Identification and Characterization of ABCG15-A Gene Required for Exocarp Color Differentiation in Pear.

Exocarp color is a commercially essential quality for pear which can be divided into two types: green and russet. The occurrence of russet color is associated with deficiencies and defects in the cuticular and epidermal layers, which affect the structure of the cell wall and the deposition of suberin. Until now, the genetic basics triggering this trait have not been well understood, and limited genes have been identified for the trait. To figure out the gene controlling the trait of exocarp color, we perform a comprehensive genome-wide association study, and we describe the candidate genes. One gene encoding the ABCG protein has been verified to be associated with the trait, using an integrative analysis of the metabolomic and transcriptomic data. This review covers a variety of omics resources, which provide a valuable resource for identifying gene-controlled traits of interest. The findings in this study help to elucidate the genetic components responsible for the trait of exocarp color in pear, and the implications of these findings for future pear breeding are evaluated.

Changes of Volatile Organic Compounds of Different Flesh Texture Pears during Shelf Life Based on Headspace Solid-Phase Microextraction with Gas Chromatography-Mass Spectrometry.

Aroma is an important sensory factor in evaluating the quality of pear fruits. This study used headspace solid-phase microextraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS) to analyze the volatile organic compounds (VOCs) of three crispy pears and five soft pears during shelf life, and the changes in soluble solids content (SSC) were analyzed. The results showed that the SSC of the soft pears such as Nanguoli, Jingbaili and Louis was always higher than that of the crispy pears throughout shelf life. A total of 160 VOCs were detected in the eight pear varieties. Orthogonal partial least squares discriminant analysis (OPLS-DA) and hierarchical cluster analysis (HCA) combined with predictor variable importance projection (VIP) showed that the eight pear varieties could be obviously classified into six groups according to the differences in their VOCs, and 31 differential VOCs were screened out, which could be used to differentiate between pears with different flesh textures. The results of clustering heat map analysis showed that, with the extension of shelf life, the content of each different VOC did not change much in crispy pears, whereas the difference in soft pears was larger. This study confirmed the potential of determining the optimal shelf life of different pear varieties about aroma evaluation and studying the mechanism of differences in VOCs in the future.

Metabolomic and transcriptomic analyses highlight the influence of lipid changes on the post-harvest softening of Pyrus ussurian Max. 'Zaoshu Shanli'.

How lipids influence post-harvest softening in pears is not well understood. LC-MS/MS (Liquid chromatography-tandem mass spectrometry) and RNA-Seq analyses of 'Zaoshu Shanli' (ZSSL) pears were conducted during post-harvest storage. This approach enabled the identification of 98 different metabolites that upregulated and 95 that downregulated at 18 days post-harvest in ZSSL fruits to day 0. Metabolites were significantly enriched in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways including glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis. When comparing fruits from day 18 to those from day 0 post-harvest, RNA-seq analyses further highlighted 6496 differentially expressed genes (DEGs) in ZSSL fruits that were significantly enriched in KEGG pathways including glycerophospholipid metabolism and fatty acid degradation. Overall, these results suggested that glycerophospholipid metabolism is closely related to the post-harvest softening of pears. Further research will be essential in order to fully explore the functional implications of and mechanistic basis for these findings.

[Prediction of potential geographical distribution patterns of Pyrus xerophila under different climate scenarios.] / ä¸åŒæ°”å€™æƒ æ™¯ä¸‹æœ¨æ¢¨æ½œåœ¨åœ°ç†åˆ†å¸ƒæ ¼å±€å˜åŒ–çš„é¢„æµ‹.

Pyrus xerophila has strong resistance to drought, cold, salt, and rust. It is one of the main rootstock types of pear in Northwest China, with high production value. However, its habitat is seriously damaged. The prediction of the geographical distribution of P. xerophila under different climate scenarios will provide important scientific basis for rational development and utilization of resources and the protection of diversity. Based on MaxEnt model and ArcGIS spatial analysis, the potential spatial distribution pattern of P. xerophila in the current and future (2050, 2070) was constructed using comprehensive and accurate distribution records and high-resolution environmental data, and the relative importance of environmental factors was evaluated. The results showed that the suitable habitat area of P. xerophila was 3.32×105 km2, mainly located in eastern Qinghai, southern Gansu, southern Ningxia, central Shaanxi, southern Shanxi and western Henan. Mean UV-B of the month with lowest UV-B and altitude were identified as the critical factors shaping habitat availability for P. xerophila. Overall, with global warming, the potential habitat for P. xerophila might decrease in 2050 and 2070 under different CO2 climate scenarios. Real-time monitoring of P. xerophila populations should be enhanced.

De novo assembly of a wild pear (Pyrus betuleafolia) genome.

China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide-binding site (NBS)-type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR-NBS-LRR (TNL)-type genes, which represented the greatest number of TNL-type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism-related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high-quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.

Postharvest metabolomic changes in Pyrus ussuriensis Maxim. wild accession 'Zaoshu Shanli'.

There are strong economic drivers for understanding the process of fruit post-harvest softening. In this study, liquid chromatography with electrospray ionization tandem mass spectrometry was used to analyze metabolite changes in 'Zaoshu Shanli' fruit after different storage periods; this wild accession of Pyrus ussuriensis presents good fruit quality and relatively low flesh firmness after fruit storage. The lipid metabolites in 'Zaoshu Shanli' fruit were significantly higher at 18 days of storage compared with those at 0 days of storage, and glycerophospholipid metabolism was different metabolic pathway. It was therefore speculated that lipid metabolism play an important role in pear fruit post-harvest processes and softening. Furthermore, the abscisic acid and trans-zeatin contents in 'Zaoshu Shanli' fruit at 18 days of storage were significantly greater than those at 0 days of storage. Therefore, it was speculated that the abovementioned hormones play an important role in pear fruit post-harvest softening. Together, these results provide fundamental insight into the reasonable control of pear fruit post-harvest softening and lay a solid foundation for additional research.

Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia.

Asian pear plays an important role in the world pear industry, accounting for over 70% of world total production volume. Commercial Asian pear production relies on four major pear cultivar groups, Japanese pear (JP), Chinese white pear (CWP), Chinese sand pear (CSP), and Ussurian pear (UP), but their origins remain controversial. We estimated the genetic diversity levels and structures in a large sample of existing local cultivars to investigate the origins of Asian pears using twenty-five genome-covering nuclear microsatellite (simple sequence repeats, nSSR) markers and two non-coding chloroplast DNA (cpDNA) regions (trnL-trnF and accD-psaI). High levels of genetic diversity were detected for both nSSRs (HE = 0.744) and cpDNAs (Hd = 0.792). The major variation was found within geographic populations of cultivated pear groups, demonstrating a close relationship among cultivar groups. CSPs showed a greater genetic diversity than CWPs and JPs, and lowest levels of genetic differentiation were detected among them. Phylogeographical analyses indicated that the CSP, CWP, and JP were derived from the same progenitor of Pyrus pyrifolia in China. A dissemination route of cultivated P. pyrifolia estimated by approximate Bayesian computation suggested that cultivated P. pyrifolia from the Middle Yangtze River Valley area contributed the major genetic resources to the cultivars, excluding those of southwestern China. Three major genetic groups of cultivated Pyrus pyrifolia were revealed using nSSRs and a Bayesian statistical inference: (a) JPs; (b) cultivars from South-Central China northward to northeastern China, covering the main pear production area in China; (c) cultivars from southwestern China to southeastern China, including Yunnan, Guizhou, Guangdong, Guangxi, and Fujian Provinces. This reflected the synergistic effects of ecogeographical factors and human selection during cultivar spread and improvement. The analyses indicated that UP cultivars might be originated from the interspecific hybridization of wild Pyrus ussuriensis with cultivated Pyrus pyrifolia. The combination of uniparental DNA sequences and nuclear markers give us a better understanding of origins and genetic relationships for Asian pear groups and will be beneficial for the future improvement of Asian pear cultivars.

[Leaf morphology and photosynthetic characteristics of wild Ussurian pear in China].

The wild Ussurian pear was the most important wild pear resource in northern China, belonging to the most hardiness species. Taking 48 accessions of wild Ussurian pear and 2 accessions of cultivated Ussurian pear as test materials, this paper studied the morphology of leaves, chlorophyll content, and photosynthetic characteristics. We compared the difference between the wild and cultivated Ussurian pear, analyzed the photosynthetic characteristics of wild Ussurian pear, clarified the interrelationships between the indices, and established significant linear equations of photosynthesis and water-related physiological indices. The results showed that the leaf morphological index, chlorophyll content and photosynthetic indices for cultivated Ussurian pear were significantly lower than their average values for wild Ussurian pear. The specific leaf area (SLA), leaf dry matter content ( LDMC) , and intercellular CO2 concentration had low coefficients of variation, and the other 8 indices had variation coefficient indices between 0.12-0.41. So, the level of diversity was high, indicating obvious difference in photosynthetic characteristic of wild pear resources in China. The photosynthetic indices were significantly correlated with chlorophyll composition (Chl a/b) and LDMC. The photosynthetic rate had significant exponential correlation with the intercellular CO2 concentration, transpiration rate, and stomatal conductance. The photosynthetic rate was mainly affected by stomatal limitation. The wild variety 'Jinzhoushanli' was selected as high photosynthetic genetic resource.

Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli' (Pyrus sinkiangensis Yu) by digital transcript abundance measurements.

BACKGROUND: 'Kuerlexiangli' (Pyrus sinkiangensis Yu), a native pear of Xinjiang, China, is an important agricultural fruit and primary export to the international market. However, fruit with persistent calyxes affect fruit shape and quality. Although several studies have looked into the physiological aspects of the calyx abscission process, the underlying molecular mechanisms remain unknown. In order to better understand the molecular basis of the process of calyx abscission, materials at three critical stages of regulation, with 6000 × Flusilazole plus 300 × PBO treatment (calyx abscising treatment) and 50 mg.L-1GA3 treatment (calyx persisting treatment), were collected and cDNA fragments were sequenced using digital transcript abundance measurements to identify candidate genes. RESULTS: Digital transcript abundance measurements was performed using high-throughput Illumina GAII sequencing on seven samples that were collected at three important stages of the calyx abscission process with chemical agent treatments promoting calyx abscission and persistence. Altogether more than 251,123,845 high quality reads were obtained with approximately 8.0 M raw data for each library. The values of 69.85%-71.90% of clean data in the digital transcript abundance measurements could be mapped to the pear genome database. There were 12,054 differentially expressed genes having Gene Ontology (GO) terms and associating with 251 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. The differentially expressed genes correlated with calyx abscission were mainly involved in photosynthesis, plant hormone signal transduction, cell wall modification, transcriptional regulation, and carbohydrate metabolism. Furthermore, candidate calyx abscission-specific genes, e.g. Inflorescence deficient in abscission gene, were identified. Quantitative real-time PCR was used to confirm the digital transcript abundance measurements results. CONCLUSIONS: We identified candidate genes that showed highly dynamic changes in expression during the calyx abscission process. These genes are potential targets for future functional characterization and should be valuable for exploration of the mechanisms of calyx abscission, and eventually for developing methods based on small molecule application to induce calyx abscission in fruit production.

Evaluation of the volatile profile of 33 Pyrus ussuriensis cultivars by HS-SPME with GC-MS.

Evaluation of the volatile compounds in fruit provides useful information for plant breeding for improved fruit aroma. In this study, headspace solid-phase microextraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS) was used to assess the volatile profile of 33 cultivars of the Chinese pear Pyrus ussuriensis. In all, 108 volatile compounds were identified and there were significant differences in the composition and concentration of volatiles among cultivars. On the basis of principal components analysis (PCA), the cultivars could be divided into four groups: Group 1 contained Reli, Jinxiang, Hongbalixiang, Baibalixiang and Fuwuxiang, cultivars with a high concentration of esters and a low concentration of hydrocarbons. Group 2 contained Qiuxiang, Fuanjianba, Longxiang, Guanhongxiao, Shanli24 and Wuxiangli, cultivars with high concentrations of hydrocarbons and low concentrations of esters. Group 3 contained Shatangli and Manyuanxiang, cultivars with high concentrations of aldehydes. Group 4 contained the other 25 cultivars.

Molecular identification of two new self-incompatible alleles (S-alleles) in Chinese pear (Pyrus bretschneideri).

Self-incompatibility (SI) is an important intraspecific reproductive barrier in flowering plants. To identify the S-alleles of Chinese pear species (Pyrus pyrifolia, P. bretschneideri, P. ussuriensis and P. sinkiangenis etc.), S-RNase-specific PCR amplification, sequence analyses and field pollination tests were performed using two cultivars 'Jingxiang' and 'Esu' of P. bretschneideri as materials. Two new S-RNase genes were identified from the two cultivars. They were 1,122 bp and 1,058 bp in length, and designated as S37-RNase (GenBank accession no. DQ839238) and S38-RNase (GenBank accession no. DQ839239). By comparison of their deduced amino acid sequences with those of S1-to S36-alleles of Oriental pear, it can be seen that both the two new S-alleles had their conserved regions C1 and C2, but their hypervariable regions (HV) were quite different from those of the others. S37 showed a higher similarity (96%) to S38 in the amino acid sequences deduced from them, whereas both of them displayed the highest similarity (98%) to S15 and the lowest (63%) to S32. The two S-alleles had introns of 786 bp and 723 bp, respectively, similar in size to that of S15 (777 bp). Finally, the S-genotypes of 'Jinxiang' and 'Esu' were unambiguously determined as S34S37 and S15S38, respectively.