Although the genome of Chinese white pear (‘Dangshansuli’) has been released, little is known about the functions, evolutionary history and expression patterns of NAC families in this species to date. In this study, we identified a total of 183 NAC transcription factors (TFs) in the pear genome, among which 146 pear NAC (PbNAC) members were mapped onto 16 chromosomes, and 37 PbNAC genes were located on scaffold contigs. No PbNAC genes were mapped to chromosome 2. Based on gene structure, protein motif analysis, and topology of the phylogenetic tree, the pear PbNAC family was classified into 33 groups. By comparing and analyzing the unique NAC subgroups in Rosaceae, we identified 19 NAC subgroups specific to pear. We also found that whole-genome duplication (WGD)/segmental duplication played critical roles in the expansion of the NAC family in pear, such as the 83 PbNAC duplicated gene pairs dated back to the two WGD events. Further, we found that purifying selection was the primary force driving the evolution of PbNAC family genes. Next, we used transcriptomic data to study responses to drought and cold stresses in pear, and we found that genes in groups C2f, C72b, and C100a were related to drought and cold stress response. Through the phylogenetic, evolutionary, and expression analyses of the NAC gene family in Chinese white pear, we indentified 11 PbNAC TFs associated with abiotic stress in pear.

Large quantities of thinned young pears, a natural source of bioactive compounds, are abandoned as agricultural by-products in many orchards. Hence, ten thinned young pear varieties were systematically investigated in terms of their chemical composition and antioxidant potential. Through ultra-performance liquid chromatography coupled with electrospray ionization triple quadrupole mass spectrometry (UPLC-Q TRAP-MS/MS), 102 polyphenols and 16 triterpenoids were identified and individually quantified within a short time using multiple reaction monitoring (MRM). Subsequently, the antioxidant capacities of these pears were determined with DPPH assays, and the correlation between total antioxidant activity and each component was analyzed. The results indicated that the bioactive compound content and antioxidant capacity in thinned pears were considerably high. Regarding chemical composition, chlorogenic acid, quinic acid and arbutin were the primary polyphenols and ursolic acid was the predominant triterpenoid, whereas 27 polyphenolic compounds, especially chlorogenic acid and most of the flavan-3-ols, were the main antioxidants in young pears. These findings should provide a scientific basis for the further use of pear fruit by-products.

Nitrogen (N) is an important element for plant growth, and a suitable N supply is crucial to ensure optimal yields from fruit trees. Frequently, application of N fertilizers to fruit trees is often excessive, which not only leads to environmental pollution, but also reduces the output from fruit trees through N toxicity. To evaluate the effects of different concentrations of nitrate on plant growth, root-morphological traits, and other nutritional element’s responses in pear, pear seedlings (Pyrus betulifolia Bunge) were treated with five levels of N. Both N-deficiency and an excess of N inhibited the growth and development of pear rootstocks. However, different visible symptoms were observed among treated leaves and roots. Leaf yellowing, the stimulation of root elongation, a decrease in nitrate reductase activity and chlorophyll content were observed under N-deficiency conditions. On the other hand, dark green leaves accompanied by coking, the suppression of root elongation, and a decrease in nitrate reductase activity and chlorophyll content were displayed under regimes of excess N. In addition, not only the N content, but also the content of other mineral nutrients was influenced by nitrate treatments. Taken together, these results suggested that a careful choice of N fertilizer supply is crucial to ensure normal growth and development in pear trees.

In plants, ERF genes participate in a variety of regulatory pathways, such as plant growth and biotic and/or abiotic stress responses. Although the genome of Chinese white pear (‘Dangshansuli’) has been released, knowledge regarding the ERF family in pear, such as gene functions, evolutionary history and expression patterns, remains limited. In our study, a total of 155 members of ERF families were identified in pear (Pyrus bretschneideri). The Ka and Ks values suggested that whole-genome duplication (WGD) and dispersed duplication have effectively contributed to the expansion of the pear ERF family. Gene structure and phylogeny analysis divided the PbrERF family into 12 groups, and their gene functions were predicted by comparative analysis. qRT-PCR was carried out to verify the relative expression levels of 7 genes in group III using wild and cultivated pear fruits at three key developmental stages. Wild samples had higher expression of these genes than cultivated samples, especially at the enlarged fruit stage. The transcriptome data of pear seedlings subjected to dehydration treatment further revealed that 4 of the 7 genes responded to drought conditions. The AP2/ERF gene family is greatly expanded in pear. Comparative analysis revealed the probability of ERF genes performing functional roles in multiple pathways. Expression analysis at different stages of pear fruit development in wild and cultivated samples indicated that genes in group III might be involved in abiotic and/or biotic stresses. Further transcriptome data on seedlings subjected to drought treatment verified the potential role of ERF genes in stress response. These results will provide a valuable reference for understanding the function and evolution of the ERF family in higher plants.

To examine the biochemical metabolism of aroma volatiles derived from fatty acids, pear fruits were incubated in vitro with metabolic precursors of these compounds. Aroma volatiles, especially esters, were significantly increased, both qualitatively and quantitatively, in pear fruits fed on fatty acid metabolic precursors. Cultivars having different flavor characteristics had distinctly different aroma volatile metabolisms. More esters were formed in fruity-flavored “Nanguoli” fruits than in green-flavored “Dangshansuli” fruits fed on the same quantities of linoleic acid and linolenic acid. Hexanal and hexanol were more efficient metabolic intermediates for volatile synthesis than linoleic acid and linolenic acid. Hexyl esters were the predominant esters produced by pear fruits fed on hexanol, and their contents in “Dangshansuli” fruits were higher than in “Nanguoli” fruits. Hexyl esters and hexanoate esters were the primary esters produced in pear fruits fed on hexanal, however the content of hexyl ester in “Dangshansuli” was approximately three times that in “Nanguoli”. The higher contents of hexyl esters in “Dangshansuli” may have resulted from a higher level of hexanol derived from hexanal. In conclusion, the synthesis of aroma volatiles was largely dependent on the metabolic precursors presented.

Hybrid crops often exhibit increased yield and greater resilience, yet the genomic mechanism(s) underlying hybrid vigor or heterosis remain unclear, hindering our ability to predict the expression of phenotypic traits in hybrid breeding. Here, we generated haplotype-resolved T2T genome assemblies of two pear hybrid varieties, 'Yuluxiang' (YLX) and 'Hongxiangsu' (HXS), which share the same maternal parent but differ in their paternal parents. We then used these assemblies to explore the genome-scale landscape of allele-specific expression (ASE) and create a pangenome graph for pear. ASE was observed for close to 6000 genes in both hybrid cultivars. A subset of ASE genes related to aspects of fruit quality such as sugars, organic acids, and cuticular wax were identified, suggesting their important contributions to heterosis. Specifically, Ma1, a gene regulating fruit acidity, is absent in the paternal haplotypes of HXS and YLX. A pangenome graph was built based on our assemblies and seven published pear genomes. Resequencing data for 139 cultivated pear genotypes (including 97 genotypes sequenced here) were subsequently aligned to the pangenome graph, revealing numerous structural variant hotspots and selective sweeps during pear diversification. As predicted, the Ma1 allele was found to be absent in varieties with low organic acid content, and this association was functionally validated by Ma1 overexpression in pear fruit and calli. Overall, these results reveal the contributions of ASE to fruit-quality heterosis and provide a robust pangenome reference for high-resolution allele discovery and association mapping.