pSBVB: A versatile simulation tool to evaluate genomic selection in polyploid species
Ver/Abrir
Fecha de publicación
2018-12-20ISSN
2160-1836
Resumen
Genomic Selection (GS) is the procedure whereby molecular information is used to predict complex phenotypes and it is standard in many animal and plant breeding schemes. However, only a small
number of studies have been reported in horticultural crops, and in polyploid species in particular. In this
paper, we have developed a versatile forward simulation tool, called polyploid Sequence Based Virtual
Breeding (pSBVB), to evaluate GS strategies in polyploids; pSBVB is an efficient gene dropping software
that can simulate any number of complex phenotypes, allowing a very flexible modeling of phenotypes
suited to polyploids. As input, it takes genotype data from the founder population, which can vary from
single nucleotide polymorphisms (SNP) chips up to sequence, a list of causal variants for every trait and their heritabilities, and the pedigree. Recombination rates between homeologous chromosomes can be
specified, so that both allo- and autopolyploid species can be considered. The program outputs phenotype and genotype data for all individuals in the pedigree. Optionally, it can produce several genomic relationship matrices that consider exact or approximate genotype values. pSBVB can therefore be used to evaluate GS strategies in polyploid species (say varying SNP density, genetic architecture or population size, among other factors), or to optimize experimental designs for association studies. We illustrate pSBVB with SNP data from tetraploid potato and partial sequence data from octoploid strawberry, and we show that GS is a promising breeding strategy for polyploid species but that the actual advantage critically depends on the underlying genetic architecture. Source code, examples and a complete manual are freely available in GitHub
Tipo de documento
Artículo
Versión del documento
Versión publicada
Lengua
Inglés
Materias (CDU)
633 - Cultivos y producciones
Páginas
8
Publicado por
Genetics Society of America
Publicado en
G3
Citación
Zingaretti, Laura, Amparo Monfort, and Miguel Pérez-Enciso. 2018. "Psbvb: A Versatile Simulation Tool To Evaluate Genomic Selection In Polyploid Species". G3&Amp;#58; Genes|Genomes|Genetics, g3.200942.2018. Genetics Society of America. doi:10.1534/g3.118.200942.
Número del acuerdo de la subvención
MINECO/Programa Estatal de fomento de la investigación científica y técnica de excelencia/SEV-2015-0533/ES/ /
INIA/Programa Estatal de promoción del talento y su empleabilidad en I+D+I/RTA2013-00010-00-00/ES/Análisis genético del aroma de las fresas silvestre y cultivada: desarrollo de marcadores moleculares para su selección en fresa cultivada/
MINECO/Programa Estatal de I+D+I orientada a los retos de la sociedad/AGL2016-78709-R/ES/UTILIZACION DE SECUENCIAS COMPLETAS PARA LA MEJORA DE ESPECIES DOMESTICAS/
Program
Genòmica i Biotecnologia
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