Genome-wide association mapping and genomic prediction of yield-related traits and starch pasting properties in cassava

• Published in: Theoretical and applied genetics Vol. 135; no. 1; pp. 145 - 171
• Main Authors: Phumichai, Chalermpol, Aiemnaka, Pornsak, Nathaisong, Piyaporn, Hunsawattanakul, Sirikan, Fungfoo, Phasakorn, Rojanaridpiched, Chareinsuk, Vichukit, Vichan, Kongsil, Pasajee, Kittipadakul, Piya, Wannarat, Wannasiri, Chunwongse, Julapark, Tongyoo, Pumipat, Kijkhunasatian, Chookiat, Chotineeranat, Sunee, Piyachomkwan, Kuakoon, Wolfe, Marnin D., Jannink, Jean-Luc, Sorrells, Mark E.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 2022; Springer Nature B.V
• Subjects: Agricultural production; Agriculture; Bayesian analysis; Biochemistry; Biomedical and Life Sciences; Biotechnology; Breeding; Cassava; Chromosome Mapping; Chromosomes, Plant; Edible Grain; Food industry; Gene mapping; Gene polymorphism; Genetic Markers; Genome, Plant; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Genotyping; Heritability; Life Sciences; Linkage Disequilibrium; Manihot - genetics; Manihot - growth & development; Mathematical models; Molecular modelling; Original Article; Plant Biochemistry; Plant Breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Predictions; Quantitative trait loci; Single-nucleotide polymorphism; Starch
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-021-03956-2

Key message
GWAS identified eight yield-related, peak starch type of waxy and wild-type starch and 21 starch pasting property-related traits (QTLs). Prediction ability of eight GS models resulted in low to high predictability, depending on trait, heritability, and genetic architecture.
Cassava is both a food and an industrial crop in Africa, South America, and Asia, but knowledge of the genes that control yield and starch pasting properties remains limited. We carried out a genome-wide association study to clarify the molecular mechanisms underlying these traits and to explore marker-based breeding approaches. We estimated the predictive ability of genomic selection (GS) using parametric, semi-parametric, and nonparametric GS models with a panel of 276 cassava genotypes from Thai Tapioca Development Institute, International Center for Tropical Agriculture, International Institute of Tropical Agriculture, and other breeding programs. The cassava panel was genotyped via genotyping-by-sequencing, and 89,934 single-nucleotide polymorphism (SNP) markers were identified. A total of 31 SNPs associated with yield, starch type, and starch properties traits were detected by the fixed and random model circulating probability unification (FarmCPU), Bayesian-information and linkage-disequilibrium iteratively nested keyway and compressed mixed linear model, respectively. GS models were developed, and forward predictabilities using all the prediction methods resulted in values of − 0.001–0.71 for the four yield-related traits and 0.33–0.82 for the seven starch pasting property traits. This study provides additional insight into the genetic architecture of these important traits for the development of markers that could be used in cassava breeding programs.