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Allele-specific gene responses are picked up in this workflow as gene loci displaying genotype-specific differential expression that often have single amino acid polymorphisms. If the resources are sufficient, a genotype-specific mRNAseq database is recommended where a link is made to the allele-specific transcription levels. If the resources are limited, allele-specific proteins can be detected by the detection of genotype-specific peptides and the identification against existing genomics libraries of the parents.Tomato is a major crop
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