Genomic selection for productive traits in biparental cassava breeding populations

PLoS One. 2019 Jul 25;14(7):e0220245. doi: 10.1371/journal.pone.0220245. eCollection 2019.

Abstract

Cassava improvement using traditional breeding strategies is slow due to the species' long breeding cycle. However, the use of genomic selection can lead to a shorter breeding cycle. This study aimed to estimate genetic parameters for productive traits based on pedigree (pedigree and phenotypic information) and genomic (markers and phenotypic information) analyses using biparental crosses at different stages of selection. A total of 290 clones were genotyped and phenotyped for fresh root yield (FRY), dry matter content (DMC), dry yield (DY), fresh shoot yield (FSY) and harvest index (HI). The clones were evaluated in clonal evaluation trials (CET), preliminary yield trials (PYT), advanced yield trials (AYT) and uniform yield trials (UYT), from 2013 to 2018 in ten locations. The breeding stages were analyzed as follows: one stage (CET), two stages (CET and PYT), three stages (CET, PYT and AYT) and four stages (CET, PYT, AYT and UYT). The genomic predictions were analyzed via k-fold cross-validation based on the genomic best linear unbiased prediction (GBLUP) considering a model with genetic additive effects and genotype × location interactions. Genomic and pedigree accuracies were moderate to high (0.56-0.72 and 0.62-0.78, respectively) for important starch-related traits such as DY and FRY; when considering one breeding stage (CET) with the aim of early selection, the genomic accuracies ranged from 0.60 (DMC) to 0.71 (HI). Moreover, the correlations between the genomic estimation breeding values of one-stage genomic analysis and the estimated breeding values of the four-stage (full data set) pedigree analysis were high for all traits as well as for a selection index including all traits. The results indicate great possibilities for genomic selection in cassava, especially for selection early in the breeding cycle (saving time and effort).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agriculture / economics
  • Agriculture / methods
  • Breeding / methods*
  • Crosses, Genetic
  • Economics
  • Genomics / methods*
  • Genotype
  • Inheritance Patterns
  • Manihot / economics
  • Manihot / genetics*
  • Manihot / growth & development
  • Models, Genetic
  • Pedigree
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Quantitative Trait, Heritable*
  • Selection, Genetic*

Grants and funding

LGT was supported by scholarships from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) MDVR, FFS and EJO was supported by research productivity scholarships from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). The authors are grateful for the financial support provided by Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). This work was also partially supported by the NEXTGEN Cassava project, through a grant to Cornell University by the Bill & Melinda Gates Foundation and the UK Department for International Development. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.