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Pigmentation in sand pear (Pyrus pyrifolia) fruit: biochemical characterization, gene discovery and expression analysis with exocarp pigmentation mutant

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Abstract

Exocarp color of sand pear is an important trait for the fruit production and has caused our concern for a long time. Our previous study explored the different expression genes between the two genotypes contrasting for exocarp color, which indicated the different suberin, cutin, wax and lignin biosynthesis between the russet- and green-exocarp. In this study, we carried out microscopic observation and Fourier transform infrared spectroscopy analysis to detect the differences of tissue structure and biochemical composition between the russet- and green-exocarp of sand pear. The green exocarp was covered with epidermis and cuticle which was replaced by a cork layer on the surface of russet exocarp, and the chemicals of the russet exocarp were characterized by lignin, cellulose and hemicellulose. We explored differential gene expression between the russet exocarp of ‘Niitaka’ and its green exocarp mutant cv. ‘Suisho’ using Illumina RNA-sequencing. A total of 559 unigenes showed different expression between the two types of exocarp, and 123 of them were common to the previous study. The quantitative real time-PCR analysis supports the RNA-seq-derived gene with different expression between the two types of exocarp and revealed the preferential expression of these genes in exocarp than in mesocarp and fruit core. Gene ontology enrichment analysis revealed divorced expression of lipid metabolic process genes, transport genes, stress responsive genes and other biological process genes in the two types of exocarp. Expression changes in lignin metabolism-related genes were consistent with the different pigmentation of russet and green exocarp. Increased transcripts of putative genes involved the suberin, cutin and wax biosynthesis in ‘Suisho’ exocarp could facilitate deposition of the chemicals and take a role in the mutant trait responsible for the green exocarp. In addition, the divorced expression of ATP-binding cassette transporters involved in the trans-membrane transport of lignin, cutin, and suberin precursors suggests that the transport process could also affect the composition of exocarp and take a role in the regulation of exocarp pigmentation. Results from this study provide a base for the analysis of the molecular mechanism underlying sand pear russet/green exocarp mutation, and presents a comprehensive list of candidate genes that could be used to further investigate the trait mutation at the molecular level.

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Acknowledgments

This study was partially supported by The Special Funds for China “Twelfth Five-Year” National Science and Technology Project for Pear Molecular Breeding and Germplasm Enhancement (2011AA10020602), the Special Funds for China Agriculture Research System (CARS-29-04), The Key Project for New Agricultural Cultivar Breeding in Zhejiang Province, China (2012C112904-2) and The Program for Zhejiang Leading Team of Scientific and Technology Innovation (Grant No. 2009R50033). Fruits of ‘Suisho’ Pear and ‘Niitaka’ Pear used in the study were provided by researcher Yingtao Wang of Fruit Research Institute of Hebei Academy of Agricultural and Forestry Sciences, China. Researcher Yong Li and Dr. Yongbo Wang gave their helps in the materials preparation.

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  1. Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang Province, China

    Yue-zhi Wang, Shujun Zhang, Mei-song Dai & Ze-bin Shi

  2. Jining Forestry Bureau, Jining, 272019, Shandong Province, China

    Shujun Zhang

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  1. Yue-zhi Wang
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Correspondence to Ze-bin Shi.

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Yue-zhi Wang and Shujun Zhang have contributed equally to this work.

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11103_2014_173_MOESM1_ESM.doc

Suppl_Figure 1 Cluster analysis of genes (83 in total) that were differentially expressed between the russet exocarp of ‘Niitaka’ (S3) and the green exocarp of ‘Suisho’ (S4) and verified by the gene expression data for sand pear exocarp russet/green variation. Cluster analysis of genes was performed using Hierarchical cluster analysis. Rows represent differentially expressed genes, columns represent contrast groups. Black and red boxes represent genes showing lower and higher expression level, respectively. The unit of measurement used by Cufflinks to estimate transcript abundance is Fragments Per Kilobase of exon per Million fragments mapped (FPKM). Annotations of genes see Supplemental Table S3 (DOC 77 kb)

11103_2014_173_MOESM2_ESM.doc

Suppl_Figure 2. KEGG pathway of cutin, suberine and wax biosynthesis (ID: ko00073). The arrow indicates the regulation direction of pathways (red) and genes (black) involved in the cutin, suberine and wax biosynthesis in sand pear russet pericarp (expression level of corresponding genes in green exocarp was used as reference) (DOC 303 kb)

11103_2014_173_MOESM3_ESM.doc

Suppl_Figure 3 qRT-PCR analysis of differentially expressed genes detected by the RNA-seq analysis between the exocarps of sand pear cv. ‘Niitaka’ and ‘Suisho’. A1 ~ A3 and B1 ~ B3 represent the exocarp, mesocarp and core of ‘Niitaka’ fruits and ‘Suisho’ fruits, respectively (DOC 1321 kb)

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Wang, Yz., Zhang, S., Dai, Ms. et al. Pigmentation in sand pear (Pyrus pyrifolia) fruit: biochemical characterization, gene discovery and expression analysis with exocarp pigmentation mutant. Plant Mol Biol 85, 123–134 (2014). https://doi.org/10.1007/s11103-014-0173-1

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