Transcriptome profiling of cultivar-specific apple fruit ripening and texture attributes

Molecular events regulating apple fruit ripening and sensory quality are largely unknown. Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, Honeycrisp (HC) and Cripps Pink (CP), which have distinct ripening features and texture attributes. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and representing 23,997 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes. Using a single color labeling system, a total of 24 microarray slides were utilized, one for each cortex tissue sample, for transcriptome profiling analysis. 2 cultivars x 3 developmental stages x 4 biological replicates.

调控苹果果实成熟与感官品质的分子机制目前仍未得到充分阐明。此类研究认知对于基因组辅助苹果育种与采后品质管理均具有重要意义。本研究针对成熟特性与质地属性存在显著差异的两个苹果品种——蜜脆（Honeycrisp, HC）与粉红佳人（Cripps Pink, CP），开展了平行转录组谱分析、扫描电子显微镜（scanning electron microscopy, SEM）检测及系统性生理特性表征。基于每周采集的成熟度数据对果实成熟过程进行系统性生理表征，结果显示在同等成熟阶段，两个品种的果实脆度与硬度存在显著差异。对同等成熟度果实的皮层组织进行扫描电镜观察发现，细胞壁厚度或与观测到的果实硬度及脆度表型密切相关。本研究在NimbleGen芯片平台上制备了一款高密度长寡核苷酸苹果基因芯片：该芯片包含190,135对无交叉杂交的50~70-mer等温探针，可覆盖23,997个UniGene簇（UniGene clusters）。转录组谱分析结果显示，在蜜脆与粉红佳人的皮层组织中，分别有1793个和1209个UniGene簇在果实成熟过程中呈现差异表达。参与激素代谢与响应、细胞壁生物合成与修饰，以及编码转录因子的UniGene均属于显著富集的功能类群。两个品种间多数鉴定出的UniGene在果实成熟过程中的表达调控模式相似；但存在一小部分基因家族或特定家族成员在两品种间呈现出截然不同的表达模式，此类基因或可作为调控品种特异性苹果果实成熟模式与品质属性的候选基因。本研究采用单颜色标记系统，共使用24张基因芯片对皮层组织样本进行转录组谱分析，样本分组为2个品种×3个发育阶段×4次生物学重复。