全基因组精细定位影响猪小肠长度的基因位点（QTL）
摘要
小肠是动物胃肠道系统一个重要器官,多种营养物质,如碳水化合物、蛋白质、微生素和矿物质等,在这里被吸收。为了鉴别影响猪小肠长度的的数量性状基因位点(QTL),本研究测量了白色杜洛克×二花脸资源群体F2代1034个体的240日龄小肠长度。结果显示,在该F2代群体中,小肠长度和生长性状及胴体长呈强相关性。利用覆盖猪基因组的183个微卫星标记对此F2群体进行全基因组扫描,分别在猪的8条染色体上鉴别到了10个影响小肠长度的QTL,其中2,4,7和8号染色体上的4个QTL达到1%基因组显著水平,12号染色体上1个QTL达到5%基因组显著水平,5、7、13和14号染色体上存在5个5%染色体组显著水平QTL。二花脸的QTL等位基因,除了7号和13号染色体上的位点外,均导致更短的小肠长度。4号染色体上的小肠长度QTL与前人报道的QTL有部分重叠,位于2,8和12号染色体上的主效QTL与已有的报道相一致,7号染色体上发现的QTL则尚属第一次报道。本研究中鉴别的所有QTL均与此前已报道的影响生长性状的QTL区域相重叠,由此可见,小肠长度在猪的生长发育过程中扮演着一个至关重要的角色。
为了进一步精细定位影响猪小肠长度的QTL,本研究利用猪全基因组60K芯片,判定929头白色杜洛克×二花脸资源家系F2代个体的基因型,并针对小肠长度性状开展了全基因组关联分析(GWAS),结果在1、2、3、4、5、7、8、9、10、11、13和15号等12条染色体上检测到18个影响小肠长度的显著区域(P<2.68e-7),这些位点共解释31.5%的表型变异。研究结果不仅验证了上述基于微卫星标记连锁分析所定位的大部分QTL,还在3、9、10、11和15号染色体上鉴别到新的影响小肠长度的位点。此外,在显著SNP位点所在区段发现了令人感兴趣的候选基因。例如,4号染色体位于78.63Mb处INRA0014995标记附近的PLAG1基因以及7号染色体位于34.55Mb处MARC0058766标记附近的HMGA1基因处于同一个影响动物解剖形态的分子网络中,这两个候选基因值得深入研究。最后,基于18个显著SNP位点的信息,利用基于似然率比的统计方法推测了小肠长度变化和猪生长快慢的因果关系,结果表明小肠长度变化会影响猪生长快慢。本研究结果反映了小肠长度变异遗传机理的复杂性,所鉴别的显著位点及其相关候选基因为下一步精细定位和独立群体验证工作奠定了基础。
The small intestine is a vital organ in animal gastrointestinal system, in which a large variety of nutrients are absorbed. To identify quantitative trait loci (QTL) for the length of porcine small intestine, phenotypic values were measured in1034individuals at240days from a White-Duroc×Chinese Erhualian intercross F2population. The length of small intestine showed strong correlation with growth traits and carcass length in this population. A whole-genome scan was performed based on183microsatellites covering the pig genome in the F2population. A total of10QTL for this trait were identified on8pig chromosomes (SSC), including four1%genome-wide significant QTL on SSC2,4,7and8, one5%genome-wide significant QTL on SSC12, and five5%chromosome-wide significant QTL on SSC5,7,13and14. The Erhualian alleles were generally associated with shorter length of the small intestine except the alleles on SSC7and13. The QTL on SSC4overlapped with the previously reported QTL for the length of small intestine. Several significant QTL on SSC2,8and12were consistent with previous reports. The significant QTL detected on SSC7was reported for the first time. All QTL identified in this study coincided to the known QTL regions significantly affected the growth traits, supporting the important role of the length of small intestine in pig growth.
To refine the location of the above-mentioned QTL, we further genotyped929F2animals from the White Duroc×Erhualian resource population using porcine60K SNP chips. A genome-wide association analysis (GWAS) was performed and a total of18significant regions around18most significant SNP (P<2.68e-7) were evidenced on12chromosomes, namely, SSC1,2,3,4,5,7,8,9,10,11,13and15. Most of the QTL detected by microsatellite markers based linkage analysis were replicated in GWAS, while the significant regions on SSC3,9,10,11and15were detected for the first time. The18significant SNP jointly explained31.5%of the phenotypic variance. We found some interesting candidate genes in the significant regions, e.g., the PLAG1near INRA0014995at78.63Mb on SSC4and HMGA1near MARC0058766at34.55Mb on SSC7are strong candidate genes that are worthwhile for further investigation, given that the two genes reside in the same molecular networks that are enriched for genes related to anatomical structure morphogenesis. Based on the genotypes of the18significant SNPs, we inferred the causal relationship between small intestine length and growth related traits like carcass weight and average daily gain using a likelihood ratio test which compared the likelihood of two reciprocal causal models. The resulting statistics supported that the change of small intestine length can be one of the causatives to variation in growth traits. These findings reflect the complex genetic architecture of porcine small intestine length, and provide a more detailed landscape of genomic regions and candidate genes underlying variation in pig intestine length compared with previous reports.
为了进一步精细定位影响猪小肠长度的QTL,本研究利用猪全基因组60K芯片,判定929头白色杜洛克×二花脸资源家系F2代个体的基因型,并针对小肠长度性状开展了全基因组关联分析(GWAS),结果在1、2、3、4、5、7、8、9、10、11、13和15号等12条染色体上检测到18个影响小肠长度的显著区域(P<2.68e-7),这些位点共解释31.5%的表型变异。研究结果不仅验证了上述基于微卫星标记连锁分析所定位的大部分QTL,还在3、9、10、11和15号染色体上鉴别到新的影响小肠长度的位点。此外,在显著SNP位点所在区段发现了令人感兴趣的候选基因。例如,4号染色体位于78.63Mb处INRA0014995标记附近的PLAG1基因以及7号染色体位于34.55Mb处MARC0058766标记附近的HMGA1基因处于同一个影响动物解剖形态的分子网络中,这两个候选基因值得深入研究。最后,基于18个显著SNP位点的信息,利用基于似然率比的统计方法推测了小肠长度变化和猪生长快慢的因果关系,结果表明小肠长度变化会影响猪生长快慢。本研究结果反映了小肠长度变异遗传机理的复杂性,所鉴别的显著位点及其相关候选基因为下一步精细定位和独立群体验证工作奠定了基础。
The small intestine is a vital organ in animal gastrointestinal system, in which a large variety of nutrients are absorbed. To identify quantitative trait loci (QTL) for the length of porcine small intestine, phenotypic values were measured in1034individuals at240days from a White-Duroc×Chinese Erhualian intercross F2population. The length of small intestine showed strong correlation with growth traits and carcass length in this population. A whole-genome scan was performed based on183microsatellites covering the pig genome in the F2population. A total of10QTL for this trait were identified on8pig chromosomes (SSC), including four1%genome-wide significant QTL on SSC2,4,7and8, one5%genome-wide significant QTL on SSC12, and five5%chromosome-wide significant QTL on SSC5,7,13and14. The Erhualian alleles were generally associated with shorter length of the small intestine except the alleles on SSC7and13. The QTL on SSC4overlapped with the previously reported QTL for the length of small intestine. Several significant QTL on SSC2,8and12were consistent with previous reports. The significant QTL detected on SSC7was reported for the first time. All QTL identified in this study coincided to the known QTL regions significantly affected the growth traits, supporting the important role of the length of small intestine in pig growth.
To refine the location of the above-mentioned QTL, we further genotyped929F2animals from the White Duroc×Erhualian resource population using porcine60K SNP chips. A genome-wide association analysis (GWAS) was performed and a total of18significant regions around18most significant SNP (P<2.68e-7) were evidenced on12chromosomes, namely, SSC1,2,3,4,5,7,8,9,10,11,13and15. Most of the QTL detected by microsatellite markers based linkage analysis were replicated in GWAS, while the significant regions on SSC3,9,10,11and15were detected for the first time. The18significant SNP jointly explained31.5%of the phenotypic variance. We found some interesting candidate genes in the significant regions, e.g., the PLAG1near INRA0014995at78.63Mb on SSC4and HMGA1near MARC0058766at34.55Mb on SSC7are strong candidate genes that are worthwhile for further investigation, given that the two genes reside in the same molecular networks that are enriched for genes related to anatomical structure morphogenesis. Based on the genotypes of the18significant SNPs, we inferred the causal relationship between small intestine length and growth related traits like carcass weight and average daily gain using a likelihood ratio test which compared the likelihood of two reciprocal causal models. The resulting statistics supported that the change of small intestine length can be one of the causatives to variation in growth traits. These findings reflect the complex genetic architecture of porcine small intestine length, and provide a more detailed landscape of genomic regions and candidate genes underlying variation in pig intestine length compared with previous reports.
引文
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