Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)

Abstract Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included:...

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Autores principales:	Qi Bin Kwong, Ai Ling Ong, Chee Keng Teh, Fook Tim Chew, Martti Tammi, Sean Mayes, Harikrishna Kulaveerasingam, Suat Hui Yeoh, Jennifer Ann Harikrishna, David Ross Appleton
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/92d804c2a3ad404f873bb46c7cdb96ac
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spelling	oai:doaj.org-article:92d804c2a3ad404f873bb46c7cdb96ac2021-12-02T11:40:57ZGenomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)10.1038/s41598-017-02602-62045-2322https://doaj.org/article/92d804c2a3ad404f873bb46c7cdb96ac2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02602-6https://doaj.org/toc/2045-2322Abstract Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: shell-to-fruit ratio (S/F, %), mesocarp-to-fruit ratio (M/F, %), kernel-to-fruit ratio (K/F, %), fruit per bunch (F/B, %), oil per bunch (O/B, %) and oil per palm (O/P, kg/palm/year). Genomic heritabilities of these traits were estimated to be in the range of 0.40 to 0.80. GS methods assessed were RR-BLUP, Bayes A (BA), Cπ (BC), Lasso (BL) and Ridge Regression (BRR). All methods resulted in almost equal prediction accuracy. The accuracy achieved ranged from 0.40 to 0.70, correlating with the heritability of traits. By selecting the most important markers, RR-BLUP B has the potential to outperform other methods. The marker density for certain traits can be further reduced based on the linkage disequilibrium (LD). Together with in silico breeding, GS is now being used in oil palm breeding programs to hasten parental palm selection.Qi Bin KwongAi Ling OngChee Keng TehFook Tim ChewMartti TammiSean MayesHarikrishna KulaveerasingamSuat Hui YeohJennifer Ann HarikrishnaDavid Ross AppletonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qi Bin Kwong Ai Ling Ong Chee Keng Teh Fook Tim Chew Martti Tammi Sean Mayes Harikrishna Kulaveerasingam Suat Hui Yeoh Jennifer Ann Harikrishna David Ross Appleton Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)
description	Abstract Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: shell-to-fruit ratio (S/F, %), mesocarp-to-fruit ratio (M/F, %), kernel-to-fruit ratio (K/F, %), fruit per bunch (F/B, %), oil per bunch (O/B, %) and oil per palm (O/P, kg/palm/year). Genomic heritabilities of these traits were estimated to be in the range of 0.40 to 0.80. GS methods assessed were RR-BLUP, Bayes A (BA), Cπ (BC), Lasso (BL) and Ridge Regression (BRR). All methods resulted in almost equal prediction accuracy. The accuracy achieved ranged from 0.40 to 0.70, correlating with the heritability of traits. By selecting the most important markers, RR-BLUP B has the potential to outperform other methods. The marker density for certain traits can be further reduced based on the linkage disequilibrium (LD). Together with in silico breeding, GS is now being used in oil palm breeding programs to hasten parental palm selection.
format	article
author	Qi Bin Kwong Ai Ling Ong Chee Keng Teh Fook Tim Chew Martti Tammi Sean Mayes Harikrishna Kulaveerasingam Suat Hui Yeoh Jennifer Ann Harikrishna David Ross Appleton
author_facet	Qi Bin Kwong Ai Ling Ong Chee Keng Teh Fook Tim Chew Martti Tammi Sean Mayes Harikrishna Kulaveerasingam Suat Hui Yeoh Jennifer Ann Harikrishna David Ross Appleton
author_sort	Qi Bin Kwong
title	Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)
title_short	Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)
title_full	Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)
title_fullStr	Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)
title_full_unstemmed	Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)
title_sort	genomic selection in commercial perennial crops: applicability and improvement in oil palm (elaeis guineensis jacq.)
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/92d804c2a3ad404f873bb46c7cdb96ac
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Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)

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