Genetic and Transcriptomic Analysis Reveal the Molecular Basis of Photoperiod-Regulated Flowering in Xishuangbanna Cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan)

Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan), is a botanical variety of cucumber cultivars native to southwest China that possesses excellent agronomic traits for cucumber improvement. However, breeding utilization of XIS cucumber is limited due to the current poor understanding of its photoperiod-sensitive flowering characteristics. In this study, genetic and transcriptomic analysis were conducted to reveal the molecular basis of photoperiod-regulated flowering in XIS cucumber. A major-effect QTL locus DFF1.1 was identified that controls the days to first flowering (DFF) of XIS cucumbers with a span of 1.38 Mb. Whole-genome re-sequencing data of 9 cucumber varieties with different flowering characteristics in response to photoperiod suggested that CsaNFYA1 was the candidate gene of DFF1.1, which harbored a single non-synonymous mutation in its fifth exon. Transcriptomic analysis revealed the positive roles of auxin and ethylene in accelerating flowering under short-day (SD) light-dark cycles when compared with equal-day/night treatment. Carbohydrate storage and high expression levels of related genes were important reasons explaining early flowering of XIS cucumber under SD conditions. By combining with the RNA-Seq data, the co-expression network suggested that CsaNFYA1 integrated multiple types of genes to regulate the flowering of XIS cucumber. Our findings explain the internal regulatory mechanisms of a photoperiodic flowering pathway. These findings may guide the use of photoperiod shifts to promote flowering of photoperiod-sensitive crops.

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Identification of A Key Major-Effect QTL Associated With Pre-Harvest Sprouting in Cucumber (Cucumis Sativus L.) Using the QTL-Seq Method

10.21203/rs.3.rs-137478/v1 ◽

2021 ◽

Author(s):

Ming ming Cao ◽

Shu ju Li ◽

Qiang Deng ◽

Hui zhe Wang ◽

Rui huan Yang

Keyword(s):

Cucumis Sativus ◽

Molecular Mechanisms ◽

Bulked Segregant Analysis ◽

Resistance Breeding ◽

Major Effect ◽

Chromosome 4 ◽

Cucumis Sativus L ◽

Whole Genome Resequencing ◽

Candidate Regions ◽

Segregating Population

Abstract Background: Cucumber (Cucumis sativusL.) is cultivated worldwide, and it is essential to produce enough high-quality seeds to meet demand. Pre-harvest sprouting (PHS) in cucumber is a critical problem and causes serious damage to seed production and quality. Nevertheless, the genetic basis and molecular mechanisms underlying cucumber PHS remain unclear. QTL-seq is an efficient approach for rapid quantitative trait loci (QTL) identificationthat simultaneously takes advantage of bulked-segregant analysis (BSA) and whole-genome resequencing. In the present research, QTL-seq analysis was performed to identify QTLs associated with PHS in cucumber using an F2 segregating population.Results: Two QTLs that spanned 7.3 Mb on Chromosome 4 and 0.15 Mb on Chromosome 5 were identified by QTL-seq and named qPHS4.1and qPHS5.1, respectively. Subsequently, SNP and InDel markers selected fromthe candidate regions were used to refine the intervals using the extended F2populations grown in the 2016 and 2017 seasons. Finally, qPHS4.1 was narrowed to 0.53 Mb on chromosome 4 flanked by the markers SNP-16 and SNP-24 and was found to explain 19-22% of the phenotypic variation in cucumber PHS. These results reveal that qPHS4.1 is the key major-effect QTL associated with PHS in cucumber. Based on gene annotations and qRT-PCR expression analyses, Csa4G622760and Csa4G622800 were proposed as the candidate genes. Conclusions: These results provide novel insights into the genetic mechanism controlling PHS in cucumber and highlight the potential for marker-assisted selection of PHS resistance breeding.

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Transcriptomic Analysis Implies That GA Regulates Sex Expression via Ethylene-Dependent and Ethylene-Independent Pathways in Cucumber (Cucumis sativus L.)

Frontiers in Plant Science ◽

10.3389/fpls.2017.00010 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 3

Author(s):

Yan Zhang ◽

Guiye Zhao ◽

Yushun Li ◽

Ning Mo ◽

Jie Zhang ◽

...

Keyword(s):

Cucumis Sativus ◽

Sex Expression ◽

Transcriptomic Analysis ◽

Cucumis Sativus L

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Identification of a major-effect QTL associated with pre-harvest sprouting in cucumber (Cucumis sativus L.) using the QTL-seq method

BMC Genomics ◽

10.1186/s12864-021-07548-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Mingming Cao ◽

Shuju Li ◽

Qiang Deng ◽

Huizhe Wang ◽

Ruihuan Yang

Keyword(s):

Cucumis Sativus ◽

Molecular Mechanisms ◽

Bulked Segregant Analysis ◽

Resistance Breeding ◽

Major Effect ◽

Chromosome 4 ◽

Cucumis Sativus L ◽

Whole Genome Resequencing ◽

Candidate Regions ◽

Segregating Population

Abstract Background Cucumber (Cucumis sativus L.) is cultivated worldwide, and it is essential to produce enough high-quality seeds to meet demand. Pre-harvest sprouting (PHS) in cucumber is a critical problem and causes serious damage to seed production and quality. Nevertheless, the genetic basis and molecular mechanisms underlying cucumber PHS remain unclear. QTL-seq is an efficient approach for rapid quantitative trait loci (QTL) identification that simultaneously takes advantage of bulked-segregant analysis (BSA) and whole-genome resequencing. In the present research, QTL-seq analysis was performed to identify QTLs associated with PHS in cucumber using an F2 segregating population. Results Two QTLs that spanned 7.3 Mb on Chromosome 4 and 0.15 Mb on Chromosome 5 were identified by QTL-seq and named qPHS4.1 and qPHS5.1, respectively. Subsequently, SNP and InDel markers selected from the candidate regions were used to refine the intervals using the extended F2 populations grown in the 2016 and 2017 seasons. Finally, qPHS4.1 was narrowed to 0.53 Mb on chromosome 4 flanked by the markers SNP-16 and SNP-24 and was found to explain 19–22% of the phenotypic variation in cucumber PHS. These results reveal that qPHS4.1 is a major-effect QTL associated with PHS in cucumber. Based on gene annotations and qRT-PCR expression analyses, Csa4G622760 and Csa4G622800 were proposed as the candidate genes. Conclusions These results provide novel insights into the genetic mechanism controlling PHS in cucumber and highlight the potential for marker-assisted selection of PHS resistance breeding.

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