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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Publications at this Location » Publication #322635

Title: Apple function genomics: from fruit to root

item Zhu, Yanmin

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/12/2014
Publication Date: 10/14/2014
Citation: Zhu, Y. 2014. Apple function genomics: from fruit to root. Meeting Abstract. n/a.

Interpretive Summary:

Technical Abstract: The genotype-specific fruit ripening patterns of apple (Malus x domestica Borkh) are closely associated with the at-harvest quality and the post-harvest storability. To elucidate the molecular networks and identify the key genes regulating apple fruit maturation and ripening processes, large-scale approaches such as microarray and RNA-seq technology as well as candidate gene based methods have been used to uncover the underlying molecular mechanisms controlling fruit ripening patterns, texture, flavor and storability. Using custom-made NimbleGen high-density long-oligo apple microarray which included 23,999 apple unigenes, a comparative transcriptomics on the maturation progression was performed on two distinct apple cultivars “Honeycrisp” and “Cripps Pink”. Multiple pathways related to auxin, jasmonate and gibberellin signaling and cell wall metabolisms appear to be critical in regulating cultivar-specific fruit ripening and texture changes. Related to this analysis, based on the expression patterns of an apple pre-climacteric ethylene biosynthesis gene, MdACS3, among 12 apple cultivars; the observations suggest that MdACS3 acts as an apple fruit ripening “accelerator” through timely activation of MdACS1expression, which is responsible for apple climacteric ethylene biosynthesis. Based on the results of transcriptome analysis, the studies on eight candidate genes with annotated function in auxin transport and homeostasis suggest that auxin plays a role in signaling the regulation of timing for ethylene pathway activation through interaction with MdACS3. Genome-wide identification of fruit tissues expressed jasmonate biosynthetic genes and their expression profiles during apple fruit maturation also suggest that MdACS3 interact with JA in determining genotype-specific fruit ripening progression. Very limited information on the defense responses of plant root tissue to soilborne pathogens is available, particularly so for perennial tree crops such as apple. Apple replant disease (ARD) is caused by a complex of soilborne necrotrophic fungi and oomycetes including P. ultimum. High-resolution transcriptome profiling using a large-scale and high-throughput RNA-seq technology, the molecular networks regulating defense responses in apple root tissue during infection by P. ultimum was investigated. Differentially expressed genes functioning in plant hormone signaling such as the jasmonate and ethylene pathways, secondary metabolisms and defense related proteins appeared to be the major molecular framework of apple root defense action to soil borne pathogens. Tissue-culture based procedures are being used to generate genetically uniform seedlings from multiple rootstock germplasm, such as the core apple rootstock genotypes of M26, B9, M9, G41, G935 and G214 and more than 90 individual genotypes from ‘Ottawa 3’ × ‘Robusta 5’ for subsequent comparative transcriptomics and genotype-phenotype association.