Genomic preselection with genotyping-by-sequencing increases performance of commercial oil palm hybrid crosses

BMC Genomics
David CrosTristan Durand-Gasselin

Abstract

There is great potential for the genetic improvement of oil palm yield. Traditional progeny tests allow accurate selection but limit the number of individuals evaluated. Genomic selection (GS) could overcome this constraint. We estimated the accuracy of GS prediction of seven oil yield components using A × B hybrid progeny tests with almost 500 crosses for training and 200 crosses for independent validation. Genotyping-by-sequencing (GBS) yielded +5000 single nucleotide polymorphisms (SNPs) on the parents of the crosses. The genomic best linear unbiased prediction method gave genomic predictions using the SNPs of the training and validation sets and the phenotypes of the training crosses. The practical impact was illustrated by quantifying the additional bunch production of the crosses selected in the validation experiment if genomic preselection had been applied in the parental populations before progeny tests. We found that prediction accuracies for cross values plateaued at 500 to 2000 SNPs, with high (0.73) or low (0.28) values depending on traits. Similar results were obtained when parental breeding values were predicted. GS was able to capture genetic differences within parental families, requiring at least 2000 SNPs with...Continue Reading

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Citations

Jun 21, 2020·Scientific Reports·Javier HerreroEnrique Ritter
Nov 17, 2020·Frontiers in Plant Science·Andrés J CortésLarry E Bedoya-Canas
Mar 16, 2021·Frontiers in Genetics·Marlee R LabrooJessica E Rutkoski
Sep 10, 2020·Plant Science : an International Journal of Experimental Plant Biology·Achille NyoumaDavid Cros
Feb 26, 2019·G3 : Genes - Genomes - Genetics·David T AshtonMaren Wellenreuther
Nov 11, 2021·Omics : a Journal of Integrative Biology·Muliyar Krishna RajeshThottethodi Subrahmanya Keshava Prasad

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Methods Mentioned

BETA
genotyping
PCR
two hybrid

Software Mentioned

custom
GBLUP
R script
R
PBLUP
Bowtie2
ADNid
TBLUP
Tassel GBS
BEAGLE

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