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Variations in the number of fruit spines among cultivars PI183967, XTMC, YD, 65G, and 02245. a Fruit spine counting method and the phenotype of five parents with different fruit spine densities. b The number of fruit spines among five parents. c The origin of the LM, YR, HR, and HP populations and phenotyping environments
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Key message
Quantitative Trait Loci (QTL) analysis of multiple populations in multiple environments revealed that the fsd6.2 locus, which includes the candidate gene Csgl3, controls high fruit spine density in natural cucumbers. GWAS identified a novel locus fsd6.1, which regulates ultra-high fruit spine density in combination with Csgl3, and evolv...
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Abstract
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Citations
... This result is further confirmed by examining the phenotypic data of recombinants defined by markers SSR01234, CSWCT5B, and SSR18251. Notably, the 566 kb candidate region covered the previously identified QTL fsd6.2 and Csgl3, both of which have been proposed to regulate high fruit spine density in natural cucumber populations [24][25][26][27]. ...
IL52 is a valuable introgression line obtained from interspecific hybridization between cultivated cucumber (Cucumis sativus L., 2n = 14) and the wild relative species C. hystrix Chakr. (2n = 24). IL52 exhibits high resistance to a number of diseases, including downy mildew, powdery mildew, and angular leaf spot. However, the ovary- and fruit-related traits of IL52 have not been thoroughly investigated. Here, we conducted quantitative trait loci (QTL) mapping for 11 traits related to ovary size, fruit size, and flowering time using a previously developed 155 F7:8 RIL population derived from a cross between CCMC and IL52. In total, 27 QTL associated with the 11 traits were detected, distributed on seven chromosomes. These QTL explained 3.61% to 43.98% of the phenotypic variance. Notably, we identified a major-effect QTL (qOHN4.1) on chromosome 4 associated with the ovary hypanthium neck width and further delimited it into a 114-kb candidate region harboring 13 candidate genes. Furthermore, the QTL qOHN4.1 is co-localized with the QTL detected for ovary length, mature fruit length, and fruit neck length, all residing within the consensus QTL FS4.1, suggesting a plausible pleiotropic effect.
... The numerousspine trait is recessive to the few-spine trait and is controlled by a recessive single gene, ns , and forked trichomes, and dialytic stamens may be regulated by a recessive gene, the dl gene (Chang et al., 2016). The fruit spine densities of cucumber were measured in multiple populations in multiple environments; the results indicated that the fruit spine density was controlled by a major-effect quantitative trait locus (QTL) (Bo et al., 2019). In this study, the F 2 population derived by crossing accession 16 and accession 63 was constructed. ...
... In this study, the F 2 population derived by crossing accession 16 and accession 63 was constructed. Trichome densities, rather than trichome size or development, were significantly different in the F 2 population, which was similar to the fruit spine densities of cucumber (Bo et al., 2019). Trichome density exhibited quantitative characteristic inheritance in zucchini. ...
Plant trichomes are specialized structures that develop from epidermal cells and are widely present on the surface of the aboveground tissues in plants. Trichomes play a significant role in plant development, the biotic and abiotic adaptations, and some of them have important commercial value. Trichome micromorphology of the aboveground parts of zucchini germplasm resources was observed, and the results showed that zucchini trichomes are multicellular, and they consist of head, stem, and basal cells. Zucchini trichomes were classified into seven types: type I, II, III, and VII trichomes were nonglandular, and type IV, V, and VI trichomes were glandular. Each type had a unique structure and morphology, and type I and II trichomes were long and pointy, which could easily be observed. According to the presence of type I and II trichomes, the zucchini germplasm resources were divided into long dense trichome (LDT) groups (presence of type I and II trichomes) and sparse micro trichome (SMT) groups (absence of type I and II trichomes). The F2 population derived by crossing typical LDT 16 and typical SMT 63 was constructed, and the density of type I and type II petiole trichomes was found significantly different. Petiole trichome density exhibited quantitative characteristic inheritance and was controlled by multiple genes. A study of the structure and morphology of zucchini trichomes can deepen the understanding of multicellular trichomes and lay the foundation for the morphological development of zucchini trichomes and the identification of trichome density genes, which could have important theoretical and practical application value for the selection of new zucchini varieties in the future.
... Fruit peels of the ns mutants and ns knock outs exhibited reduced auxin levels and decreased expression of Aux/IAA transcriptional repressors, indicating a central role for auxin in initiation of cucumber fruit spines. Other loci associated with naturally occurring variation in spine number include QTL on chromosome 6, fsd6.1 and fsd6.2 [88]. fsd6.2, which originated in China, promotes ultra-high spine density when in combination with fsd6.1. ...
... Fine mapping of fsd6.2 identified a homolog of the tomato HD-ZIP IV factor Wooly, essential for multicellular trichome formation in tomato [89], as the candidate gene for fsd6.2 [named Csgl3 (glabrous3) in cucumber] [88]. ...
... Our understanding of genetic control of morphological features such as spines, warts, color, and waxes also has greatly increased in recent years. The presence and density of trichomes and warts has been associated with homologs of numerous transcription factors regulating trichome development in other species as well as genes influencing auxin and cytokinin levels and transport [87,88,90,[96][97][98]111,113,114]. Variation in traits such as cuticle thickness and composition and skin and flesh color has been found to be mediated by structural genes encoding biosynthetic enzymes for cutin, wax, chlorophyll, and beta-carotene synthesis, as well as transcription factors regulating cuticle deposition and pigment biosynthesis [118,120,124,127,[135][136][137][138][139][140][141]143]. ...
Cucumber (Cucumis sativus L.) fruits, which are eaten at an immature stage of development, can vary extensively in morphological features such as size, shape, waxiness, spines, warts, and flesh thickness. Different types of cucumbers that vary in these morphological traits are preferred throughout the world. Numerous studies in recent years have added greatly to our understanding of cucumber fruit development and have identified a variety of genetic factors leading to extensive diversity. Candidate genes influencing floral organ establishment, cell division and cell cycle regulation, hormone biosynthesis and response, sugar transport, trichome development, and cutin, wax, and pigment biosynthesis have all been identified as factors influencing cucumber fruit morphology. The identified genes demonstrate complex interplay between structural genes, transcription factors, and hormone signaling. Identification of genetic factors controlling these traits will facilitate breeding for desired characteristics to increase productivity, improve shipping, handling, and storage traits, and enhance consumer-desired qualities. The following review examines our current understanding of developmental and genetic factors driving diversity of cucumber fruit morphology.
... In terms of cucumber fruit quality traits, Shang [13] detected the bitterness gene Bi in 115 cucumber germplasm resources by GWAS. Bo [14,15] found a new locus fsd6.1 associated with spines and two loci, qgf5.1 and qgf3.1, related to green fruit flesh in cucumber. For cucumber disease-resistance traits, 395 cucumber germplasm resources were used to analyze downy mildew resistance, and 18 loci were related to downy mildew resistance, five candidate genes were predicted at the major effect loci [16][17][18]. ...
The stem diameter, an important agronomic trait, affects cucumber growth and yield. However, no genes responsible for cucumber stem diameter have been identified yet. In this study, the stem diameter of 88 cucumber core germplasms were measured in spring 2020, autumn 2020 and autumn 2021, and a genome-wide association study (GWAS) was carried out based on the gene sequence and stem diameter of core germplasms. A total of eight loci (gSD1.1, gSD2.1, gSD3.1, gSD3.2, gSD4.1, gSD5.1, gSD5.2, and gSD6.1) significantly associated with cucumber stem diameter were detected. Of these, five loci (gSD1.1, gSD2.1, gSD3.1, gSD5.2, and gSD6.1) were repeatedly detected in two or more seasons and were considered as robust and reliable loci. Based on the linkage disequilibrium sequences of the associated SNP loci, 37 genes were selected. By further investigating the five loci via analyzing Arabidopsis homologous genes and gene haplotypes, five genes (CsaV3_1G028310, CsaV3_2G006960, CsaV3_3G009560, CsaV3_5G031320, and CsaV3_6G031260) showed variations in amino acid sequence between thick stem lines and thin stem lines. Expression pattern analyses of these genes also showed a significant difference between thick stem and thin stem lines. This study laid the foundation for gene cloning and molecular mechanism study of cucumber stem development.
... According to the density of spines, it can be roughly divided into four types: numerous spines, dense spines, few spines and no spines (Zhang et al. 2016b;Xie et al. 2018;Bo et al. 2019b). Several genes controlling fruit spines density and fruit spines size have been reported, and there is a degree of linkage between them, such as ns and ss, ns for numerous spines, ss for small spines. ...
... Fsd4.1, fsd6.2 and fsd6.1 are loci controlling fruit spine density in cucumber, Csgl3 was identified as the candidate gene for fsd6.2 and Csa6G421750 for fsd6.1, respectively. Among them, fsd6.2 controls the formation of high fruit spine density, while fsd6.1 and Csgl3 combined with fsd6.2 regulates the formation of ultra-high fruit spine density (Bo et al. 2019b). A gene that controls few spines, fs1, was obtained from CNS2, a wild-type cucumber, with a higher density of fruit spines, which mapped to chromosome 6 of cucumber. ...
... Xue et al. (2019) demonstrated for a signal that both phytohormones and environmental factors were closely associated with trichome development. However, details on multi-cellular trichome formation and fruit spine density in cucumber and related genes may require further investigation (Bo et al. 2019b). Finding genes responsible for fruit trichomes and their molecular mechanism will have great impact to improve cucumber appearance and to improve economic benefits. ...
Key message
Recent 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.
Abstract
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.
... 56 ); but higher density spines in Chinese Long cucumber seem to require both CsGL3 and the QTL fsd6.1 (ref. 57 ). Some cucumbers have numerous (ns) but small spines (ss) with the ns being a homolog for the gene encoding an auxin transporter-like protein 3 (CsLAX3) 58,59 . ...
Cucumber, Cucumis sativus L. (2n = 2x = 14), is an important vegetable crop worldwide. It was the first specialty crop with a publicly available draft genome. Its relatively small, diploid genome, short life cycle, and self-compatible mating system offers advantages for genetic studies. In recent years, significant progress has been made in molecular mapping, and identification of genes and QTL responsible for key phenotypic traits, but a systematic review of the work is lacking. Here, we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or characterized in cucumber. We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped. For each gene, detailed information was compiled including chromosome locations, allelic variants and associated polymorphisms, predicted functions, and diagnostic markers that could be used for marker-assisted selection in cucumber breeding. We also documented 322 QTL for 42 quantitative traits, including 109 for disease resistances against seven pathogens. By alignment of these QTL on the latest version of cucumber draft genomes, consensus QTL across multiple studies were inferred, which provided insights into heritable correlations among different traits. Through collaborative efforts among public and private cucumber researchers, we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a useful resource for the cucurbit research community.
... To detect QTLs for thermotolerance in cucumber seedlings, the phenotypic data for thermotolerance (HII) from HR and HP in two environments (Supplementary Materials Tables S1 and S2) and their genetic maps that we previously constructed [17] were used for QTL mapping, respectively. Details of each QTL detected, including chromosome number, physical position, length of interval, peak logarithm of odds (LOD) support value, and percentages of total phenotypic variances explained (R 2 ) are shown in Table 2. ...
... 17,744,278-18,744.278) associated with heat tolerance by genome-wide association study analysis (Wei et al. 2019). It is worth noting that qHT4.2 identified in our study was very close to gHII4.1 and gHII4.2, ...
... Genetic maps of HR and HP that were previously generated in our lab [17] were employed for QTL analysis in this study. QTL analysis was performed as previously described in our lab [33]. ...
High temperature is one of the major abiotic stresses that affect cucumber growth and development. Heat stress often leads to metabolic malfunction, dehydration, wilting and death, which has a great impact on the yield and fruit quality. In this study, genetic analysis and quantitative trait loci (QTL) mapping for thermotolerance in cucumber seedlings was investigated using a recombinant inbred line (RILs; HR) population and a doubled haploid (DH; HP) population derived from two parental lines '65G' (heat-sensitive) and '02245' (heat-tolerant). Inheritance analysis suggested that both short-term extreme and long-term mild thermotolerance in cucumber seedlings were determined by multiple genes. Six QTLs for heat tolerance including qHT3.1, qHT3.2, qHT3.3, qHT4.1, qHT4.2, and qHT6.1 were detected. Among them, the major QTL, qHT3.2, was repeatedly detected for three times in HR and HP at different environments, explained 28.3% of the phenotypic variability. The 481.2 kb region harbored 79 genes, nine of which might involve in heat stress response. This study provides a basis for further identifying thermotolerant genes and helps understanding the molecular mechanism underlying thermotolerance in cucumber seedlings.
... It also identified two SNPs on chromosome 1 as being responsible for the PA phenotype. GWAS was used to map other important agronomic traits in watermelon, melon and cucumber (Nimmakayala et al., 2016;Yagcioglu et al., 2016;Dou et al., 2018a;Dou et al., 2018b;Hou et al., 2018;Wang et al., 2018;Bo et al., 2019b;Bo et al., 2019a;Oren et al., 2019). The major sex-determining gene for monoecy/ andromonoecy in melon (CmACS7) was also successfully detected using the GWAS approach (Gur et al., 2017;, but so far no other andromonoecy locus had been found in cucurbits. ...
The sexual expression of watermelon plants is the result of the distribution and occurrence of male, female, bisexual and hermaphrodite flowers on the main and secondary stems. Plants can be monoecious (producing male and female flowers), andromonoecious (producing male and hermaphrodite flowers), or partially andromonoecious (producing male, female, bisexual, and hermaphrodite flowers) within the same plant. Sex determination of individual floral buds and the distribution of the different flower types on the plant, are both controlled by ethylene. A single missense mutation in the ethylene biosynthesis gene CitACS4, is able to promote the conversion of female into hermaphrodite flowers, and therefore of monoecy (genotype MM) into partial andromonoecy (genotype Mm) or andromonoecy (genotype mm). We phenotyped and genotyped, for the M/m locus, a panel of 207 C. lanatus accessions, including five inbreds and hybrids, and found several accessions that were repeatedly phenotyped as PA (partially andromonoecious) in several locations and different years, despite being MM. A cosegregation analysis between a SNV in CitACS4 and the PA phenotype, demonstrated that the occurrence of bisexual and hermaphrodite flowers in a PA line is not dependent on CitACS4, but conferred by an unlinked recessive gene which we called pa. Two different approaches were performed to map the pa gene in the genome of C. lanatus: bulk segregant analysis sequencing (BSA-seq) and genome wide association analysis studies (GWAS). The BSA-seq study was performed using two contrasting bulks, the monoecious M-bulk and the partially andromonoecious PA-bulk, each one generated by pooling DNA from 20 F2 plants. For GWAS, 122 accessions from USDA gene bank, already re-sequenced by genotyping by sequencing (GBS), were used. The combination of the two approaches indicates that pa maps onto a genomic region expanding across 32.24–36.44 Mb in chromosome 1 of watermelon. Fine mapping narrowed down the pa locus to a 867 Kb genomic region containing 101 genes. A number of candidate genes were selected, not only for their function in ethylene biosynthesis and signalling as well as their role in flower development and sex determination, but also by the impact of the SNPs and indels differentially detected in the two sequenced bulks.
... found a candidate gene related to callus regeneration by GWAS combined with QTL mapping [25]. Bo et al. (2019) identi ed a novel locus fsd6.1 combined with fsd6.2 (Csgl3) which regulates fruit spine density by GWAS [26]. GWAS has been widely used for gene mapping of multiple species and complex traits. ...
Background
Downy mildew (DM) is one of the most serious diseases in cucumber and brings the loss of yield and profit. Multiple QTLs for DM resistance have been detected, however, no loci related to resistance was reported using genome-wide association analysis (GWAS). In this study, the core germplasm (CG) of cucumber lines that had been constructed and resequenced were used to identify DM resistance Loci using GWAS technology.
Results
Thirteen loci (dmG1.1, dmG1.2, dmG2.1, dmG2.2, dmG3.1, dmG4.1, dmG4.2, dmG5.1, dmG5.2, dmG6.1, dmG6.2, dmG7.1 and dmG7.2) associated with DM resistance were detected on all the seven chromosomes. Among these loci, dmG2.1 and dmG7.1 were novel loci compared with previous studies. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlations, Csa1G575030 could be the most likely candidate gene of dmG1.2; Csa2G059820 and Csa2G060360 could be the candidate gene of dmG2.1. A WRKY transcription factor Csa5G606470 could be the candidate gene of dmG5.2. Csa7G004020 could be the candidate gene of dmG7.1.
Conclusions
These results identify five candidate genes for four loci related to DM resistance in cucumber which provide theoretical basis for gene cloning and genetic breeding of DM resistance in cucumber.
... The SNPs that are identical within each bulk but different between two bulks may be highly associated with the target phenotype. With this method, Li et al. (2016) quickly narrowed the Cn locus into a 16-kb region, and Bo et al. (2019) fine-mapped the fruit spine density related major QTL qfsd6.2 to a 50-kb region, and finally identified the candidate gene Csgl3. ...
... With this method in cucumber, Li et al. (2016) quickly narrowed the interval around the gene controlling carpel number from a 1.9 Mb region down to 16 kb. Bo et al. (2019) also used this method to fine-map the fruit spine density related major QTL (qfsd6.2) to a 50 kb region, and finally identified the candidate gene Csgl3 for the trait. In our study, the phenotypic data obtained in two replicated experiments were consistent, and the genotype sequencing depth reached 30 X, therefore this method was employed to narrow the target region. ...
Cucumber (Cucumis sativus L.) is an economically important vegetable crop worldwide, but it is sensitive to low temperatures. Cucumber seedlings exposed to long-term low temperature stress (LT), i.e., below 20°C during the day, and 8°C at night, exhibit leaf yellowing, accelerated senescence, and reduced yield, therefore posing a threat to cucumber production. Studying the underlying mechanisms involved in LT tolerance in cucumber seedlings, and developing germplasm with improved LT-tolerance could provide fundamental solutions to the problem. In this study, an F2 population was generated from two parental lines, “CG104” (LT-tolerant inbred line) and “CG37” (LT-sensitive inbred line), to identify loci that are responsible for LT tolerance in cucumber seedlings. Replicated phenotypic analysis of the F2-derived F3 family using a low-temperature injury index (LTII) suggested that the LT tolerance of cucumber seedlings is controlled by multiple genes. A genetic map of 990.8 cM was constructed, with an average interval between markers of 5.2 cM. One quantitative trait loci (QTL) named qLTT5.1 on chromosome 5, and two QTLs named qLTT6.1 and qLTT6.2 on chromosome 6 were detected. Among them, qLTT6.2 accounted for 26.8 and 24.1% of the phenotypic variation in two different experiments. Single-nucleotide polymorphism (SNP) variations within the region of qLTT6.2 were analyzed using two contrasting in silico bulks generated from the cucumber core germplasm. Result showed that 214 SNPs were distributed within the 42-kb interval, containing three candidate genes. Real-time quantitative reverse transcription PCR and sequence analysis suggested that two genes Csa6G445210, an auxin response factor, and Csa6G445230, an ethylene-responsive transmembrane protein, might be candidate genes responsible for LT tolerance in cucumber seedlings. This study furthers the understanding of the molecular mechanism underlying LT tolerance in cucumber seedlings, and provides new markers for molecular breeding.
