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Pear is an important fruit tree that is widely distributed around the world. The first pear genome map was reported from our laboratory approximately 10 years ago. To further study global protein expression patterns in pear, we generated pear proteome data based on 24 major tissues. The tissue-resolved profiles provided evidence of the expression of 17 953 proteins. We identified 4294 new coding events and improved the pear genome annotation via the proteogenomic strategy based on 18 090 peptide spectra with peptide spectrum matches >1. Among the eight randomly selected new short coding open reading frames that were expressed in the style, four promoted and one inhibited the growth of pear pollen tubes. Based on gene coexpression module analysis, we explored the key genes associated with important agronomic traits, such as stone cell formation in fruits. The network regulating the synthesis of lignin, a major component of stone cells, was reconstructed, and receptor-like kinases were implicated as core factors in this regulatory network. Moreover, we constructed the online database PearEXP (http://www.peardb.org.cn) to enable access to the pear proteogenomic resources. This study provides a paradigm for in-depth proteogenomic studies of woody plants. A quantitative atlas of pear proteomes is presented, including 17 953 proteins from 24 tissues. The pear genome annotation is improved based on the 4 294 newly identified coding events. An interactive database, PearEXP (http://www.peardb.org.cn), has been established to facilitate the utilization of the proteomic and genomic information derived from this study. [ABSTRACT FROM AUTHOR]

Pear is one of the most important fruits in the world. In recent years, many new varieties have been bred. However, little is known about these new varieties, including pollen germination, self-(in)compatibility, and the best pollinator for the varieties. In this study, by surveying the length of the pollen tubes that grew into the self styles, pollen germination and self-(in)compatibility of the 127 pear cultivars were determined. All tested pollen germinated on the self stigmas, but the lengths of pollen tube growth into the self styles were different among the pear cultivars. Of these 127 cultivars, 56, 58, and 8 cultivars presented strong, intermediate, and weak self-incompatibility, respectively. Moreover, 5 cultivars presented self-compatibility because their pollen tubes grew to the bottom of the self styles and higher fruit sets with self-pollination were verified in the field. Furthermore, to assign the best pollinator for fruit production and/or new variety breeding, the S-RNase alleles that shared almost identical sequences were integrated together and then re-designated to discern different function-specificity. As a result, the original 68 S-RNase alleles in eastern pear were integrated into 48 re-designated function-specific S-RNase alleles. This integration is promising for assigning the best pollinator for the 36 main pear cultivars in China. Unless the integrated S-RNase alleles, in addition, the S-RNase alleles, which have extremely high identities in amino acid sequences, should be excluded to avoid cross-incompatibility between two parents, leading to poor fruit production and the loss of genetic information in this chromosome [ABSTRACT FROM AUTHOR]

Flower buds are very important for pear yield; non-germinated flower buds become wizened and drop from the branch, reducing pear production. However, little research has focused on the study of wizened flower bud (WB) formation in spring. In order to elucidate the mechanism of WB formation in pear, physiological indices relating to plant hormones and antioxidases were measured. We found that activities of peroxidase (POD) and superoxide dismutase (SOD) were higher and lower, respectively, in WBs than in normal flower buds (NBs). The contents of indole acetic acid (IAA), gibberellin (GA), and cytokinin (CTK) were lower in WBs, while the level of addition of abscisic acid (ABA) was higher in WBs than in NBs. Differentially expressed genes (DEGs) were surveyed between WBs and NBs. In total, 23 DEGs relating to POD and SOD were detected from GO (Gene Ontology) enrichment, and 29 DEGs associated with plant hormone biosynthesis were found from the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway. Notably, the expression patterns of these 52 genes were consistent with variations of antioxidase activities or hormone contents. Because POD and SOD are stress-response enzymes, the differences in POD and SOD activities between NBs and WBs indicated that WB formation in pear could result from ambient environmental stresses that influence expression levels of hormone biosynthesis genes. [ABSTRACT FROM PUBLISHER]

Self-incompatibility is a genetic mechanism in flowering plants that promotes outcrossing and prevents inbreeding. In this study, the reported 15 S-RNase alleles were isolated from 18 pear accessions that contained 14 different S -genotypes. The S-RNase alleles were only expressed in the style, not in the root, stem, leaf, fruit, sepal, and pollen. Pollen tube grew into self-styles and self-pollinated fruit set involved the breakdown of self-incompatibility in cv. Xinxue. However, the two S-RNase alleles in cv. Xinxue had identical amino acid sequences to those self-incompatible cultivars, and S 5 - and S 6 -RNase were normally expressed in style, indicating that the loss of self-incompatibility in cv. Xinxue likely resulted from pollen-part mutation. Further, S 5 S 5 and S 6 S 6 genotyped individuals were identified in self-pollinated progeny, indicating that S 5 and S 6 genotyped pollen were compatible with the self-styles of cv. Xinxue. A genetic analysis showed that the segregation ratio of S 5 S 5 , S 5 S 6 , and S 6 S 6 was approximately 0:2:1 (χ 2  = 3.505 < χ 2 0.05, 2  = 5.99), which did not fit the theoretical ratio of 1:2:1 (χ 2  = 13.340 > χ 2 0.05, 2  = 5.99), suggesting that the breakdown of self-incompatibility could be caused by modified factor(s) located outside of the S -locus. These results are useful for parental assignment and understanding self-incompatibility reaction. [ABSTRACT FROM AUTHOR]

Ein3-binding F-box (EBF) proteins have been determined to modulate ethylene response processes by regulating EIN3/EIL protein degradation in Arabidopsis and tomato. However, the function of pear PbrEBFs in ethylene-dependent responses during fruit ripening remains unclear. In this study, PbrEBF1 , PbrEBF2 , and PbrEBF3 display contrasting expression patterns in response to ethylene and 1-MCP treatment. PbrEBF3 displayed potential fruit ripening-associated function in a transient expression experiment. Yeast two-hybrid (Y2H) and Firefly luciferase complementation imaging (LCI) assays indicated that PbrEBF3 interacts with PbrEIL1, PbrEIL2, and PbrEIL3 proteins. In turn, the transcription of PbrEBF3 is directly regulated by PbrEILs via a feedback loop. PbrEILs trigger a transcriptional cascade of PbrERF24 and finally affect ethylene synthesis. Overall, PbrEBF3 plays a central role in pear fruit ripening through mediation of the ethylene signaling pathway. • PbrEBF3 displayed potential fruit ripening-associated function in transient expression experiments. • PbrEBF3 can interact with EIN3/EIL protein PbrEIL1, PbrEIL2, and PbrEIL3 proteins. • The transcription of PbrEBF3 is directly regulated by PbrEILs via a feedback loop. • PbrEBF3 plays a central role in pear fruit ripening through mediation of the ethylene signaling pathway. [ABSTRACT FROM AUTHOR]

F-box gene family, as one of the largest gene families in plants, plays crucial roles in regulating plant development, reproduction, cellular protein degradation and responses to biotic and abiotic stresses. However, comprehensive analysis of the F-box gene family in pear ( Pyrus bretschneideri Rehd.) and other Rosaceae species has not been reported yet. Herein, we identified a total of 226 full-length F-box genes in pear for the first time. And these genes were further divided into various subgroups based on specific domains and phylogenetic analysis. Intriguingly, we observed that whole-genome duplication and dispersed duplication have a major contribution to F-box family expansion. Furthermore, the dynamic evolution for different modes of gene duplication was dissected. Interestingly, we found that dispersed and tandem duplicate have been evolving at a high rate. In addition, we found that F-box genes exhibited functional specificity based on GO analysis, and most of the F-box genes were significantly enriched in the protein binding (GO: 0005515) term, supporting that F-box genes might play a critical role for gene regulation in pear. Transcriptome and digital expression profiles revealed that F-box genes are involved in the development of multiple pear tissues. Overall, these results will set stage for elaborating the biological role of F-box genes in pear and other plants. [ABSTRACT FROM AUTHOR]

• Pear fruit exhibited a single sigmoid pattern during fruit development. • Fruit size was determined by both of cell number and cell size during fruit development. • 342 differentially expressed genes (DEGs) were screened in the fruits early and late enlargement. • 14 DEGs were located within the reported quantitative trait locus (QTL) regions related to fruit size. Fruit size, one of the crucial traits of fruit, affects pear fruit quality. Usually, both velocity and duration of swelling determines fruit size. However, fruit enlargement studies involving gene regulation during pear fruit development are very limited. In this study, fruit weight, transverse and longitudinal diameters, fruit core, and flesh volume were measured. Cell sizes were presented by paraffin sections, and the number of cells was counted from fruitlet to mature fruit of the CG, XQ, and HS cultivars. Results revealed that pear fruit enlargement was a single sigmoid pattern and was determined by cell number and cell size during fruit development. In addition, transcriptome sequencing was conducted for the fruitlet, early enlargement, late enlargement, and ripening stages. By analyzing the Venn diagram, 156 and 186 differentially expressed genes (DEGs) were selected and identified for the early and late enlargement of pear fruit, respectively. Of these genes, we performed to analysis of gene function annotation and chromosome location. Furthermore, 14 DEGs were located in the reported quantitative trait locus (QTL) regions associated with pear fruit size. Taken together, the results of this study provide information on fruit size from transcriptome analysis and the potential molecular mechanism of candidate genes regulating fruit size in pear. [ABSTRACT FROM AUTHOR]