhang L, Xu C, Xu H, Shao J, Xia G. 2020. Correlations between single nucleotide polymorphisms in FABP4 and meat quality and lipid metabolism gene expression in Yanbian yellow cattle. Plos One, 15, e0234328.

Yu G, Wang L-G, Han Y, He Q-Y. 2012. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics: a journal of integrative biology, 16, 284-287.

YUJIA, SUN, JING, XUE, WENJIAO, GUO, MENJIAO, LI, YONGZHEN, HUANG. 2013. Haplotypes of bovine FoxO1 gene sequence variants and association with growth traits in Qinchuan cattle. Journal of Genetics, 93, 1-7.

Zhang F L, Zhang X Y, Zhao J X, Zhu K X, Liu S Q, Zhang T, Sun Y J, Wang J J, Shen W. 2022. Multispecies comparative analysis reveals transcriptional specificity during Mongolian horse testicular development. Reprod Domest Anim, 57, 1295-1306.

Zhao B, Luo H, Huang X, Wei C, Di J, Tian Y, Fu X, Li B, Liu G E, Fang L, Zhang S, Tian K. 2021. Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep. Genet Sel Evol, 53, 56.

No related articles found!
No Suggested Reading articles found!