Effects of marker density and population structure on the genomic prediction accuracy for growth trait in Pacific white shrimp Litopenaeus vannamei

BMC Genetics
Quanchao WangJianhai Xiang

Abstract

Due to the great advantages in selection accuracy and efficiency, genomic selection (GS) has been widely studied in livestock, crop and aquatic animals. Our previous study based on one full-sib family of Litopenaeus vannamei (L. vannamei) showed that GS was feasible in penaeid shrimp. However, the applicability of GS might be influenced by many factors including heritability, marker density and population structure etc. Therefore it is necessary to evaluate the major factors affecting the prediction ability of GS in shrimp. The aim of this study was to evaluate the factors influencing the GS accuracy for growth traits in L. vannamei. Genotype and phenotype data of 200 individuals from 13 full-sib families were used for this analysis. In the present study, the heritability of growth traits in L. vannamei was estimated firstly based on the full set of markers (23 K). It was 0.321 for body weight and 0.452 for body length. The estimated heritability increased rapidly with the increase of the marker density from 0.05 K to 3.2 K, and then it tended to be stable for both traits. For genomic prediction on the growth traits in L. vannamei, three statistic models (RR-BLUP, BayesA and Bayesian LASSO) showed similar performance for the pr...Continue Reading

References

Aug 3, 2006·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·L R Schaeffer
Mar 27, 2007·Bioinformatics·Yurii S AulchenkoCornelia M van Duijn
Dec 14, 2007·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·M E Goddard, B J Hayes
Oct 15, 2008·PloS One·Hans D DaetwylerJohn A Woolliams
Jan 24, 2009·Journal of Dairy Science·B J HayesM E Goddard
Jul 2, 2009·Genetics, Selection, Evolution : GSE·Anna K Sonesson, Theo H E Meuwissen
Dec 9, 2009·Animal Genetics·Z-Q DuM F Rothschild
Jan 2, 2010·Genetics, Selection, Evolution : GSE·Gerhard MoserHerman W Raadsma
May 23, 2012·Nature Methods·Shi WangMikhail V Matz
Jun 30, 2012·Genetics·Gustavo de Los CamposMario P L Calus
Oct 17, 2013·Genetics, Selection, Evolution : GSE·Marie LillehammerAnna K Sonesson
Jan 5, 2014·Genetics and Molecular Biology·Fabyano Fonseca E SilvaSimone E F Guimarães
Jan 24, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Zhigang GuoGilles Gay
Mar 1, 2014·Genetics, Selection, Evolution : GSE·Haroldo H R NevesJosé Fernando Garcia
Dec 9, 2014·Frontiers in Genetics·Jørgen OdegårdTheo H E Meuwissen
Jul 1, 2016·Genetics, Selection, Evolution : GSE·Hsin-Yuan TsaiRoss D Houston
Sep 23, 2016·G3 : Genes - Genomes - Genetics·Christos PalaiokostasLuca Bargelloni

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Citations

Feb 29, 2020·International Journal of Molecular Sciences·Samuel LanFrank M You
Jun 11, 2020·PloS One·Frances R ThistlethwaiteYousry A El-Kassaby
Apr 18, 2020·Nature Reviews. Genetics·Ross D HoustonDiego Robledo
Apr 4, 2021·Animals : an Open Access Journal From MDPI·Fotis Pappas, Christos Palaiokostas
Oct 31, 2018·G3 : Genes - Genomes - Genetics·Alfred OzimatiJean-Luc Jannink
Nov 3, 2020·Journal of Invertebrate Pathology·Iasmim Santos Mangabeira-SilvaDaniel Carlos Ferreira Lanza

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Methods Mentioned

BETA
electrophoresis
genotyping
MDS

Software Mentioned

LASSO
GenABEL
rrBLUP
Beagle
BayesA
R
MAS
R package rrBLUP
RADtyping
R package BGLR

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