Performance Comparison of Two Efficient Genomic Selection Methods(gsbay & MixP ) Applied in Aquacultural Organisms  

作　　者：SU Hailin LI Hengde WANG Shi WANG Yangfan BAO Zhenmin 

机构地区：[1]College of Marine Life Science, Ocean University of China [2]The Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences

出　　处：《Journal of Ocean University of China》2017年第1期137-144,共8页中国海洋大学学报（英文版）

基　　金：supported by the National High-Tech R&D Program (863 Program No. 2012AA10A405);the earmarked fund for Modern Agro-industry Technology Research System;the National Natural Science Foundation of China (No. 31302182)

摘　　要：Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools Mix P and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop(Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction(GBLUP) method which has been applied widely. Our results showed that both Mix P and gsbay could accurately estimate single-nucleotide polymorphism(SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values(GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by Mix P; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by Mix P and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with Mix P the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by Mix P and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools MixP and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop (Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction (GBLUP) method which has been applied widely. Our results showed that both MixP and gsbay could accurately estimate single-nucleotide polymorphism (SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values (GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by MixP; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by MixP and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with MixP the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by MixP and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.

关 键 词：GENOMIC SELECTION SCALLOP BREEDING method comparison 

分 类 号：S917.4[农业科学—水产科学]