Zengrong Zhang , Mohan Qiu , Huarui Du , Qingyun Li , Chunlin Yu , Wu Gan , Han Peng , Bo Xia , Xia Xiong , Xiaoyan Song , Li Yang , Chenming Hu , Jialei Chen , Chaowu Yang , Xiaosong Jiang
{"title":"全基因组重测序鉴定出藏鸡独特的单核苷酸多态性、插入/缺失和与缺氧相关的结构变异","authors":"Zengrong Zhang , Mohan Qiu , Huarui Du , Qingyun Li , Chunlin Yu , Wu Gan , Han Peng , Bo Xia , Xia Xiong , Xiaoyan Song , Li Yang , Chenming Hu , Jialei Chen , Chaowu Yang , Xiaosong Jiang","doi":"10.1016/j.gep.2021.119181","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><p><span>The adaptation to hypoxia in high altitude areas has great research value in the field of biological sciences. Tibetan chicken has unique adaptability to high-altitude, low pressure and anoxic conditions, and served as a </span>biological model<span> to search for genetic diversity of hypoxia adaption.</span></p></div><div><h3>Methods</h3><p>The whole genome re-sequencing technology was conducted to investigate the genetic diversity.</p></div><div><h3>Results</h3><p><span>In this study, we obtained quantity genetic resource, contained 5164926 single nucleotide polymorphisms (SNPs), 237504 Insertion/Deletion (InDel), 55606 structural variation types in all chromosomes of Tibetan chicken. Moreover, 17154 non-synonymous mutations, 45763 synonymous mutations, 258 InDel mutations and 9468 structural mutations were detected in coding sequencing (CDS) region. Furthermore, SNPs occur in 591 genes, including </span>HIF1A<span><span><span>, VEGF, MAPK 8/9/10/11, PPARA/D/G, NOTCH2, and ABCs, which were involved in 14 hypoxia-related pathways, such as VEGF </span>signaling pathway, MAPK signaling pathway, </span>PPAR<span> signaling pathway and Notch signaling pathway. Among them, 19 genes with non-synonymous SNP variation in CDS were identified. Moreover, structure variation in CDS also occurred in the mentioned above genes with SNPs.</span></span></p></div><div><h3>Conclusions</h3><p>This study provides useful targets for clarifying the hypoxia adaptability of the domestication of chickens in Tibetan and may help breeding efforts to develop improved breeds for the highlands.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.0000,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gep.2021.119181","citationCount":"4","resultStr":"{\"title\":\"Whole genome re-sequencing identifies unique adaption of single nucleotide polymorphism, insertion/deletion and structure variation related to hypoxia in Tibetan chickens\",\"authors\":\"Zengrong Zhang , Mohan Qiu , Huarui Du , Qingyun Li , Chunlin Yu , Wu Gan , Han Peng , Bo Xia , Xia Xiong , Xiaoyan Song , Li Yang , Chenming Hu , Jialei Chen , Chaowu Yang , Xiaosong Jiang\",\"doi\":\"10.1016/j.gep.2021.119181\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><p><span>The adaptation to hypoxia in high altitude areas has great research value in the field of biological sciences. Tibetan chicken has unique adaptability to high-altitude, low pressure and anoxic conditions, and served as a </span>biological model<span> to search for genetic diversity of hypoxia adaption.</span></p></div><div><h3>Methods</h3><p>The whole genome re-sequencing technology was conducted to investigate the genetic diversity.</p></div><div><h3>Results</h3><p><span>In this study, we obtained quantity genetic resource, contained 5164926 single nucleotide polymorphisms (SNPs), 237504 Insertion/Deletion (InDel), 55606 structural variation types in all chromosomes of Tibetan chicken. Moreover, 17154 non-synonymous mutations, 45763 synonymous mutations, 258 InDel mutations and 9468 structural mutations were detected in coding sequencing (CDS) region. Furthermore, SNPs occur in 591 genes, including </span>HIF1A<span><span><span>, VEGF, MAPK 8/9/10/11, PPARA/D/G, NOTCH2, and ABCs, which were involved in 14 hypoxia-related pathways, such as VEGF </span>signaling pathway, MAPK signaling pathway, </span>PPAR<span> signaling pathway and Notch signaling pathway. Among them, 19 genes with non-synonymous SNP variation in CDS were identified. 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Whole genome re-sequencing identifies unique adaption of single nucleotide polymorphism, insertion/deletion and structure variation related to hypoxia in Tibetan chickens
Background
The adaptation to hypoxia in high altitude areas has great research value in the field of biological sciences. Tibetan chicken has unique adaptability to high-altitude, low pressure and anoxic conditions, and served as a biological model to search for genetic diversity of hypoxia adaption.
Methods
The whole genome re-sequencing technology was conducted to investigate the genetic diversity.
Results
In this study, we obtained quantity genetic resource, contained 5164926 single nucleotide polymorphisms (SNPs), 237504 Insertion/Deletion (InDel), 55606 structural variation types in all chromosomes of Tibetan chicken. Moreover, 17154 non-synonymous mutations, 45763 synonymous mutations, 258 InDel mutations and 9468 structural mutations were detected in coding sequencing (CDS) region. Furthermore, SNPs occur in 591 genes, including HIF1A, VEGF, MAPK 8/9/10/11, PPARA/D/G, NOTCH2, and ABCs, which were involved in 14 hypoxia-related pathways, such as VEGF signaling pathway, MAPK signaling pathway, PPAR signaling pathway and Notch signaling pathway. Among them, 19 genes with non-synonymous SNP variation in CDS were identified. Moreover, structure variation in CDS also occurred in the mentioned above genes with SNPs.
Conclusions
This study provides useful targets for clarifying the hypoxia adaptability of the domestication of chickens in Tibetan and may help breeding efforts to develop improved breeds for the highlands.
期刊介绍:
Gene Expression Patterns is devoted to the rapid publication of high quality studies of gene expression in development. Studies using cell culture are also suitable if clearly relevant to development, e.g., analysis of key regulatory genes or of gene sets in the maintenance or differentiation of stem cells. Key areas of interest include:
-In-situ studies such as expression patterns of important or interesting genes at all levels, including transcription and protein expression
-Temporal studies of large gene sets during development
-Transgenic studies to study cell lineage in tissue formation