RAD-seq技术在大白猪繁殖性状基因组选择上的应用

发布时间：2018-06-26 12:04

本文选题：简化基因组测序技术(RAD-seq) + 基因组选择　；参考：《农业生物技术学报》2017年09期

【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。
[Abstract]:Reproductive performance is one of the main target traits in breeding selection of pigs (Sus scrofa). Because reproductive traits belong to low heritability quantitative traits, it is difficult to make great genetic progress in conventional breeding. In order to investigate the predictive performance of restriction-site associated DNA sequencing technique (RAD-seq) in breeding traits of pigs, In this study, 725 sows with total litter size (total number), litter size (number born (number born) and newborn litter weight (litter weight) were collected, and 618 sows were genotyped by RAD-seq technique. 79,725 SNP markers covering the genome were obtained by quality control. In order to verify the validity of RAD-seq technique in genome selection, the sequencing population was divided into reference group and validation group according to the approximate 4:1 scale. When the phenotypic value of the group is unknown (simulating early selection), the traditional optimal linear unbiased prediction (best linear unbiased prediction method and two genome breeding prediction methods, genomic blup (genomic BLUPSS-GBLUP) and one-step blup (single-step genomic BLUPSS-GBLUP), are investigated respectively. The accuracy and bias of the value prediction. The results showed that the accuracy of GBLUP in predicting individual breeding value of verified populations was increased from 0.109 (TNB) 0.067 (NBA) and 0.009 (LW) of blup to 0.220 (TNB) 0.184 (NBA) and 0.205 (LW), respectively, while the prediction accuracy of SS-GBLUP was almost the same as that of GBLUP. In addition, GBLUP and SS-GBLUP significantly improved the bias of breeding value prediction. The results showed that the genome selection method based on RADseq technique was effective in predicting breeding value of breeding traits. The results have important theoretical and practical significance for the breeding of improved breeds of pigs.
【作者单位】：深圳华大基因研究院;深圳动物基因组辅助育种工程实验室;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;深圳市农牧实业有限公司;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;
【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)
【分类号】：S828

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