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The apple (Malus × domestica Borkh.) is an economically and culturally important crop grown worldwide. Growers of this long-lived perennial must produce fruit of adequate quality while also combatting abiotic and biotic stress. Traditional apple breeding can take up to 20 yr from initial cross to commercial release, but genomics-assisted breeding can help accelerate this process. To advance genomics-assisted breeding in apple, we performed genome-wide association studies (GWAS) and genomic prediction in a collection of 172 apple accessions by linking over 55,000 single nucleotide polymorphisms (SNPs) with 10 phenotypes collected over 2 yr. Genomewide association studies revealed several known loci for skin color, harvest date and firmness at harvest. Several significant GWAS associations were detected for resistance to a major fungal pathogen, apple scab (Venturia ineaqualis [Cke.] Wint.), but we demonstrate that these hits likely represent a single ancestral source. Using genomic prediction, we show that most phenotypes are sufficiently predictable using genome-wide SNPs to be candidates for genomic selection. Finally, we detect a signal for firmness retention after storage on chromosome 10 and show that it may not stem from variation in PG1, a gene repeatedly identified in bi-parental mapping studies and widely believed to underlie a major QTL for firmness on chromosome 10. We provide evidence that this major QTL is more likely due to variation in a neighboring ethylene response factor (ERF) gene. The present study showcases the superior mapping resolution of GWAS compared to bi-parental linkage mapping by identifying a novel candidate gene underlying a well-studied, major QTL involved in apple firmness.

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Cut tissues from distinct anatomical locations in iceberg lettuce (Lactuca sativa L.) were subjected to washing in cold (4 degrees C) and warm (47 degrees C) water with or without chlorine to assess their propensity to discoloration during storage. Total protein (Bradford method) and phenolic (TPH; Folin-Ciocalteu method) contents and polyphenol oxidase (PPO; spectrophotometric method using catechol as a substrate), peroxidase (POD; guaiacol substrate), and phenylalanine ammonia-lyase (PAL; phenylalanine substrate) activities were determined in photosynthetic and vascular tissue from outer and inner leaves. Unprocessed photosynthetic and inner leaf tissues had significantly higher (P < 0.05) levels of protein and TPH and PPO and POD activities than vascular and outer leaf tissues. PAL activities (on a fresh weight basis) were similar in all tissues. Changes in browning (light reflectance measurement) and phenolic metabolism in all four tissue types were observed during aerobic storage at 5 degrees C over 10 days. PAL activity increased in all tissues after 1-2 days of storage and then gradually decreased. POD activity also increased steadily for the storage duration. Protein content and PPO activity remained constant. Edge browning (measured with a Minolta Chroma Meter) and TPH increased in all tissues, especially in outer vascular tissue. Cut photosynthetic and vascular tissues washed at 4 and 47 degrees C with and without 100 microg mL(-1) chlorine for 3 min were analyzed during 7 days in storage at 5 degrees C. Enzyme activities and accumulation of phenolics in all tissues washed at 47 degrees C were significantly (P < 0.05) lower compared to controls or tissues washed at 4 degrees C. Chlorine had no additional effect at 47 degrees C but significantly (P < 0.05) reduced browning and accumulation of phenolics in lettuce washed at 4 degrees C. These results showed that inherent differences between tissues affect phenolic metabolism and browning in stored, fresh-cut lettuce.

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