Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits.

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.

Impact of wild solanaceae rootstocks on morphological and physiological response, yield, and fruit quality of tomato (Solanum lycopersicum L.) grown under deficit irrigation conditions.

It has been established that climate change has a direct impact on water availability, an essential resource for agricultural development. As a result, controlling, mitigating, and adapting to water deficit requires the advancement of research on promising wild flora species. As recent studies have shown, wild relatives of certain cultivars are tolerant to adverse factors, enabling the development of sustainable and resilient agriculture. The present study evaluated the morpho-physiology and productivity of tomato scions grafted on wild Solanaceae (Datura stramonium, Solanum sisymbriifolium, Solanum quitoense, and Cyphomandra betacea) grown under water deficit conditions (100% ETc - high level, 75% ETc - moderate level, 50% ETc - medium level, and 25% ETc - low level). The results showed that tomato plants grafted on Datura stramonium rootstocks performed better morpho-physiologically under deficit irrigation. The improved osmoregulation caused by a higher relative water content (98.49%) allowed the scion to be more tolerant to water stress. In addition, these scions showed high water potential during their phenological stages (vegetative -0.47 MPa, flowering -0.59 MPa, and production -0.64 MPa), as well as improved photosynthetic efficiency. The overall tolerance of the scion resulted in better yield (8.14 kg/plant) with higher number of commercially valuable fruits. The D. stramonium rootstock allowed better management and use of irrigation water, increasing productivity (54.95 kg/m3); that is, it is presented as a species with potential for establishing tomato production areas in scenarios of water scarcity or cultivation under deficit irrigation.

Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple (Malus × domestica Borkh.).

Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01382-w.

Pomegranate morpho-chemodiversity: computational investigations based on in-vivo and in-vitro screening.

Pomegranate tree is cultivated since ancient times in Morocco, where a high genetic diversity is hosted mainly in traditional agroecosystems. Over the past decade, it regained importance through extension of cultivated area, but remains thus far little valued. To date, its genetic variability and chemodiversity have gone unheeded for many reasons, some of which are related to previous agricultural strategies. In this context, the present study aimed to screen an ex-situ collection of seven local cultivars and seven exotic varieties with regard to 50 fruit morphometric and biochemical descriptors. The results showed statistically significant variability within accessions (p < 0.01), based on all aforementioned traits, except for seed weight, with coefficients of variation greater than 49%. This indicated a high level of phenotypic diversity among the studied genetic pool. The 3D scatter plot built based on the principal component analysis displayed an interesting discrimination with regard to the genotypes' geographic origins with a total variance of about 50%. According to morphometric based-heatmap, four main clusters were identified distinguishing the typicality of some local cultivars compared to exotic varieties, mainly 'Sefri', 'Bzou', 'Chioukhi' and 'Djeibi'. Traits having the highest impact on discrimination between accessions were, by order of importance, fruit weight and its dimensions, juice yield, aril yield, single aril diameter, soluble sugars (glucose and fructose) along with contents in some organic acids, including citric, palmitic, linoleic and malic acids. Potential statistically significant correlations were spotted through bi-dimensional heatmap analysis, particularly between the fruit size, shape and peel traits along with some biochemical attributes. As many areas of the species chemodiversity and functional properties are still needed to be investigated further, the results of the present study are of great interest for the species valorization and for breeding programs.

Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci Linked to Fruit Quality Traits in Apricots Using Specific-Locus Amplified Fragment Sequencing.

Improving fruit quality is one of the main tasks in modern commercial apricot breeding. Because of the lack of high-density linkage maps and fine mapping, it is difficult to obtain molecular markers that can assist in breeding for quantitative inheritance of fruit quality traits. In this study, specific-locus amplified fragment sequencing was used to genotype 169 seedlings of F1 apricot (Prunus armeniaca L.) progenies derived from crossing "Chuanzhihong" (H) with "Saimaiti" (S). After aligning to the Prunus armeniaca reference genome and filtering out low-quality variants, 6,012 high-quality single nucleotide polymorphisms were obtained and employed to construct a genetic map for each parent. The genetic linkage maps showed eight linkage groups of apricot, covering a distance of 809.6 cM in "H" and 1076.4 cM in "S". The average distance between markers in "H" and "S" was 0.62 and 0.95 cM, respectively. To map quantitative trait loci (QTLs) for fruit quality, we investigated fruit quality traits, including fruit weight (FW), fruit height (FH), fruit lateral width (FL), fruit ventral width (FV), soluble solids content (SSC), and fruit firmness (FF) for all seedlings genotyped in 2018 and 2019. Eleven and nine QTLs linked to fruit quality traits were anchored on the "H" and "S" maps, respectively, and 1,138 putative candidate genes for 16 most significant regions on the corresponding chromosome were identified based on gene annotation. Among them, fruit size contained 648 genes in 11 intervals on the reference genome, SSC contained 372 genes in 3 intervals, and FF contained 117 genes in 2 intervals. Our findings uncovered the genetic basis of apricot fruit quality, and provided candidate genes for further molecular genetic studies on fruit quality and QTL targets for future marker-assisted selection of apricot quality improvement breeding.

Preliminary Insights in Sensory Profile of Sweet Cherries.

Sweet cherry (Prunus avium L.) is a fruit appreciated by consumers for its well-known physical and sensory characteristics and its health benefits. Being an extremely perishable fruit, it is important to know the unique attributes of the cultivars to develop cultivation or postharvest strategies that can enhance their quality. This study aimed to understand the influence of physicochemical characteristics of two sweet cherry cultivars, Burlat and Van, on the food quality perception. Several parameters (weight, dimensions, soluble solids content (SSC), pH, titratable acidity (TA), colour, and texture) were measured and correlated with sensory data. Results showed that cv. Van presented heavier and firmer fruits with high sugar content. In turn, cv. Burlat showed higher pH, lower TA, and presented redder and brightest fruits. The principal component analysis revealed an evident separation between cultivars. Van cherries stood out for their sensory parameters and were classified as more acidic, bitter, and astringent, and presented a firmer texture. Contrarily, Burlat cherries were distinguished as being more flavourful, succulent, sweeter, and more uniform in terms of visual and colour parameters. The results of the sensory analysis suggested that perceived quality does not always depend on and/or recognize the quality parameters inherent to the physicochemical characteristics of each cultivar.

Transcriptomic analysis of a near-isogenic line of melon with high fruit flesh firmness during ripening.

BACKGROUND: A near-isogenic line (NIL) of melon (SC10-2) with introgression in linkage group X was studied from harvest (at firm-ripe stage of maturity) until day 18 of postharvest storage at 20.5 °C together with its parental control ('Piel de Sapo', PS). RESULTS: SC10-2 showed higher flesh firmness and whole fruit hardness but lower juiciness than its parental. SC10-2 showed a decrease in respiration rate accompanied by a decrease in ethylene production during ripening, both of which fell to a greater extent than in PS. The introgression affected 11 volatile organic compounds (VOCs), the levels of which during ripening were generally higher in SC10-2 than in PS. Transcriptomic analysis from RNA-Seq revealed differentially expressed genes (DEGs) associated with the effects studied. For example, 909 DEGs were exclusive to the introgression, and only 23 DEGs were exclusive to postharvest ripening time. Major functions of the DEGs associated with introgression or ripening time were identified by cluster analysis. About 37 genes directly and/or indirectly affected the delay in ripening of SC10-2 compared with PS in general and, more particularly, the physiological and quality traits measured and, probably, the differential non-climacteric response. Of the former genes, we studied in more detail at least five that mapped in the introgression in linkage group (LG) X, and 32 outside it. CONCLUSION: There is an apparent control of textural changes, VOCs and fruit ripening by an expression quantitative trait locus located in LG X together with a direct control on them due to genes presented in the introgression (CmTrpD, CmNADH1, CmTCP15, CmGDSL esterase/lipase, and CmHK4-like) and CmNAC18. © 2020 Society of Chemical Industry.

Phenotypic and Molecular Selection of a Superior Solanum pennellii Introgression Sub-Line Suitable for Improving Quality Traits of Cultivated Tomatoes.

The Solanum pennellii Introgression Line (IL) population can be exploited to identify favorable alleles that can improve yield and fruit quality traits in commercial tomato varieties. Over the past few years, we have selected ILs that exhibit increased content of antioxidant compounds in the fruit compared to the cultivar M82, which represents the genetic background in which the different wild regions of the S. pennellii ILs were included. Recently, we have identified seven sub-lines of the IL7-3 accumulating different amounts of antioxidants in the ripe fruit. Since the wild region carried on chromosome 7 induces a low fruit production in IL7-3, the first aim of the present work was to evaluate yield performances of the selected sub-lines in three experimental fields located in the South of Italy. Another aim was to confirm in the same lines the high levels of antioxidants and evaluate other fruit quality traits. On red ripe fruit, the levels of soluble solids content, firmness, and ascorbic acid (AsA) were highly variable among the sub-lines grown in three environmental conditions, evidencing a significant genotype by environment interaction for soluble solids and AsA content. Only one sub-line (coded R182) exhibited a significantly higher firmness, even though no differences were observed for this trait between the parental lines M82 and IL7-3. The same sub-line showed significantly higher AsA content compared to M82, thus resembling IL7-3. Even though IL7-3 always exhibited a significantly lower yield, all the sub-lines showed yield variability over the three trials. Interestingly, the sub-line R182, selected for its better performances in terms of fruit quality, in all the trials showed a production comparable to that of the control line M82. A group of species-specific molecular markers was tested on R182 and on the parental genotypes in order to better define the wild genomic regions carried by the elite line R182. In these regions three candidate genes that could increase the level of AsA in the fruit were identified. In the future, the line R182 could be used as pre-breeding material in order to obtain new varieties improved for nutritional traits.

Mediterranean Long Shelf-Life Landraces: An Untapped Genetic Resource for Tomato Improvement.

The Mediterranean long shelf-life (LSL) tomatoes are a group of landraces with a fruit remaining sound up to 6-12 months after harvest. Most have been selected under semi-arid Mediterranean summer conditions with poor irrigation or rain-fed and thus, are drought tolerant. Besides the convergence in the latter traits, local selection criteria have been very variable, leading to a wide variation in fruit morphology and quality traits. The different soil characteristics and agricultural management techniques across the Mediterranean denote also a wide range of plant adaptive traits to different conditions. Despite the notorious traits for fruit quality and environment adaptation, the LSL landraces have been poorly exploited in tomato breeding programs, which rely basically on wild tomato species. In this review, we describe most of the information currently available for Mediterranean LSL landraces in order to highlight the importance of this genetic resource. We focus on the origin and diversity, the main selective traits, and the determinants of the extended fruit shelf-life and the drought tolerance. Altogether, the Mediterranean LSL landraces are a very valuable heritage to be revalued, since constitutes an alternative source to improve fruit quality and shelf-life in tomato, and to breed for more resilient cultivars under the predicted climate change conditions.