RAD-seq技术在大白猪繁殖性状基因组选择上的应用  

The Application of RAD-seq Technology on Genomic Selection of Fertility Traits for Large White Pigs(Sus scrofa)

作　　者：李勇 苗泽圃[1,2] 蒙小云 杨漫漫 魏强 郭笑峰 郑华 方铭 

机构地区：[1]深圳华大基因研究院,深圳518000 [2]深圳动物基因组辅助育种工程实验室,深圳518000 [3]华中农业大学农业动物遗传育种与繁殖教育部重点实验室/2011生猪健康养殖协同创新中心,武汉430070 [4]深圳市农牧实业有限公司,深圳518000 [5]农业基因组学国家重点实验室/广东省农作物核心资源开发应用企业重点实验室,深圳518000

出　　处：《农业生物技术学报》2017年第9期1508-1515,共8页Journal of Agricultural Biotechnology

基　　金：深圳动物基因组辅助育种工程实验室提升项目;深圳市生物产业发展专项资金现代农业生物产业扶持计划项目(No.NYSW20140326010005);国家自然科学基金面上项目(No.31672399)

摘　　要：繁殖性能是猪(Sus scrofa)育种选择中的主要目标性状之一,由于繁殖性状属于低遗传力的数量性状,常规选育难以取得较大遗传进展。为了考察限制性位点相关DNA测序技术(restriction-site associated DNA sequencing,RAD-seq)在猪繁殖性状上育种值预测的性能,本研究采集了具有窝产总仔数(total number born,TNB)、窝产活仔数(number born alive,NBA)、初生窝重(litter weight,LW)3个繁殖性状记录的母猪725头,采用RAD-seq技术对其中618头母猪进行基因组遗传分型,经过质量控制获得了覆盖基因组的79 725个SNP标记。为了验证RAD-seq技术在基因组选择中的有效性,本研究将测序群体按近似4∶1的比例划分为参考群和验证群,在验证群表型值未知(模拟早期选择)时分别考察传统的最佳线性无偏预测(best linear unbiased prediction,BLUP)方法和两种基因组育种值预测方法基因组BLUP(genomic BLUP,GBLUP)和一步法BLUP(single-step genomic BLUP,SS-GBLUP)对验证群育种值预测的准确性和偏向性。结果表明,GBLUP对验证群个体育种值预测的准确性从BLUP的0.109(TNB),0.067(NBA)和0.009(LW)分别提高至0.220(TNB)、0.184(NBA)和0.205(LW),而SS-GBLUP的预测准确性与GBLUP几乎相同;此外,GBLUP和SS-GBLUP明显改良了育种值预测的偏向性。结果表明,基于RADseq技术的基因组选择方法在种猪繁殖性状的育种值预测中是有效的。研究结果对于猪的良种选育具有重要的理论和实践意义。Fertility performance of pig （Sus scrofa） is a main objective trait in pig genetic improvement, which is difficult to achieve great genetic progress with traditional breeding method due to its relative lower heritability. To investigate the performance of the restriction association site DNA sequencing （RAD- seq） technology on genomic prediction of the breeding value for fertility traits, 725 sows with records of total number born （TNB）, number born alive （NBA） and litter weight （LW） from Shenzhen Agroi Pastoral Enterprises Co., Ltd. were collected. 618 sows in all of 725 sows with RAD-seq were sequenced and 79 725 genome-wide distributed SNPs after quality control were produced. To validate the efficiency of the RAD-seq on genomic selection, the 618 sows into two parts with 4：1 ratio were divided, which served as the reference and validation population, respectively. Then, the predictive accuracy and biasness of three methods including best linear unbiased prediction （BLUP）, genomic BLUP （GBLUP） and single-step genomic BLUP （SS- GBLUP） were studied, respectively, for validation population for which phenotypic records were masked. The results showed that GBLUP increased the prediction accuracy of breeding value from 0.109 （TNB）, 0.067 （NBA） and 0.009 （LW） with BLUP to 0.220 （TNB）, 0.184 （NBA） and 0.205 （LW）, respectively, and SS- GBLUP performed similar prediction accuracy as GBLUE Furthermore, GBLUP and SS-GBLUP improved the prediction biasness in comparison with BLUE The results suggested PAD-seq based genomic selection method was effective in breeding value prediction for fertility traits. The exploration of the application of PAD-seq technology on pig genomic selection has theoretical and practical significance.

关 键 词：简化基因组测序技术(RAD—seq) 基因组选择 繁殖性状 最佳线性无偏预测(BLUP) 

分 类 号：S828[农业科学—畜牧学]