title: Genomic Selection Using Extreme Phenotypes and Pre-Selection of SNPs in Large Yellow Croaker (Larimichthys crocea).
abstract: Genomic selection (GS) is an effective method to improve predictive accuracies of genetic values. However, high cost in genotyping will limit the application of this technology in some species. Therefore, it is necessary to find some methods to reduce the genotyping costs in genomic selection. Large yellow croaker is one of the most commercially important marine fish species in southeast China and Eastern Asia. In this study, genotyping-by-sequencing was used to construct the libraries for the NGS sequencing and find 29,748 SNPs in the genome. Two traits, eviscerated weight (EW) and the ratio between eviscerated weight and whole body weight (REW), were chosen to study. Two strategies to reduce the costs were proposed as follows: selecting extreme phenotypes (EP) for genotyping in reference population or pre-selecting SNPs to construct low-density marker panels in candidates. Three methods of pre-selection of SNPs, i.e., pre-selecting SNPs by absolute effects (SE), by single marker analysis (SMA), and by fixed intervals of sequence number (EL), were studied. The results showed that using EP was a feasible method to save the genotyping costs in reference population. Heritability did not seem to have obvious influences on the predictive abilities estimated by EP. Using SMA was the most feasible method to save the genotyping costs in candidates. In addition, the combination of EP and SMA in genomic selection also showed good results, especially for trait of REW. We also described how to apply the new methods in genomic selection and compared the genotyping costs before and after using the new methods. Our study may not only offer a reference for aquatic genomic breeding but also offer a reference for genomic prediction in other species including livestock and plants, etc.
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, People's Republic of China.
authors.forename: Linsong
authors.initials: L
authors.lastname: Dong
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, People's Republic of China.
authors.forename: Shijun
authors.initials: S
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, People's Republic of China.
authors.forename: Junwei
authors.initials: J
authors.lastname: Chen
authors.affiliation: Academy of Animal Science and Technology, Collaborative Innovation Center for Aquatic Efficient Health Production of Fisheries, Hunan Agricultural University, Changsha, Hunan, People's Republic of China.
authors.forename: Liang
authors.initials: L
authors.lastname: Wan
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, People's Republic of China. zywang@jmu.edu.cn.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Wang
mesh_terms: D000818:Animals; D001835:Body Weight; D001947:Breeding; D005260:Female; D005819:Genetic Markers; D005838:Genotype; D060005:Genotyping Techniques / Q000191:economics*; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D010473:Perciformes / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic
chemical_list: D005819:Genetic Markers
keywords: Extreme phenotype; Genome-wide association study; Genomic selection; Pre-selection of SNPs; Predictive ability