{"title":"Integrated analysis of whole genome and transcriptome sequencing uncovers genetic differences between Zi goose and Xianghai flying goose","authors":"Hongyu Ni, Yonghong Zhang, Yuwei Yang, Yijing Yin, Jing Ren, Qingxing Xiao, Puze Zhao, Xiaoqing Hong, Ziyi Zhang, Benhai Cui, Hao Sun, Xueqi Sun, Yumei Li","doi":"10.1111/age.13388","DOIUrl":null,"url":null,"abstract":"<p>Zi goose is a famous indigenous breed originating from northeast China with high annual egg production. Xianghai flying goose is a composite breed and is bred by crosses of the wild swan goose and the Zi goose. Our previous study revealed significant differences in muscle fiber characteristics between the two populations. Here, we aimed to reveal the underlying genetic basis of the above phenotype differences through whole-genome and transcriptome analysis. A total of 20 blood samples (10 Zi geese and 10 Xianghai flying geese) were used for whole genome sequencing, and eight breast muscle tissue samples (four Zi geese and four Xianghai flying geese) were used for RNA sequencing. Using the <i>F</i><sub>ST</sub> and XP-EHH analysis, some highly differentiated genome regions annotated with egg production (<i>RORB</i>, <i>WNT4</i>, <i>BMPR1B</i>) and breast muscle development (<i>WNT7B</i>) between the two populations were detected. RNA-sequencing analysis revealed differentially expressed genes related to muscle development (<i>IGF1</i>, <i>PAX7</i>). Moreover, several genes were detected by both genome and transcriptome analysis, and some of them were reported to be associated with muscle growth (<i>SLIT2</i>, <i>PREX1</i>) and intramuscular fat (<i>COL6A1</i>). These findings will help researchers better understand the genetic basis related to egg production and muscle development in geese.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 1","pages":"147-151"},"PeriodicalIF":1.8000,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Animal genetics","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/age.13388","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"AGRICULTURE, DAIRY & ANIMAL SCIENCE","Score":null,"Total":0}
引用次数: 0
Abstract
Zi goose is a famous indigenous breed originating from northeast China with high annual egg production. Xianghai flying goose is a composite breed and is bred by crosses of the wild swan goose and the Zi goose. Our previous study revealed significant differences in muscle fiber characteristics between the two populations. Here, we aimed to reveal the underlying genetic basis of the above phenotype differences through whole-genome and transcriptome analysis. A total of 20 blood samples (10 Zi geese and 10 Xianghai flying geese) were used for whole genome sequencing, and eight breast muscle tissue samples (four Zi geese and four Xianghai flying geese) were used for RNA sequencing. Using the FST and XP-EHH analysis, some highly differentiated genome regions annotated with egg production (RORB, WNT4, BMPR1B) and breast muscle development (WNT7B) between the two populations were detected. RNA-sequencing analysis revealed differentially expressed genes related to muscle development (IGF1, PAX7). Moreover, several genes were detected by both genome and transcriptome analysis, and some of them were reported to be associated with muscle growth (SLIT2, PREX1) and intramuscular fat (COL6A1). These findings will help researchers better understand the genetic basis related to egg production and muscle development in geese.
期刊介绍:
Animal Genetics reports frontline research on immunogenetics, molecular genetics and functional genomics of economically important and domesticated animals. Publications include the study of variability at gene and protein levels, mapping of genes, traits and QTLs, associations between genes and traits, genetic diversity, and characterization of gene or protein expression and control related to phenotypic or genetic variation.
The journal publishes full-length articles, short communications and brief notes, as well as commissioned and submitted mini-reviews on issues of interest to Animal Genetics readers.