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Powdery mildew (PM) is one of the most serious diseases in cucumber and causes huge yield loss. Multiple quantitative trait loci (QTLs) for PM resistance have been reported in previous studies using a limited number of cucumber accessions. In this study, a cucumber core germplasm (CG) consisting of 94 resequenced lines was evaluated for PM resistance in four trials across three years (2013, 2014, and 2016). These trials were performed on adult plants in the field with natural infection. Using genome-wide association study (GWAS), 13 loci (pmG1.1, pmG1.2, pmG2.1, pmG2.2, pmG3.1, pmG4.1, pmG4.2, pmG5.1, pmG5.2, pmG5.3, pmG5.4, pmG6.1, and pmG6.2) associated with PM resistance were detected on all chromosomes except for Chr.7. Among these loci, ten were mapped to chromosomal intervals where QTLs had been reported in previous studies, while, three (pmG2.1, pmG3.1, and pmG4.1) were novel. The loci of pmG2.1, pmG5.2, pmG5.3 showed stronger signal in four trials. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, candidate genes located in the QTL intervals were predicted. SNPs in these candidate genes were analyzed between haplotypes of highly resistant (HR) and susceptible (HS) CG lines, which were defined based on combing disease index data of all trials. Furthermore, candidate genes (Csa5G622830 and CsGy5G015660) reported in previous studies for PM resistance and cucumber orthologues of several PM susceptibility (S) genes (PMR5, PMR-6, and MLO) that are colocalized with certain QTLs, were analyzed for their potential contribution to the QTL effect on both PM and DM in the CG population. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for both PM and DM resistance, which can be exploited in cucumber breeding.
Xiaoping Liu; Xingfang Gu; Hongwei Lu; Panna Liu; Han Miao; Yuling Bai; Shengping Zhang. Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm. Genes 2021, 12, 584 .
AMA StyleXiaoping Liu, Xingfang Gu, Hongwei Lu, Panna Liu, Han Miao, Yuling Bai, Shengping Zhang. Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm. Genes. 2021; 12 (4):584.
Chicago/Turabian StyleXiaoping Liu; Xingfang Gu; Hongwei Lu; Panna Liu; Han Miao; Yuling Bai; Shengping Zhang. 2021. "Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm." Genes 12, no. 4: 584.
Heat stress during cucumber production often leads to sunburn of leaves, growth retardation of stems and roots, fruit malformation, and even plant death, which have a great impact on the fruit quality and yield. However, no studies on the genetic inheritance and quantitative trait locus mapping of heat tolerance in cucumber at the adult stage have been reported yet. In this study, a set of 86 recombinant inbred lines (RILs) derived from “99281” (heat-tolerant) and “931” (heat-sensitive) were used to identify the heat tolerance QTL in summer 2018, 2019, and 2020. Eight-week-old plants were exposed to a natural high temperature environment in the field, and the heat injury index was used to indicate the heat tolerance performance. Genetic analysis showed that the heat tolerance of adult cucumber is quantitatively inherited. One QTL named qHT1.1 on chromosome 1 was identified. It was delimited by Indel 3-3 and Indel 1-15 and explained 59.6%, 58.1%, and 40.1% of the phenotypic variation in 2018, 2019, and 2020, respectively. The efficiency of marker HT-1, which is closely linked to the locus, was tested using 62 cucumber germplasm accessions and was found to have an accuracy of 97.8% in heat sensitive plants. The qHT1.1 was delimited to a 694.5-kb region, containing 98 genes, nine of which may be involved in heat tolerance. Further sequence analysis showed that there are three single-base substitutions within the coding sequences of Csa1G004990. Gene expression analyses suggested that the expression of Csa1G004990 was significantly higher in “99281” than “931” at 14d, 35d, 42d, and 49d after transplanting. This study provides practically useful markers for heat tolerance breeding in cucumber and provides a basis for further identifying heat tolerant genes.
Yanyan Liu; Shaoyun Dong; Shuang Wei; Weiping Wang; Han Miao; Kailiang Bo; Xingfang Gu; Shengping Zhang. QTL Mapping of Heat Tolerance in Cucumber (Cucumis sativus L.) at Adult Stage. Plants 2021, 10, 324 .
AMA StyleYanyan Liu, Shaoyun Dong, Shuang Wei, Weiping Wang, Han Miao, Kailiang Bo, Xingfang Gu, Shengping Zhang. QTL Mapping of Heat Tolerance in Cucumber (Cucumis sativus L.) at Adult Stage. Plants. 2021; 10 (2):324.
Chicago/Turabian StyleYanyan Liu; Shaoyun Dong; Shuang Wei; Weiping Wang; Han Miao; Kailiang Bo; Xingfang Gu; Shengping Zhang. 2021. "QTL Mapping of Heat Tolerance in Cucumber (Cucumis sativus L.) at Adult Stage." Plants 10, no. 2: 324.
Cucumber is very sensitive to salt stress, and excessive salt content in soils seriously affects normal growth and development, posing a serious threat to commercial production. In this study, the recombinant inbred line (RIL) population (from a cross between the salt tolerant line CG104 and salt sensitive line CG37) was used to study the genetic mechanism of salt tolerance in cucumber seedlings. At the same time, the candidate genes within the mapping region were cloned and analyzed. The results showed that salt tolerance in cucumber seedlings is a quantitative trait controlled by multiple genes. In experiments carried out in April and July 2019, qST6.2 on chromosome six was repeatedly detected. It was delimited into a 1397.1 kb region, and nine genes related to salt tolerance were identified. Among these genes, Csa6G487740 and Csa6G489940 showed variations in amino acid sequence between lines CG104 and CG37. Subsequent qRT-PCR showed that the relative expression levels of both genes during salt treatment were significantly different between the two parents. These results provide a basis for the fine mapping of salt tolerant genes and further study of the molecular mechanism of salt tolerance in cucumber seedlings.
Dongrang Liu; Shaoyun Dong; Kailiang Bo; Han Miao; Caixia Li; Yanyan Zhang; Shengping Zhang; Xingfang Gu. Identification of QTLs Controlling Salt Tolerance in Cucumber (Cucumis sativus L.) Seedlings. Plants 2021, 10, 85 .
AMA StyleDongrang Liu, Shaoyun Dong, Kailiang Bo, Han Miao, Caixia Li, Yanyan Zhang, Shengping Zhang, Xingfang Gu. Identification of QTLs Controlling Salt Tolerance in Cucumber (Cucumis sativus L.) Seedlings. Plants. 2021; 10 (1):85.
Chicago/Turabian StyleDongrang Liu; Shaoyun Dong; Kailiang Bo; Han Miao; Caixia Li; Yanyan Zhang; Shengping Zhang; Xingfang Gu. 2021. "Identification of QTLs Controlling Salt Tolerance in Cucumber (Cucumis sativus L.) Seedlings." Plants 10, no. 1: 85.
The GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) proteins are a family of plant-specific transcription factors that regulate plant growth, development, and stress response. Currently, the role of GRAS transcription factors in various abiotic stress responses has not been systematically studied in cucumber (Cucumis sativus L.), a popular vegetable crop. Here, we provide a comprehensive bioinformatics analysis of the 35 GRAS genes identified in the cucumber genome. In this study, cucumber genotypes, i.e., “CG104”, which is stress-tolerant, and genotype “CG37”, which is stress-sensitive, were examined to provide insight on potential differences in the GRAS-regulated abiotic stress pathways. Transcriptional analysis by RNA-seq or qRT-PCR of these two genotypes revealed common and divergent functions of CsGRAS genes regulated by low and high temperatures, salinity, and by exposure to the phytohormones gibberellin (GA) and abscisic acid (ABA). Notably, CsGRAS2 (DELLA) and CsGRAS26 (LISCL) were regulated by all abiotic stresses and hormone treatments, suggesting that they may function in the biological cross-talk between multiple signaling pathways. This study provides candidate genes for improving cucumber tolerance to various environmental stresses.
Caixia Li; Shaoyun Dong; Xiaoping Liu; Kailiang Bo; Han Miao; Diane M. Beckles; Shengping Zhang; Xingfang Gu. Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses. Horticulturae 2020, 6, 110 .
AMA StyleCaixia Li, Shaoyun Dong, Xiaoping Liu, Kailiang Bo, Han Miao, Diane M. Beckles, Shengping Zhang, Xingfang Gu. Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses. Horticulturae. 2020; 6 (4):110.
Chicago/Turabian StyleCaixia Li; Shaoyun Dong; Xiaoping Liu; Kailiang Bo; Han Miao; Diane M. Beckles; Shengping Zhang; Xingfang Gu. 2020. "Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses." Horticulturae 6, no. 4: 110.
Downy mildew (DM) is one of the most serious diseases in cucumber. Multiple quantitative trait loci (QTLs) for DM resistance have been detected in a limited number of cucumber accessions. In this study we applied genome-wide association analysis (GWAS) to detected genetic loci for DM resistance in a core germplasm (CG) of cucumber lines that represent diverse origins and ecotypes. Phenotypic data on responses to DM infection were collected in four field trials across three years, 2014, 2015, and 2016. With the resequencing data of these CG lines, GWAS for DM resistance was performed and detected 18 loci that were distributed on all the seven cucumber chromosomes. Of these 18 loci, only six (dmG1.4, dmG4.1, dmG4.3, dmG5.2, dmG7.1, and dmG7.2) were detected in two experiments, and were considered as loci with a stable effect on DM resistance. Further, 16 out of the 18 loci colocalized with the QTLs that were reported in previous studies and two loci, dmG2.1 and dmG7.1, were novel ones identified only in this study. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, several candidate genes were identified as potential causal genes underlying the stable and novel loci, including Csa1G575030 for dmG1.4, Csa2G060360 for dmG2.1, Csa4G064680 for dmG4.1, Csa5G606470 for dmG5.2, and Csa7G004020 for dmG7.1. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for DM resistance. The potential of using these CG lines for future allele-mining of candidate genes was discussed in the context of breeding cucumber with resistance to DM.
Xiaoping Liu; Hongwei Lu; Panna Liu; Han Miao; Yuling Bai; Xingfang Gu; Shengping Zhang. Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS. Plants 2020, 9, 1659 .
AMA StyleXiaoping Liu, Hongwei Lu, Panna Liu, Han Miao, Yuling Bai, Xingfang Gu, Shengping Zhang. Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS. Plants. 2020; 9 (12):1659.
Chicago/Turabian StyleXiaoping Liu; Hongwei Lu; Panna Liu; Han Miao; Yuling Bai; Xingfang Gu; Shengping Zhang. 2020. "Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS." Plants 9, no. 12: 1659.
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.
Shaoyun Dong; Song Zhang; Shuang Wei; Yanyan Liu; Caixia Li; Kailiang Bo; Han Miao; Xingfang Gu; Shengping Zhang. Identification of Quantitative Trait Loci Controlling High-Temperature Tolerance in Cucumber (Cucumis sativus L.) Seedlings. Plants 2020, 9, 1155 .
AMA StyleShaoyun Dong, Song Zhang, Shuang Wei, Yanyan Liu, Caixia Li, Kailiang Bo, Han Miao, Xingfang Gu, Shengping Zhang. Identification of Quantitative Trait Loci Controlling High-Temperature Tolerance in Cucumber (Cucumis sativus L.) Seedlings. Plants. 2020; 9 (9):1155.
Chicago/Turabian StyleShaoyun Dong; Song Zhang; Shuang Wei; Yanyan Liu; Caixia Li; Kailiang Bo; Han Miao; Xingfang Gu; Shengping Zhang. 2020. "Identification of Quantitative Trait Loci Controlling High-Temperature Tolerance in Cucumber (Cucumis sativus L.) Seedlings." Plants 9, no. 9: 1155.
Green flesh color, resulting from the accumulation of chlorophyll, is one of the most important commercial traits for the fruits. The genetic network regulating green flesh formation has been studied in tomato, melon and watermelon. However, little is known about the inheritance and molecular basis of green flesh in cucumber. This study sought to determine the main genomic regions associated with green flesh. Three F2 and two BC1 populations derived from the 9110Gt (cultivated cucumber, green flesh color) and PI183967 (wild cucumber, white flesh color) were used for the green flesh genetic analysis. Two F2 populations of them were further employed to do the map construction and quantitative trait loci (QTL) study. Also, a core cucumber germplasms population was used to do the GWAS analysis. We identified three indexes, flesh color (FC), flesh extract color (FEC) and flesh chlorophyll content (FCC) in three environments. Genetic analysis indicated that green flesh color in 9110Gt is controlled by a major-effect QTL. We developed two genetic maps with 192 and 174 microsatellite markers respectively. Two novel inversions in Chr1 were identified between cultivated and wild cucumbers. The major-effect QTL, qgf5.1, was identified using FC, FEC and FCC index in all different environments used. In addition, the same qgf5.1, together with qgf3.1, was identified via GWAS. Further investigation of two candidate regions using pairwise LD correlations, combined with genetic diversity of qgf5.1 in natural populations, it was found that Csa5G021320 is the candidate gene of qgf5.1. Geographical distribution revealed that green flesh color formation could be due to the high latitude, which has longer day time to produce the photosynthesis and chlorophyll synthesis during cucumber domestication and evolution. We first reported the cucumber green flesh color is a quantitative trait. We detected two novel loci qgf5.1 and qgf3.1, which regulate the green flesh formation in cucumber. The QTL mapping and GWAS approaches identified several candidate genes for further validation using functional genomics or forward genetics approaches. Findings from the present study provide a new insight into the genetic control of green flesh in cucumber.
Kailiang Bo; Shuang Wei; Weiping Wang; Han Miao; Shaoyun Dong; Shengping Zhang; Xingfang Gu. QTL mapping and genome-wide association study reveal two novel loci associated with green flesh color in cucumber. BMC Plant Biology 2019, 19, 1 -13.
AMA StyleKailiang Bo, Shuang Wei, Weiping Wang, Han Miao, Shaoyun Dong, Shengping Zhang, Xingfang Gu. QTL mapping and genome-wide association study reveal two novel loci associated with green flesh color in cucumber. BMC Plant Biology. 2019; 19 (1):1-13.
Chicago/Turabian StyleKailiang Bo; Shuang Wei; Weiping Wang; Han Miao; Shaoyun Dong; Shengping Zhang; Xingfang Gu. 2019. "QTL mapping and genome-wide association study reveal two novel loci associated with green flesh color in cucumber." BMC Plant Biology 19, no. 1: 1-13.
Poor seed germination of cucumber at suboptimal temperatures is a great concern for growers wishing to take advantage of the early market. The development of low‐temperature‐tolerant varieties would be aided by understanding the inheritance of the trait and mapping its locus. In this study, a set of 140 recombinant inbred lines (RILs) derived from a cross between 65G (low‐temperature‐tolerant) and 02245 (low‐temperature‐sensitive) was used to identify the QTLs linked with low‐temperature tolerance. A linkage map was developed using 135 simple sequence repeat (SSR) markers and five insertion–deletion (Indel) markers, and three QTLs were identified, qLTG1.1, qLTG2.1 and qLTG4.1. qLTG1.1, the major one for germination rate, germination energy and germination index, explained more than 50% of the observed phenotypic variability. The major QTL for radicle length, qLTG4.1, explained 13.8% of the phenotypic variability. The results showed that qLTG1.1 and qLTG4.1 play an important role in low‐temperature tolerance during seed germination of cucumber and provide a basis for further fine mapping to determine the molecular mechanism for this trait.
Zichao Song; Weiping Wang; Lixue Shi; Song Zhang; Qing Xie; Shuang Wei; Ye Wang; Kailiang Bo; Han Miao; Shengping Zhang; Xingfang Gu. Identification of QTLs controlling low-temperature tolerance during the germination stage in cucumber (Cucumis sativusL.). Plant Breeding 2018, 137, 629 -637.
AMA StyleZichao Song, Weiping Wang, Lixue Shi, Song Zhang, Qing Xie, Shuang Wei, Ye Wang, Kailiang Bo, Han Miao, Shengping Zhang, Xingfang Gu. Identification of QTLs controlling low-temperature tolerance during the germination stage in cucumber (Cucumis sativusL.). Plant Breeding. 2018; 137 (4):629-637.
Chicago/Turabian StyleZichao Song; Weiping Wang; Lixue Shi; Song Zhang; Qing Xie; Shuang Wei; Ye Wang; Kailiang Bo; Han Miao; Shengping Zhang; Xingfang Gu. 2018. "Identification of QTLs controlling low-temperature tolerance during the germination stage in cucumber (Cucumis sativusL.)." Plant Breeding 137, no. 4: 629-637.
Leaf color mutants are common in higher plants that can be used as markers in crop breeding or as an important tool in understanding regulatory mechanisms in chlorophyll biosynthesis and chloroplast development. In virescent leaf mutants, young leaves are yellow in color, which gradually return to normal green when the seedlings grow large. In the present study, we conducted phenotypic characterization and genetic mapping of the cucumber virescent leaf mutant 9110Gt conferred by the v-1 locus. Total chlorophyll and carotenoid content in 9110Gt was reduced by 44% and 21%, respectively, as compared with its wild type parental line 9110G. Electron microscopic investigation revealed fewer chloroplasts per cell and thylakoids per chloroplast in 9110Gt than in 9110G. Fine genetic mapping allowed for the assignment of the v-1 locus to a 50.4 kb genomic DNA region in chromosome 6 with two flanking markers that were 0.14 and 0.16 cM away from v-1, respectively. Multiple lines of evidence supported CsaCNGCs as the only candidate gene for the v-1 locus, which encoded a cyclic-nucleotide-gated ion channel protein. A single nucleotide change in the promoter region of v-1 seemed to be associated with the virescent color change in 9110Gt. Real-time PCR revealed significantly lower expression of CsaCNGCs in the true leaves of 9110Gt than in 9110G. This was the first report that connected the CsaCNGCs gene to virescent leaf color change, which provided a useful tool to establish linkages among virescent leaf color change, chloroplast development, chlorophyll biosynthesis, and the functions of the CsaCNGCs gene.
Han Miao; Shengping Zhang; Min Wang; Ye Wang; Yiqun Weng; Xingfang Gu. Fine Mapping of Virescent Leaf Gene v-1 in Cucumber (Cucumis sativus L.). International Journal of Molecular Sciences 2016, 17, 1602 .
AMA StyleHan Miao, Shengping Zhang, Min Wang, Ye Wang, Yiqun Weng, Xingfang Gu. Fine Mapping of Virescent Leaf Gene v-1 in Cucumber (Cucumis sativus L.). International Journal of Molecular Sciences. 2016; 17 (10):1602.
Chicago/Turabian StyleHan Miao; Shengping Zhang; Min Wang; Ye Wang; Yiqun Weng; Xingfang Gu. 2016. "Fine Mapping of Virescent Leaf Gene v-1 in Cucumber (Cucumis sativus L.)." International Journal of Molecular Sciences 17, no. 10: 1602.
Plant volatile organic compounds, which are generated in a tissue-specific manner, play important ecological roles in the interactions between plants and their environments, including the well-known functions of attracting pollinators and protecting plants from herbivores/fungi attacks. However, to date, there have not been reports of holistic volatile profiling of the various tissues of a single plant species, even for the model plant species. In this study, we qualitatively and quantitatively analyzed 85 volatile chemicals, including 36 volatile terpenes, in 23 different tissues of cucumber (Cucumis sativus) plants using solid-phase microextraction combined with gas chromatography-mass spectrometry. Most volatile chemicals were found to occur in a highly tissue-specific manner. The consensus transcriptomes for each of the 23 cucumber tissues were generated with RNA sequencing data and used in volatile organic compound-gene correlation analysis to screen for candidate genes likely to be involved in cucumber volatile biosynthetic pathways. In vitro biochemical characterization of the candidate enzymes demonstrated that TERPENE SYNTHASE11 (TPS11)/TPS14, TPS01, and TPS15 were responsible for volatile terpenoid production in the roots, flowers, and fruit tissues of cucumber plants, respectively. A functional heteromeric geranyl(geranyl) pyrophosphate synthase, composed of an inactive small subunit (type I) and an active large subunit, was demonstrated to play a key role in monoterpene production in cucumber. In addition to establishing a standard workflow for the elucidation of plant volatile biosynthetic pathways, the knowledge generated from this study lays a solid foundation for future investigations of both the physiological functions of cucumber volatiles and aspects of cucumber flavor improvement.
Guo Wei; Peng Tian; Fengxia Zhang; Hao Qin; Han Miao; Qingwen Chen; Zhongyi Hu; Li Cao; Meijiao Wang; Xingfang Gu; Sanwen Huang; Mingsheng Chen; Guodong Wang. Integrative Analyses of Nontargeted Volatile Profiling and Transcriptome Data Provide Molecular Insight into VOC Diversity in Cucumber Plants (Cucumis sativus). Plant Physiology 2016, 172, 603 -618.
AMA StyleGuo Wei, Peng Tian, Fengxia Zhang, Hao Qin, Han Miao, Qingwen Chen, Zhongyi Hu, Li Cao, Meijiao Wang, Xingfang Gu, Sanwen Huang, Mingsheng Chen, Guodong Wang. Integrative Analyses of Nontargeted Volatile Profiling and Transcriptome Data Provide Molecular Insight into VOC Diversity in Cucumber Plants (Cucumis sativus). Plant Physiology. 2016; 172 (1):603-618.
Chicago/Turabian StyleGuo Wei; Peng Tian; Fengxia Zhang; Hao Qin; Han Miao; Qingwen Chen; Zhongyi Hu; Li Cao; Meijiao Wang; Xingfang Gu; Sanwen Huang; Mingsheng Chen; Guodong Wang. 2016. "Integrative Analyses of Nontargeted Volatile Profiling and Transcriptome Data Provide Molecular Insight into VOC Diversity in Cucumber Plants (Cucumis sativus)." Plant Physiology 172, no. 1: 603-618.