Abstract
Key messageThe 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.
Highlights
Carrot (Daucus carota subsp. sativus) is a widely cultivated vegetable crop of both significant economic importance— globally, annual carrot production exceeds 40 million metric tons (FAO 2020)—and nutritional value, representing a significant source of pro-vitamin A in the human diet (Simon 2000)
This included a highly significant SNP on chromosome 2 associated with root fill; as such, this represents the first genetic characterization of the control of the vast majority of the variance in root shape
For three of these four traits, only two QTL per trait were identified, and their effect sizes were relatively small, ranging from 0.01 to 0.06, with total phenotypic variance explained ranging from 0.06 for root fill to 0.22 for aspect ratio
Summary
Carrot (Daucus carota subsp. sativus) is a widely cultivated vegetable crop of both significant economic importance— globally, annual carrot production exceeds 40 million metric tons (FAO 2020)—and nutritional value, representing a significant source of pro-vitamin A in the human diet (Simon 2000). In this regard, the size and shape of the edible, swollen taproot are key traits which influence yield, but are the principal determinants of market class in carrot (Banga 1957; Simon et al 2008), affecting harvestability, post-harvest handling, and marketability. Processing industries (e.g., canning, freezing, dehydrating, or juicing) prefer to purchase cultivars that can produce a large, bulky root, which is typically grown as a long-season crop at relatively lower densities (500,000–1,000,000 plants per hectare). On the other hand, typically require longer, slimmer roots, which can be grown at higher densities (1,500,000–3,000,000 plants per hectare). With the mechanization of carrot production, harvest, and post-harvest handling, these particular combinations of carrot root size and shape attributes have become increasingly important breeding targets.
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