Subsampling and DNA pooling can increase gains through genomic selection in switchgrass

Abstract Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candid...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Neal Wepking Tilhou, Michael D. Casler
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	Plant culture SB1-1110 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/442dda4c1e434735a44130a167b19cc5
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:442dda4c1e434735a44130a167b19cc5
record_format	dspace
spelling	oai:doaj.org-article:442dda4c1e434735a44130a167b19cc52021-12-05T07:50:12ZSubsampling and DNA pooling can increase gains through genomic selection in switchgrass1940-337210.1002/tpg2.20149https://doaj.org/article/442dda4c1e434735a44130a167b19cc52021-11-01T00:00:00Zhttps://doi.org/10.1002/tpg2.20149https://doaj.org/toc/1940-3372Abstract Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of <5% of the predictive ability, measured using cross‐validation. Predictive ability also decreased when sequencing progressively fewer TP DNA pools, but TPs constructed from only two phenotypically contrasting DNA samples retained a mean of >80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the impact of reduced sequencing, genetic gain was calculated for seven GS scenarios with variable sequencing budgets. Reduced TP sequencing and most CP pooling methods were superior to individual sequence‐based GS when sequencing resources were restricted (2,000 DNA samples per 5‐yr cycle). Only one scenario was superior to individual sequencing when sequencing budgets were large (8,000 DNA samples per 5‐yr cycle). This study highlights multiple routes for reduced sequencing costs in GS.Neal Wepking TilhouMichael D. CaslerWileyarticlePlant cultureSB1-1110GeneticsQH426-470ENThe Plant Genome, Vol 14, Iss 3, Pp n/a-n/a (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Plant culture SB1-1110 Genetics QH426-470
spellingShingle	Plant culture SB1-1110 Genetics QH426-470 Neal Wepking Tilhou Michael D. Casler Subsampling and DNA pooling can increase gains through genomic selection in switchgrass
description	Abstract Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of <5% of the predictive ability, measured using cross‐validation. Predictive ability also decreased when sequencing progressively fewer TP DNA pools, but TPs constructed from only two phenotypically contrasting DNA samples retained a mean of >80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the impact of reduced sequencing, genetic gain was calculated for seven GS scenarios with variable sequencing budgets. Reduced TP sequencing and most CP pooling methods were superior to individual sequence‐based GS when sequencing resources were restricted (2,000 DNA samples per 5‐yr cycle). Only one scenario was superior to individual sequencing when sequencing budgets were large (8,000 DNA samples per 5‐yr cycle). This study highlights multiple routes for reduced sequencing costs in GS.
format	article
author	Neal Wepking Tilhou Michael D. Casler
author_facet	Neal Wepking Tilhou Michael D. Casler
author_sort	Neal Wepking Tilhou
title	Subsampling and DNA pooling can increase gains through genomic selection in switchgrass
title_short	Subsampling and DNA pooling can increase gains through genomic selection in switchgrass
title_full	Subsampling and DNA pooling can increase gains through genomic selection in switchgrass
title_fullStr	Subsampling and DNA pooling can increase gains through genomic selection in switchgrass
title_full_unstemmed	Subsampling and DNA pooling can increase gains through genomic selection in switchgrass
title_sort	subsampling and dna pooling can increase gains through genomic selection in switchgrass
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/442dda4c1e434735a44130a167b19cc5
work_keys_str_mv	AT nealwepkingtilhou subsamplinganddnapoolingcanincreasegainsthroughgenomicselectioninswitchgrass AT michaeldcasler subsamplinganddnapoolingcanincreasegainsthroughgenomicselectioninswitchgrass
_version_	1718372550324518912

Subsampling and DNA pooling can increase gains through genomic selection in switchgrass

Ejemplares similares