Fleshy fruit traits and seed dispersers: which traits define syndromes?

BACKGROUND AND AIMS: Fruit traits and their inter-relationships can affect foraging choices by frugivores, and hence the probability of mutualistic interactions. Certain combinations of fruit traits that determine the interaction with specific seed dispersers are known as dispersal syndromes. The dispersal syndrome hypothesis (DSH) states that seed dispersers influence the combination of fruit traits found in fruits. Therefore, fruit traits can predict the type of dispersers with which plant species interact. Here, we analysed whether relationships of fruit traits can be explained by the DSH. To do so, we estimated the inter-relationships between morphological, chemical and display groups of fruit traits. In addition, we tested the importance of each trait group defining seed dispersal syndromes. METHODS: Using phylogenetically corrected fruit trait data and fruit-seed disperser networks, we tested the relationships among morphological, chemical and display fruit traits with Pearson's correlations and phenotypic integration indices. Then, we used perMANOVA to test if the fruit traits involved in the analysis supported the functional types of seed dispersers. KEY RESULTS: Morphological traits showed strong intragroup relationships, in contrast to chemical and display traits whose intragroup trait relationships were weak or null. Accordingly, only the morphological group of traits supported three broad seed disperser functional types (birds, terrestrial mammals and bats), consistent with the DSH. CONCLUSIONS: Altogether, our results give some support to the DSH. Here, the three groups of traits interacted in different ways with seed disperser biology. Broad functional types of seed dispersers would adjust fruit consumption to anatomical limitations imposed by fruit morphology. Once this anatomical filter is sovercome, seed dispersers use almost all the range of variation in chemical and display fruit traits. This suggests that the effect of seed dispersers on fruit traits is modulated by hierarchical decisions. First, morphological constraints define which interactions can actually occur; subsequently, display and composition determine fruit preferences.

Mapping of genetic loci controlling fruit linked morphological traits of melon using developed CAPS markers.

BACKGROUND: Fruit morphology traits are important commercial traits that directly affect the market value. However, studying the genetic basis of these traits in un-explored botanical groups is a fundamental objective for crop genetic improvement through marker-assisted breeding. METHODS AND RESULTS: In this study, a quantitative trait loci (QTLs) mapping strategy was used for dissecting the genomic regions of fruit linked morphological traits by single nucleotide polymorphism (SNP) based cleaved amplified polymorphism sequence (CAPS) molecular markers. Next-generation sequencing was done for the genomic sequencing of two contrasted melon lines (climacteric and non-climacteric), which revealed 97% and 96% of average coverage over the reference melon genome database, respectively. A total of 57.51% non-synonymous SNPs and 42.49% synonymous SNPs were found, which produced 149 sets of codominant markers with a 24% polymorphism rate. Total 138-F2 derived plant populations were genotyped for linkage mapping and composite interval mapping based QTL mapping exposed 6 genetic loci, positioned over distinct chromosomes (02, 04, 08, 09, and 12) between the flanking intervals of CAPS markers, which explained an unlinked polygenic architecture in genome. Three minor QTLs of fruit weight (FWt2.1, FWt4.1, FWt9.1), one major QTL of fruit firmness (FrFir8.1), one major QTL of fruit length (FL12.1), and one major QTL of fruit shape (FS12.1) were determined and collectively explained the phenotypic variance from 5.64 to 15.64%. Fruit phenotypic correlation exhibited the significant relationship and principal component analysis also identified the potential variability. Multiple sequence alignments also indicated the significant base-mutations in the detected genetic loci, respectively. CONCLUSION: In short, our illustrated genetic loci are expected to provide the reference insights for fine QTL mapping and candidate gene(s) mining through molecular genetic breeding approaches aimed at developing the new varieties.

Genetic diversity of superior Persian walnut genotypes in Azadshahr, Iran.

Persian walnut (Juglans regia L.) is known to have originated in central and eastern Asia. Remnants of these wild populations can still be found in the Hyrcanian forest in north-eastern Iran. In this study, 102 individual walnut trees from four geographic populations in the Azadshahr province (Vamenan, Kashidar, Rudbar and Saidabad) were sampled. We characterized individual trees using 28 standard morphological traits. The range of traits varied widely for some economically important characteristics including nut weight (6.1-19.79 g), kernel weight (2.9-9.4 g), and kernel fill percentage (26.51-60.34%). After morphological evaluation, 39 superior individuals based on nut quality and kernel fill percentage were selected for further genetic analysis. Individual superior trees were genotyped using 10 simple sequence repeat markers (SSR) and genetic diversity. Number of alleles per locus ranged from 3 (WGA005) to 12 (WGA054). Clustering analysis of 10 SSR loci divided the genotypes into three main groups. PCoA analysis clearly sorted genotypes into one of four distinctive groups which aligned with the cluster analysis. All analyses showed that individuals from Saidabad were genetically distinct. Likewise, results indicated that the high level of genetic diversity in Azadshahr region walnuts may provide a diverse source for superior walnuts in walnut breeding programs.

Atlantic frugivory: a plant-frugivore interaction data set for the Atlantic Forest.

The data set provided here includes 8,320 frugivory interactions (records of pairwise interactions between plant and frugivore species) reported for the Atlantic Forest. The data set includes interactions between 331 vertebrate species (232 birds, 90 mammals, 5 fishes, 1 amphibian, and 3 reptiles) and 788 plant species. We also present information on traits directly related to the frugivory process (endozoochory), such as the size of fruits and seeds and the body mass and gape size of frugivores. Data were extracted from 166 published and unpublished sources spanning from 1961 to 2016. While this is probably the most comprehensive data set available for a tropical ecosystem, it is arguably taxonomically and geographically biased. The plant families better represented are Melastomataceae, Myrtaceae, Moraceae, Urticaceae, and Solanaceae. Myrsine coriacea, Alchornea glandulosa, Cecropia pachystachya, and Trema micrantha are the plant species with the most animal dispersers (83, 76, 76, and 74 species, respectively). Among the animal taxa, the highest number of interactions is reported for birds (3,883) followed by mammals (1,315). The woolly spider monkey or muriqui, Brachyteles arachnoides, and Rufous-bellied Thrush, Turdus rufiventris, are the frugivores with the most diverse fruit diets (137 and 121 plants species, respectively). The most important general patterns that we note are that larger seeded plant species (>12 mm) are mainly eaten by terrestrial mammals (rodents, ungulates, primates, and carnivores) and that birds are the main consumers of fruits with a high concentration of lipids. Our data set is geographically biased, with most interactions recorded for the southeast Atlantic Forest.

Revisiting the phylogeny of Bombacoideae (Malvaceae): Novel relationships, morphologically cohesive clades, and a new tribal classification based on multilocus phylogenetic analyses.

Bombacoideae (Malvaceae) is a clade of deciduous trees with a marked dominance in many forests, especially in the Neotropics. The historical lack of a well-resolved phylogenetic framework for Bombacoideae hinders studies in this ecologically important group. We reexamined phylogenetic relationships in this clade based on a matrix of 6465 nuclear (ETS, ITS) and plastid (matK, trnL-trnF, trnS-trnG) DNA characters. We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among 108 species (∼70% of the total number of known species). We analyzed the evolution of selected morphological traits: trunk or branch prickles, calyx shape, endocarp type, seed shape, and seed number per fruit, using ML reconstructions of their ancestral states to identify possible synapomorphies for major clades. Novel phylogenetic relationships emerged from our analyses, including three major lineages marked by fruit or seed traits: the winged-seed clade (Bernoullia, Gyranthera, and Huberodendron), the spongy endocarp clade (Adansonia, Aguiaria, Catostemma, Cavanillesia, and Scleronema), and the Kapok clade (Bombax, Ceiba, Eriotheca, Neobuchia, Pachira, Pseudobombax, Rhodognaphalon, and Spirotheca). The Kapok clade, the most diverse lineage of the subfamily, includes sister relationships (i) between Pseudobombax and "Pochota fendleri" a historically incertae sedis taxon, and (ii) between the Paleotropical genera Bombax and Rhodognaphalon, implying just two bombacoid dispersals to the Old World, the other one involving Adansonia. This new phylogenetic framework offers new insights and a promising avenue for further evolutionary studies. In view of this information, we present a new tribal classification of the subfamily, accompanied by an identification key.

Frugivores and cheap fruits make fruiting fruitful.

Animal seed dispersal provides an important ecosystem service by strongly benefiting plant communities. There are several theoretical studies on the ecology of plant-animal seed-disperser interactions, but few studies have explored the evolution of this mutualism. Moreover, these studies ignore plant life history and frugivore foraging behaviour. Thus, it remains an open question what the conditions for the diversification of fruit traits are, in spite of the multitude of empirical studies on fruit trait diversity. Here, we study the evolution of fruit traits using a spatially explicit individual-based model, which considers the costs associated with adaptations inducing dispersal by frugivory, as well as frugivore foraging behaviour and abundance. Our model predicts that these costs are the main determinants of the evolution of fruit traits and that when the costs are not very high, the evolution of larger fruit traits (e.g. fleshy/colourful fruits) is controlled by the choosiness and response thresholds of the frugivores as well as their numerical abundance.

Diversification and the evolution of dispersal ability in the tribe Brassiceae (Brassicaceae).

BACKGROUND AND AIMS: Dispersal and establishment ability can influence evolutionary processes such as geographic isolation, adaptive divergence and extinction probability. Through these population-level dynamics, dispersal ability may also influence macro-evolutionary processes such as species distributions and diversification. This study examined patterns of evolution of dispersal-related fruit traits, and how the evolution of these traits is correlated with shifts in geographic range size, habitat and diversification rates in the tribe Brassiceae (Brassicaceae). METHODS: The phylogenetic analysis included 72 taxa sampled from across the Brassiceae and included both nuclear and chloroplast markers. Dispersal-related fruit characters were scored and climate information for each taxon was retrieved from a database. Correlations between fruit traits, seed characters, habitat, range and climate were determined, together with trait-dependent diversification rates. KEY RESULTS: It was found that the evolution of traits associated with limited dispersal evolved only in association with compensatory traits that increase dispersal ability. The evolution of increased dispersal ability occurred in multiple ways through the correlated evolution of different combinations of fruit traits. The evolution of traits that increase dispersal ability was in turn associated with larger seed size, increased geographic range size and higher diversification rates. CONCLUSIONS: This study provides evidence that the evolution of increased dispersal ability and larger seed size, which may increase establishment ability, can also influence macro-evolutionary processes, possibly by increasing the propensity for long-distance dispersal. In particular, it may increase speciation and consequent diversification rates by increasing the likelihood of geographic and thereby reproductive isolation.

Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai).

Using an F1 population from a cross between Japanese pear (Pyrus pyrifolia Nakai) cultivars 'Akiakari' and 'Taihaku', we performed quantitative trait locus (QTL) analysis of seven fruit traits (harvest time, fruit skin color, flesh firmness, fruit weight, acid content, total soluble solids content, and preharvest fruit drop). The constructed simple sequence repeat-based genetic linkage map of 'Akiakari' consisted of 208 loci and spanned 799 cM; that of 'Taihaku' consisted of 275 loci and spanned 1039 cM. Out of significant QTLs, two QTLs for harvest time, one for fruit skin color, and one for flesh firmness were stably detected in two successive years. The QTLs for harvest time were located at the bottom of linkage group (LG) Tai3 (nearest marker: BGA35) and at the top of LG Tai15 (nearest markers: PPACS2 and MEST050), in good accordance with results of genome-wide association study. The PPACS2 gene, a member of the ACC synthase gene family, may control harvest time, preharvest fruit drop, and fruit storage potential. One major QTL associated with fruit skin color was identified at the top of LG 8. QTLs identified in this study would be useful for marker-assisted selection in Japanese pear breeding programs.

Analysis and evaluation of Camellia oleifera Abel. Germplasm fruit traits from the high-altitude areas of East Guizhou Province, China.

Camellia oleifera, a significant woody edible oil species, was examined using 48 germplasm resources from high-altitude regions in East Guizhou Province, China, to analyze fruit quality. The analysis aimed to identify high-performance germplasm, providing theoretical and research foundations for selecting and cross-breeding superior C. oleifera varieties in these regions. Fifteen primary traits of mature fruits were measured and analyzed, including four phenotypic traits (single fruit weight, transverse diameter, longitudinal diameter, peel thickness) and eleven quality traits (fresh seed yield rate, dry seed yield rate, dry kernel yield rate, seed kernel oil content, palmitic acid, palmitoleic acid, stearic acid, oleic acid, linoleic acid, α-linolenic acid, cis-11-eicosenoic acid). A comprehensive evaluation employing cluster and principal component analyses (PCA) was conducted. The cluster analysis categorized the germplasms into five groups at a squared Euclidean distance of 14, with the first category comprising 17 germplasms, the second 28, and the third, fourth, and fifth each containing one. PCA reduced the 15 traits to five principal components (PCs), with PC1 having the highest eigenvalue of 3.57 and a contribution rate of 23.8%, mainly representing phenotypic traits. PC2, contributing 20.44%, represented linoleic acid, while PC3, PC4, and PC5, with contribution rates of 12.99%, 9.13%, and 7.45% respectively, predominantly represented seed kernel oil content, fresh seed yield, and palmitoleic acid. Employing a weighted sum method, a comprehensive evaluation function was developed to calculate total scores for each superior individual, forming the basis for rankings and selections. Notable variability was detected in single fruit weight, peel thickness, and fresh and dry seed yields, while oleic acid exhibited the lowest coefficient of variation. Dry seed yield showed a robust positive correlation with seed kernel oil content and the concentrations of palmitic and linoleic acids, whereas seed kernel oil content was inversely correlated with cis-11-eicosenoic acid levels. Five PCs with eigenvalues > 1 were identified, highlighting the top ten superior individuals: QD (Qian Dong: the code of eastern Guizhou Province)-33 > QD-34 > QD-48 > QD-38 > QD-27 > QD-15 > QD-35 > QD-5 > QD-14 > QD-36. Thus, the 48 C. oleifera germplasms from East Guizhou's high-altitude areas demonstrate significant potential for enhancing traits such as single fruit weight, peel thickness, and fresh and dry seed yields. Specifically, QD-33, QD-34, and QD-48 exhibited superior comprehensive performance, designating them as prime candidates for variety selection and breeding.

Potential of reproductive traits in functional ecology: A quantitative comparison of variability in floral, fruit, and leaf traits.

Despite their claimed low intraspecific variability, plant reproductive traits are less frequently used in functional ecology. Here we focused on underrepresented plant organs, i.e. flowers and fruits, by comparing their traits with well-established leaf traits. We evaluated 16 functional traits (six floral, six fruit, and four leaf traits) in a randomly selected group of woody species under comparable environmental conditions. We aimed to assess interspecific and intraspecimen variability and explore the potential of the proposed flower and fruit traits for ecological research. Traits related to the dry mass of flowers and fruits exhibited the highest interspecific variability, while carbon content traits in flowers and leaves had the lowest. At a specimen level, specific leaf area revealed the highest variation. Carbon content traits for all organs demonstrated the least intraspecimen variability, with flower carbon content being the least variable. Our study revealed connections between the newly proposed traits and widely recognized functional traits, uncovering intriguing links between the established traits and the floral and fruit traits upon which we focused. This complements the already well-recognized variability in plant form and function with additional insights into reproductive processes.

Invasive Plant Species Driving the Biotic Homogenization of Plant-Frugivore Interactions in the Atlantic Forest Biodiversity Hotspot.

Although biological invasions are a common and intensively studied phenomenon, most studies often ignore the biotic interactions that invasive species play in the environment. Here, we evaluated how and why invasive plant species are interconnected within the overall frugivory network of the Brazilian Atlantic Forest, an important global biodiversity hotspot. To do this, we used the recently published Atlantic Frugivory Dataset to build a meta-network (i.e., a general network made of several local networks) that included interactions between 703 native and invasive plant species and 331 frugivore species. Using tools derived from complex network theory and a bootstrap simulation approach, we found that the general structure of the Atlantic Forest frugivory network (i.e., nestedness and modularity) is robust against the entry of invasive plant species. However, we observed that invasive plant species are highly integrated within the frugivory networks, since both native and invasive plant species play similar structural roles (i.e., plant status is not strong enough to explain the interactive roles of plant species). Moreover, we found that plants with smaller fruits and with greater lipid content play a greater interactive role, regardless of their native or invasive status. Our findings highlight the biotic homogenization involving plant-frugivore interactions in the Atlantic Forest and that the impacts and consequences of invasive plant species on native fauna can be anticipated based on the characteristics of their fruits.

Fruit and seed traits and vertebrate-fruit interactions of tree species occurring in Guyana, Suriname, and French Guiana.

Seed dispersal is widely considered an important mechanism for the conservation of plant diversity. In tropical regions, over 80% of woody plant species are dispersed by vertebrates, often through the consumption of fruits. Our understanding of what drives interactions between vertebrates and fruits is limited. Through a systematic literature search, we compiled a database of fruit and seed traits and vertebrate-fruit interactions for tree and vertebrate species occurring in the Guianas, with the aim of facilitating research into seed dispersal and seed predation of tree species in the Guianas. The database was compiled by extracting data from 264 published sources. It consists of 21,082 records, of which 19,039 records contain information about 19 different fruit and seed traits belonging to 1622 different tree species. The other 2043 records contain information on vertebrate-fruit interactions between 161 vertebrate species and 464 tree species. Our analyses showed a taxonomic bias, particularly in the interaction data, toward large-bodied vertebrates, with most interactions recorded for the bearded saki (Chiropotes chiropotes), followed by the lowland tapir (Tapirus terrestris). For plants we found an overrepresentation of the Sapotaceae and Moraceae families and an underrepresentation of the Rubiaceae, Myrtaceae, and Lauraceae families in the interactions. There are no copyright restrictions on the data set; please cite this publication when using these data.

Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Paeonia rockii) Using Association Mapping.

Allelic variation in floral quantitative traits, including the elements of flowers and fruits, is caused by extremely complex regulatory processes. In the genetic improvement of flare tree peony (Paeonia rockii), a unique ornamental and edible oil woody species in the genus Paeonia, a better understanding of the genetic composition of these complex traits related to flowers and fruits is needed. Therefore, we investigated the genetic diversity and population structure of 160 P. rockii accessions and conducted single-marker association analysis for 19 quantitative flower and fruit traits using 81 EST-SSR markers. The results showed that the population had a high phenotypic diversity (coefficients of variation, 11.87-110.64%) and a high level of genetic diversity (mean number of alleles, N A = 6.09). These accessions were divided into three subgroups by STRUCTURE analysis and a neighbor-joining tree. Furthermore, we also found a low level of linkage disequilibrium between these EST-SSRs and, by single-marker association analysis, identified 134 significant associations, including four flower traits with 11 EST-SSRs and 10 fruit traits with 32 EST-SSRs. Finally, based on the sequence alignment of the associated markers, P280, PS2, PS12, PS27, PS118, PS131, and PS145 may be considered potential loci to increase the yield of flare tree peony. These results laid the foundation for further analysis of the genetic structure of some key traits in P. rockii and had an obvious potential application value in marker-assisted selection breeding.

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines.

Cucurbita maxima Duchesne squash and pumpkins are cultivated world-wide. Cucurbita maxima fruits are produced for fresh market and are valuable for food processing. Therefore, fruit characteristics and yield are the traits of high economic importance for breeders. To date, the genetic basis of fruit-associated traits in C. maxima have been poorly understood. In the present study, we evaluated fruit-associated traits and conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross of two inbred lines with different fruit morphotypes. Phenotypic data for nine fruit traits (earliness, weight, number per plant, yield per plant, length and diameter, shape index, flesh thickness, sucrose content and dry matter content) were collected for RILs in two open-field experiments. Pairwise analysis of the phenotypic data revealed correlations among the fruit and yield-associated traits. Using a previously developed genetic map, we identified 26 QTLs for eight traits. The QTLs were found in 10 locations on eight chromosomes of C. maxima. The QTLs were detected across experiments and explained up to 41.4% of the observed phenotypic variations. Major-effect QTLs for multiple fruit-associated traits were clustered on chromosome 4, suggesting that this genomic region has been under selection during diversification and/or domestication of C. maxima.

Quality preservation of sweet cherry cv. 'staccato' by using glycine-betaine or Ascophyllum nodosum.

Pre-harvest application of exogenous compounds has been employed in many crops, as a cultural practice, to promote their adaptation to a new climate-changing environment. Effect of foliar pre-harvest application of salicylic acid, glycine-betaine complex and seaweed extract (Ascophyllum nodosum) on the cherry quality from 'Staccato' cultivar was studied. Treatments significantly affected (p < 0.01) the fruit size, soluble solids content, pH, colour, polyphenols, vitamin C and antioxidant activity. Glycine-betaine and A. nodosum treated cherries presented higher dimensions, soluble solids content and pH and lower acidity. In addition, these cherries had a higher content of polyphenols and vitamin C and antioxidant capacity, but lower values of L*, C*ab and hue angle, meaning that both treatments can rise the fruit ripening process. Therefore, the pre-harvest application of glycine-betaine and A. nodosum can be a good alternative to promote the adaptation of sweet cherry tree to stressful environmental conditions, without compromising the fruit quality.

Genome-Wide Association Study Reveals Candidate Genes Involved in Fruit Trait Variation in Persian Walnut (Juglans regia L.).

Elucidating the genetic determinants of fruit quality traits in walnut is essential to breed new cultivars meeting the producers and consumers' needs. We conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of Juglans regia from the INRAE walnut germplasm collection, previously genotyped using the AxiomTM J. regia 700K SNP array. We phenotyped the panel for 25 fruit traits related to morphometrics, shape, volume, weight, ease of cracking, and nutritional composition. We found more than 60 marker-trait associations (MTAs), including a highly significant SNP associated with nut face diameter, nut volume and kernel volume on chromosome 14, and 5 additional associations were detected for walnut weight. We proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to be involved in fruit development in other species. We also confirmed associations on chromosomes 5 and 11 with nut suture strength, recently reported by the University of California, Davis. Our results enhance knowledge of the genetic control of important agronomic traits related to fruit quality in walnut, and pave the way for the development of molecular markers for future assisted selection.

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.).

Association mapping has been proposed as an efficient approach to assist plant breeding programs to investigate the genetic basis of agronomic traits. In this study, we evaluated 18 traits related to yield, (FWP, NF, FWI, and FWII), fruit size-shape (FP, FA, MW, WMH, MH, HMW, DI, FSI, FSII, OVO, OBO), and fruit quality (FIR, CF, and SST), in a diverse collection of 100 accessions of Physalis peruviana including wild, landraces, and anther culture derived lines. We identified seven accessions with suitable traits: fruit weight per plant (FWP) > 7,000 g/plant and cracked fruits (CF) < 4%, to be used as parents in cape gooseberry breeding program. In addition, the accessions were also characterized using Genotyping By Sequencing (GBS). We discovered 27,982 and 36,142 informative SNP markers based on the alignment against the two cape gooseberry references transcriptomes. Besides, 30,344 SNPs were identified based on alignment to the tomato reference genome. Genetic structure analysis showed that the population could be divided into two or three sub-groups, corresponding to landraces-anther culture and wild accessions for K = 2 and wild, landraces, and anther culture plants for K = 3. Association analysis was carried out using a Mixed Linear Model (MLM) and 34 SNP markers were significantly associated. These results reveal the basis of the genetic control of important agronomic traits and may facilitate marker-based breeding in P. peruviana.

Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri).

Pear is an important fruit crop of the Rosaceae family and has experienced two rounds of ancient whole-genome duplications (WGDs). However, whether different types of gene duplications evolved differently after duplication remains unclear in the pear genome. In this study, we identified the different modes of gene duplication in pear. Duplicate genes derived from WGD, tandem, proximal, retrotransposed, DNA-based transposed or dispersed duplications differ in genomic distribution, gene features, selection pressure, expression divergence, regulatory divergence and biological roles. Widespread sequence, expression and regulatory divergence have occurred between duplicate genes over the 30-45 million years of evolution after the recent genome duplication in pear. The retrotransposed genes show relatively higher expression and regulatory divergence than other gene duplication modes. In contrast, WGD genes underwent a slower sequence divergence and may be influenced by abundant gene conversion events. Moreover, the different classes of duplicate genes exhibited biased functional roles. We also investigated the evolution and expansion patterns of the gene families involved in sugar and organic acid metabolism pathways, which are closely related to the fruit quality and taste in pear. Single-gene duplications largely account for the extensive expansion of gene families involved in the sorbitol metabolism pathway in pear. Gene family expansion was also detected in the sucrose metabolism pathway and tricarboxylic acid cycle pathways. Thus, this study provides insights into the evolutionary fates of duplicated genes.

Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers.

Tomato (Solanum lycopersicum) fruit weight (FW), soluble solid content (SSC), fruit shape and fruit color are crucial for yield, quality and consumer acceptability. In this study, a 192 accessions tomato association panel comprising a mixture of wild species, cherry tomato, landraces, and modern varieties collected worldwide was genotyped with 547 InDel markers evenly distributed on 12 chromosomes and scored for FW, SSC, fruit shape index (FSI), and color parameters over 2 years with three replications each year. The association panel was sorted into two subpopulations. Linkage disequilibrium ranged from 3.0 to 47.2 Mb across 12 chromosomes. A set of 102 markers significantly (p < 1.19-1.30 × 10-4) associated with SSC, FW, fruit shape, and fruit color was identified on 11 of the 12 chromosomes using a mixed linear model. The associations were compared with the known gene/QTLs for the same traits. Genetic analysis using F2 populations detected 14 and 4 markers significantly (p < 0.05) associated with SSC and FW, respectively. Some loci were commonly detected by both association and linkage analysis. Particularly, one novel locus for FW on chromosome 4 detected by association analysis was also identified in F2 populations. The results demonstrated that association mapping using limited number of InDel markers and a relatively small population could not only complement and enhance previous QTL information, but also identify novel loci for marker-assisted selection of fruit traits in tomato.