Genetic structure and domestication of carrot (<i>Daucus carota</i> subsp. <i>sativus</i>) (Apiaceae)

Iorizzo, Massimo; Senalik, Douglas; Ellison, Shelby; Grzebelus, Dariusz; Cavagnaro, Pablo Federico; Allender, Charlotte J.; Brunet, Johanne; Spooner, David M.; Deynze, Allen Van; Simon, Philipp W.

doi:10.3732/ajb.1300055

Cited by 171 publications

(184 citation statements)

References 72 publications

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“…In contrast, western cultivars clearly separated from wild and eastern cultivated carrots, and some inbred lines (I3 and I4) have a purified genetic pattern shared with western cultivated accessions, reflecting the intensive breeding practiced in western regions. Nucleotide diversity (π) 25 estimates showed that wild carrots have a slightly higher level of genetic diversity than cultivated carrots (Supplementary Table 18), indicating the occurrence of a limited domestication bottleneck, consistent with previous findings 3,26 . When D. carota subspecies, which have morphological characteristics contributing to their sexual isolation relative to carrot 27 , were excluded from diversity estimates, this observation was more evident from comparative analysis (wild, π = 9.5 × 10 −4 versus cultivated, π = 8.6 × 10 −4 ).…”

Section: A R T I C L E Ssupporting

confidence: 88%

“…We identified 3,267 (10% of the total) regulatory genes in carrot, a number similar to that in tomato (3,209 regulatory genes) and rice (3,203 npg regulatory gene expansion, with ~33% of these genes retained after the two carrot WGDs, demonstrating the evolutionary impact of large-scale duplications on plant regulatory network diversity 34 (Supplementary Table 27). Six regulatory gene families involved in lineage-specific duplications were expanded in carrot (Supplementary Table 28).…”

Section: Regulatory Genesmentioning

confidence: 85%

“…2a). Eastern wild accessions were most closely related to cultivated carrots, further demonstrating a primary center of carrot domestication in the Middle East and Central Asia 3 . Cluster analysis showed extensive allelic admixture (Fig.…”

Section: A R T I C L E Smentioning

confidence: 90%

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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

et al. 2016

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5 7Carrot (Daucus carota subsp. carota L.; 2n = 2x = 18) is a globally important root crop whose production has quadrupled between 1976 and 2013 (FAO Statistics; see URLs), outpacing the overall rate of increase in vegetable production and world population growth (FAO Statistics; see URLs) through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions 1 .The first documented colors for domesticated carrot root were yellow and purple in Central Asia approximately 1,100 years ago 2,3 , with orange carrots not reliably reported until the sixteenth century in Europe 4,5 . The popularity of orange carrots is fortuitous for modern consumers because the orange pigmentation results from high quantities of alpha-and beta-carotene, making carrots the richest source of provitamin A in the US diet 6 . Carrot breeding has substantially increased nutritional value, with a 50% average increase in carotene content in the United States as compared to 40 years ago 6 . Lycopene and lutein in red and yellow carrots, respectively, are also nutritionally important carotenoids, making carrot a model system to study storage root development and carotenoid accumulation.Carrot is the most important crop in the Apiaceae family, which includes numerous other vegetables, herbs, spices, and medicinal plants that enhance the epicurean experience 7 , including celery, parsnip, arracacha, parsley, fennel, coriander, and cumin. The Apiaceae family belongs to the euasterid II clade, which includes important crops such as lettuce and sunflower 8 . Genome sequences of euasterid I species have been reported, but only two genomes 9,10 have been published among the other euasterid II species.Here we report a high-quality genome assembly of a doubledhaploid orange carrot, characterization of the mechanism controlling carotenoid accumulation in storage roots, and the resequencing of 35 accessions spanning the genetic diversity of the Daucus genus. Our comprehensive genomic analyses provide insights into the evolution of the asterids and several gene families. These results will facilitate biological discovery and crop improvement in carrot and other crops.A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions caro...

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Section: A R T I C L E Ssupporting

confidence: 88%

Section: Regulatory Genesmentioning

confidence: 85%

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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

et al. 2016

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“…However, this is not always the case, since in some crops, e.g., in carrot (Daucus carota subsp. sativus), no decrease of genetic diversity occurred during domestication (Iorizzo et al 2013).…”

Section: Resultsmentioning

confidence: 99%

New microsatellite loci for annatto (Bixa orellana), a source of natural dyes from Brazilian Amazonia

Dequigiovanni

Ramos

Lopes

et al. 2018

Crop Breed. Appl. Biotechnol.

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“…Furthermore, new mutations may be important and the impact of epigenetic changes remains substantially unexplored. In many self-incompatible crops, such as many fruit trees [108], carrot (Daucus carota) [109], or scarlet runner bean (Phaseolus coccineus [110]), genetic diversity will remain high in cultivated forms and may be equivalent to wild relatives. Furthermore, the practice of grafting may preserve within-individual heterozygosity, while leading to very low stand or population level variation (e.g., [103]).…”

Section: Reduced Genetic Diversity Of Cropsmentioning

confidence: 99%

The Impact of Genetic Changes during Crop Domestication

et al. 2018

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Abstract:Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These "selective sweeps" can allow mildly deleterious...

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Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae)

Cited by 171 publications

References 72 publications

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

New microsatellite loci for annatto (Bixa orellana), a source of natural dyes from Brazilian Amazonia

The Impact of Genetic Changes during Crop Domestication

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