Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values

• Published in: Theoretical and applied genetics Vol. 135; no. 2; pp. 605 - 622
• Main Authors: Brainard, Scott H., Ellison, Shelby L., Simon, Philipp W., Dawson, Julie C., Goldman, Irwin L.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.02.2022; Springer; Springer Nature B.V
• Subjects: Agriculture; Association analysis; Biochemistry; Biomedical and Life Sciences; Biotechnology; Breeding; Carrots; Daucus; Daucus carota - genetics; Genetic analysis; Genetic aspects; Genetic control; Genetic diversity; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomic analysis; Genomics; Genomics - methods; Image processing; Life Sciences; Methods; Original; Original Article; Phenotype; Phenotypes; Physiological aspects; Plant Biochemistry; Plant Breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Polygenic inheritance; Polymorphism, Single Nucleotide; Production processes; Quantitative trait loci; Roots; Roots (Botany); United States
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-021-03988-8

Key message The principal phenotypic determinants of market class in carrot—the size and shape of the root—are under primarily additive, but also highly polygenic, genetic control. The size and shape of carrot roots are the primary determinants not only of yield, but also market class. These quantitative phenotypes have historically been challenging to objectively evaluate, and thus subjective visual assessment of market class remains the primary method by which selection for these traits is performed. However, advancements in digital image analysis have recently made possible the high-throughput quantification of size and shape attributes. It is therefore now feasible to utilize modern methods of genetic analysis to investigate the genetic control of root morphology. To this end, this study utilized both genome wide association analysis (GWAS) and genomic-estimated breeding values (GEBVs) and demonstrated that the components of market class are highly polygenic traits, likely under the influence of many small effect QTL. Relatively large proportions of additive genetic variance for many of the component phenotypes support high predictive ability of GEBVs; average prediction ability across underlying market class traits was 0.67. GWAS identified multiple QTL for four of the phenotypes which compose market class: length, aspect ratio, maximum width, and root fill, a previously uncharacterized trait which represents the size-independent portion of carrot root shape. By combining digital image analysis with GWAS and GEBVs, this study represents a novel advance in our understanding of the genetic control of market class in carrot. The immediate practical utility and viability of genomic selection for carrot market class is also described, and concrete guidelines for the design of training populations are provided.