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Adansonia digitata L. is a large tree with diverse socioeconomic and ecological benefits in the dryland ecosystems. Despite its significance, the natural habitat and its survival are under threat, particularly manifested by the poor regeneration and lack of juvenile individuals. Domestication and cultivation of this key species requires understanding of its seed germination ecology. This study characterizes the fruit morphology, examines seed quality parameters and determines the best pre-sowing treatments for optimum seed germination of Adansonia digitata. The International Seed Test Association's (ISTA) standards were used for the seed quality parameter tests. Further, the germination experiment was conducted in a completely randomized design (CRD) with four replications of five pre-sowing treatments (control, H 2 SO 4 , nicking, cold water and hot water). Adansonia digitata from the Metema provenance exhibit variations in the fruit morphological traits with mean values of 20.11 ± 3.24cm length, 10.71 ± 1.49cm width, 316.8 ± 112.17g weight, 123.03 ± 53.61g seed weight, 30.49 ± 11.25g pulp weight, and 194.43 ± 102.53 seeds per fruit. Furthermore, the viability, purity, and moisture content of Adansonia digitata seeds were 94 ± 0.02%, 95.5 ± 0.71% and 5.63 ± 0.11%, respectively. Regarding the thousands seed weight, 1978-1995 seeds were contained in a kilogram of pure Adansonia digitata seed. Thus, from 1875 to1919, seedlings could be produced from one kilogram of pure A. digitata seeds. The germination trial revealed that Adansonia digitata seeds have a strong dormancy problem, depicted by no (0%) germination in 45 days with the controlled group and 3.75 ± 2.5% with the cold water pre-sowing treatment. Statistically significant variation (P = 0.001) was observed in Adansonia digitata seed germination percentage, germination index, germination mean time, and germination period among the tested pre-sowing treatments. Nicking resulted in the highest germination (91.25 ± 4.8%), followed by H 2 SO 4 (85 ± 5.8%) and hot water pre-sowing treatment (35 ± 4.1%). However, the cold water pre-sowing treatment gave the lowest germination result. Generally, the study highlighted the strong physical dormancy of Adansonia digitata seeds, which resulted from the hard seed coat. Hence, nicking is recommended as the best pre-sowing treatment for enhanced germination of Adansonia digitata. The findings of the current study have implications for the conservation and domestication efforts of this tree species and consequently, for the promotion of its ecological and economical benefits.

Background Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored. Results Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800 , which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1 , regulates flat shape formation. Conclusions The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.

The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.

In east Anatolia region in Turkey, there are special microclimates, which famous for its fruit production. One of the most important microclimates in the region is Aras valley. The major fruit in the valley is apricot, which grown both cultivated and wild forms. This study aimed to assess some important fruit morphological and biochemical characteristics of 26 wild apricots and cv. Aprikoz grown in Kagizman district in Aras valley. Harvest date, tree growth habit, fruit weight, fruit shape, fruit firmness, fruit color, flesh/seed ratio, aroma, kernel taste, soluble solid content, titratable acidity, maturity index, vitamin C, total phenolic, total carotenoid and antioxidant capacity were determined. The wild grown apricots exhibited a wide variation on most of the fruit morphological and biochemical characteristics. Harvest date, fruit shape, fruit weight, fruit firmness and fruit color were the most distinct morphological characteristics of wild grown apricots. Harvest dates and fruit weight were found between 02 July (KA18) and 06 August (KA13); 16.28 g (KA6) and 33.14 g (KA2) among wild grown apricots, respectively. The main cultivar cv. Aprikoz harvested at 04 July and had 38.67 g fruit weight. The wild apricots had flesh/seed ratio between 8.41 (KA21) and 12.25 (KA10) while cv. Aprikoz had 11.69 flesh/seed ratio. Total antioxidant capacity, total carotenoid and total phenolic content were the highest in most of wild apricot fruits than cv. Aprikoz. Our results showed that there is potential for promoting wild apricot fruit from specific geographical regions because they contained elevated concentrations of antioxidant polyphenolic compounds.

Fruits represent an important part of the human diet and show extensive variation in size and shape between and within cultivated species. The genetic basis of such variation has been studied most extensively in tomato, where currently six quantitative trait loci (QTLs) involving these traits have been fine-mapped and the genes underlying the QTLs identified. The genes responsible for the cloned QTLs belong to families with a few to many members. FASCIATED is encoded by a member of the YABBY family, CNR/FW2.2 by a member of the Cell Number Regulator family, SIKLUH/FW3.2 by a cytochrome P450 of the 78A class (CYP78A), LOCULE NUMBER by a member of the WOX family including WUSCHEL, OVATE by a member of the Ovate Family Proteins (OFP), and SUN by a member of the IQ domain family. A high portion of the history and current diversity in fruit morphology among tomato cultivars can be explained by modifications at four of these cloned QTLs. In melon, a number of QTLs involved in fruit morphology have been mapped, but the molecular basis for these QTLs is unknown. In the present review, we examine the current knowledge on the molecular basis of fruit morphology in tomato and transfer that information in order to define candidate genes of melon fruit shape and size QTLs. We hypothesize that different members of the gene families identified in tomato may have a role in the regulation of fruit morphology in other species. We anchored the published melon QTL map on the genome sequence and identified the melon family members of the six cloned tomato QTLs in the genome. We investigated the co-localization of melon fruit morphology QTLs and the candidate genes. We found that QTLs for fruit weight co-localized frequently with members of the CNR/FW2.2 and KLUH/FW3.2 families, as well as co-localizations between OFP family members and fruit-shape QTLs, making this family the most suitable to explain fruit shape variation among melon accessions.

Key messageRecent molecular studies revealed new opportunities to improve cucumber fruit quality. However, the fruit color and spine traits molecular basis remain vague despite the vast sources of genetic diversity.Cucumber is agriculturally, economically and nutritionally important vegetable crop. China produces three-fourths of the world’s total cucumber production. Cucumber fruit quality depends on a number of traits such as the fruit color (peel and flesh color), spine (density, size and color), fruit shape, fruit size, defects, texture, firmness, taste, maturity stage and nutritional composition. Fruit color and spine traits determine critical quality attributes and have been the interest of researchers at the molecular level. Evaluating the molecular mechanisms of fruit quality traits is important to improve production and quality of cucumber varieties. Genes and qualitative trait locus (QTL) that are responsible for cucumber fruit color and fruit spine have been identified. The purpose of this paper is to reveal the molecular research progress of fruit color and spines as key quality traits of cucumber. The markers and genes identified so far could help for marker-assisted selection of the fruit color and spine trait in cucumber breeding and its associated nutritional improvement. Based on the previous studies, peel color and spine density as examples, we proposed a comprehensive approach for cucumber fruit quality traits improvement. Moreover, the markers and genes can be useful to facilitate cloning-mediated genetic breeding in cucumber. However, in the era of climate change, increased human population and high-quality demand of consumers, studies on molecular mechanisms of cucumber fruit quality traits are limited.

Background Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops. Results Here, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of the PpOFP2 gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes that PpOFP2 is causal for flat-fruit shape. Conclusions Thus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.

Background Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools. Results In order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: “Védrantais”, from the cantalupensis group, and “Piel de Sapo”, from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits. Conclusion Several QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map.

Background The widely cultivated pepper ( Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and F st statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index ( p  < 0.0001). Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

Summary Domestication and improvement are two important stages in crop evolution. Melon (Cucumis melo L.) is an important vegetable crop with wide phenotypic diversity in many horticultural traits, especially fruit size, flesh thickness and aroma, which are likely the results of long‐term extensive selection during its evolution. However, selective signals in domestication and improvement stages for these remarkable variations remain unclear. We resequenced 297 wild, landrace and improved melon accessions and obtained 2 045 412 high‐quality SNPs. Population structure and genetic diversity analyses revealed independent and two‐step selections in two subspecies of melon: ssp. melo and ssp. agrestis during melon breeding. We detected 233 (~18.35 Mbp) and 159 (~17.71 Mbp) novel potential selective signals during the improvement stage in ssp. agrestis and spp. melo, respectively. Two alcohol acyltransferase genes (CmAATs) unique to the melon genome compared with other cucurbit crops may have undergone stronger selection in ssp. agrestis for the characteristic aroma as compared with other cucurbits. Genome‐wide association analysis identified eight fruit size and seven flesh thickness signals overlapping with selective sweeps. Compared with thin‐skinned ssp. agrestis, thick‐skinned ssp. melo has undergone a stronger selection for thicker flesh. In most melon accessions, CmCLV3 has pleiotropic effects on carpel number and fruit shape. Findings from this study provide novel insights into melon crop evolution, and new tools to advance melon breeding.