Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content.
Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content.
复制标题
检测腹部脂肪含量不同的两个鸡品系的全基因组拷贝数变异
DOI：
10.1186/1471-2164-15-517
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发表时间：
2014-06-24
期刊：
影响因子：
4.4
通讯作者：
Li H
中科院分区：
文献类型：
--
作者：
Zhang H;Du ZQ;Dong JQ;Wang HX;Shi HY;Wang N;Wang SZ;Li H
鸡（Gallus gallus）是一种重要的模式生物，在哺乳动物和其他脊椎动物的进化中起着重要的桥梁作用。拷贝数变异（Copy number variations，CNVs）是基因组结构变异的一种形式，广泛分布于基因组中。CNV分析最近获得了更大的关注和动力，因为CNV的鉴定有助于更好地理解对人类和其他动物都很重要的性状。为了检测鸡CNVs，我们使用鸡60 K SNP阵列对来自两个肉鸡品系的475只动物进行基因分型，这是一种广泛用于鸡基因组学研究的高通量方法。结果使用PennCNV算法，我们在瘦肉和脂肪品系中分别检测到438和291个CNVs，对应于271和188个CNV区域（CNVRs），其通过合并重叠的CNV获得。在这些CNVR中，99%也被CNVPartition程序确认。这些CNVR分别覆盖了瘦肉型和脂肪型鸡基因组的40.26和30.60 Mb。此外，CNVR包括瘦线中的176个损失、68个增加和27个两者（即相同区域内的损失和增加）事件，以及脂肪线中的143个损失、25个增加和20个两者事件。选择10个CNVR用于使用qPCR方法的验证实验，并且所有CNVR均在至少一次qPCR测定中得到确认。我们共发现886个基因位于这些CNVRs中，基因本体论（GO）和京都基因和基因组百科全书（KEGG）的途径分析表明，它们可以在许多生物过程中发挥各种作用。综合CNVRs、已知数量性状基因座（QTL）和腹部脂肪含量选择性扫描的结果表明，（包括SLC9A3、GNAL、SPOCK 3、ANXA 10、HELIOS、MYLK、CCDC 14、SPAG 9、SOX 5、VSNL 1、SMC 6、GEN 1、MSGN 1和ZPAX）可能对鸡腹脂沉积起重要作用。从而有助于我们理解基因组结构变异及其在鸡腹部脂肪含量中的潜在作用。
BackgroundThe chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals. To detect chicken CNVs, we genotyped 475 animals derived from two broiler chicken lines divergently selected for abdominal fat content using chicken 60 K SNP array, which is a high-throughput method widely used in chicken genomics studies.ResultsUsing PennCNV algorithm, we detected 438 and 291 CNVs in the lean and fat lines, respectively, corresponding to 271 and 188 CNV regions (CNVRs), which were obtained by merging overlapping CNVs. Out of these CNVRs, 99% were confirmed also by the CNVPartition program. These CNVRs covered 40.26 and 30.60 Mb of the chicken genome in the lean and fat lines, respectively. Moreover, CNVRs included 176 loss, 68 gain and 27 both (i.e. loss and gain within the same region) events in the lean line, and 143 loss, 25 gain and 20 both events in the fat line. Ten CNVRs were chosen for the validation experiment using qPCR method, and all of them were confirmed in at least one qPCR assay. We found a total of 886 genes located within these CNVRs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed they could play various roles in a number of biological processes. Integrating the results of CNVRs, known quantitative trait loci (QTL) and selective sweeps for abdominal fat content suggested that some genes (includingSLC9A3,GNAL,SPOCK3,ANXA10,HELIOS,MYLK,CCDC14,SPAG9,SOX5,VSNL1,SMC6,GEN1,MSGN1andZPAX) may be important for abdominal fat deposition in the chicken.ConclusionsOur study provided a genome-wide CNVR map of the chicken genome, thereby contributing to our understanding of genomic structural variations and their potential roles in abdominal fat content in the chicken.
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