Science · 2017 · 844 citations · 32 references
AgricultureCrop SciencesGeneticsGenomicsPlant GeneticsPlant GenomicsCrop GenomicsFlavor BreedingFlavor ChemistryFlavor DevelopmentFlavor EvaluationFlavor Quality BreedingFlavor IdentificationFlavor PhenotypingFlavor-related Gene DiscoveryGenetic Control Of FlavorHeirloom CropsHeirloom VarietiesPlant Breeding For FlavorVegetable Flavor Improvement
Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavor-associated chemicals in 398 modern, heirloom, and wild accessions. A subset of these accessions was evaluated in consumer panels, identifying the chemicals that made the most important contributions to flavor and consumer liking. We found that modern commercial varieties contain significantly lower amounts of many of these important flavor chemicals than older varieties. Whole-genome sequencing and a genome-wide association study permitted identification of genetic loci that affect most of the target flavor chemicals, including sugars, acids, and volatiles. Together, these results provide an understanding of the flavor deficiencies in modern commercial varieties and the information necessary for the recovery of good flavor through molecular breeding.
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The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text
Haploview: analysis and visualization of LD and haplotype maps
Jeffrey C. Barrett, Ben Fry, Julian Maller et al. · Bioinformatics · 2004 · 14.7K citations · Full text