3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

Plant Methods

Methodology

Maxime de Ronne¹  François Belzile¹  Davoud Torkamaneh²  Gaétan Légaré³  Brian Boyle³ 

[1] Département de Phytologie, Université Laval, Quebec, Canada;Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada;Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Quebec, Canada;Département de Phytologie, Université Laval, Quebec, Canada;Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada;Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Quebec, Canada;Institut intelligence et données (IID), Université Laval, Quebec, Canada;Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada;

关键词: Genotyping-by-sequencing;    Ultra-high-throughput genotyping;    Multiplexing;    Next-generation sequencing;    Genomic selection;    Single-nucleotide polymorphism;   

DOI  :  10.1186/s13007-023-00990-7

 received in 2022-11-01, accepted in 2023-01-31,  发布年份 2023

来源: Springer

【 摘 要 】

Despite the increased efficiency of sequencing technologies and the development of reduced-representation sequencing (RRS) approaches allowing high-throughput sequencing (HTS) of multiplexed samples, the per-sample genotyping cost remains the most limiting factor in the context of large-scale studies. For example, in the context of genomic selection (GS), breeders need genome-wide markers to predict the breeding value of large cohorts of progenies, requiring the genotyping of thousands candidates. Here, we introduce 3D-GBS, an optimized GBS procedure, to provide an ultra-high-throughput and ultra-low-cost genotyping solution for species with small to medium-sized genome and illustrate its use in soybean. Using a combination of three restriction enzymes (PstI/NsiI/MspI), the portion of the genome that is captured was reduced fourfold (compared to a “standard” ApeKI-based protocol) while reducing the number of markers by only 40%. By better focusing the sequencing effort on limited set of restriction fragments, fourfold more samples can be genotyped at the same minimal depth of coverage. This GBS protocol also resulted in a lower proportion of missing data and provided a more uniform distribution of SNPs across the genome. Moreover, we investigated the optimal number of reads per sample needed to obtain an adequate number of markers for GS and QTL mapping (500–1000 markers per biparental cross). This optimization allows sequencing costs to be decreased by ~ 92% and ~ 86% for GS and QTL mapping studies, respectively, compared to previously published work. Overall, 3D-GBS represents a unique and affordable solution for applications requiring extremely high-throughput genotyping where cost remains the most limiting factor.

【 授权许可】

CC BY   
© The Author(s) 2023

【 图 表 】

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