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

Content Provider	Springer Nature : BioMed Central
Author	Cros, David Bocs, Stéphanie Riou, Virginie Ortega-Abboud, Enrique Tisné, Sébastien Argout, Xavier Pomiès, Virginie Nodichao, Leifi Lubis, Zulkifli Cochard, Benoit Durand-Gasselin, Tristan
Abstract	Background 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. Results 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 less than 5% missing data, imputed using pedigrees. Genomic preselection could have increased the selected hybrids bunch production by more than 10%. Conclusions Finally, preselection for yield components using GBS is the first possible application of GS in oil palm. This will increase selection intensity, thus improving the performance of commercial hybrids. Further research is required to increase the benefits from GS, which should revolutionize oil palm breeding.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-017-4179-3.pdf
Ending Page	17
Page Count	17
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-017-4179-3
Journal	BMC Genomics
Issue Number	1
Volume Number	18
Language	English
Publisher	BioMed Central
Publisher Date	2017-11-02
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetic gain Genomic selection Genotyping-by-sequencing Hybrid Oil palm Reciprocal recurrent selection
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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