QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber

Lü, Hongfeng; Lin, Tao; Klein, Joel D.; Wang, Shenhao; Qi, Jianjian; Zhou, Qian; Sun, Junling; Zhang, Zhonghua; Weng, Yiqun; Huang, Sanwen

doi:10.1007/s00122-014-2313-z

Cited by 260 publications

(201 citation statements)

References 36 publications

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“…QTL-seq is proposed as an efficient strategy for rapid identification of QTLs, which takes advantage of bulked-segregant analysis and high-throughput genotyping using next-generation sequencing (NGS). This approach has been applied to detecting QTLs in rice, cucumber, tomato, and chickpea1516171819. Previously we constructed a high-density cucumber genetic map compromising 1800 SNPs using F 2 populations derived from CC3 × NC76.…”

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confidence: 99%

Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis

Wei

Wang

et al. 2016

Sci Rep

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The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes.

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confidence: 99%

Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis

Wei

Wang

et al. 2016

Sci Rep

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“…Joint QTL-seq and traditional QTL analysis delimited Ef1.1 to an 890 kb genomic region. A cucumber gene, Csa1G651710, was identified in this region, which is a homolog of the FLOWERING LOCUS T (FT), the main flowering switch gene in Arabidopsis [34].…”

Section: The Utility Of Ngs In Mapping Technologymentioning

confidence: 99%

Next generation sequencing and omics in cucumber ( Cucumis sativus L.) breeding directed research

et al. 2016

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“…Conventional QTL mapping verified the candidate QTLs detected by the QTL-seq, and the method was validated by simulation analysis. QTL-seq has also been used in cucumber to map a QTL involved in flowering trait [101]. Likewise, the deployment of QTL-seq for rapid identification and fine mapping of QTLs was reported in chickpea [102] and sorghum [103].…”

Section: Qtl Identificationmentioning

confidence: 99%

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Gedil¹,

Ferguson²,

Girma³

et al. 2016

Next Generation Sequencing - Advances, Applications and Challenges

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The persistent challenge of insufficient food, unbalanced nutrition, and deteriorating natural resources in the most vulnerable nations, characterized by fast population growth, calls for utilization of innovative technologies to curb constraints of crop production. Enhancing genetic gain by using a multipronged approach that combines conventional and genomic technologies for the development of stress-tolerant varieties with high yield and nutritional quality is necessary. The advent of nextgeneration sequencing (NGS) technologies holds the potential to dramatically impact the crop improvement process. NGS enables whole-genome sequencing (WGS) and re-sequencing, transcriptome sequencing, metagenomics, as well as high-throughput genotyping, which can be applied for genome selection (GS). It can also be applied to diversity analysis, genetic and epigenetic characterization of germplasm and pathogen detection, identification, and elimination. High-throughput phenotyping, integrated data management, and decision support tools form the necessary supporting environment for effective utilization of genome sequence information. It is important that these opportunities for mainstreaming innovative breeding strategies, enabled by cutting-edge "Omics" technologies, are seized in Africa; however, several constraints must be addressed before the benefit of NGS can be fully realized. African breeding programs must have access to high-throughput genotyping facilities, capacity in the application of genome selection and marker-assisted breeding must be built and supported by capacity in genomic analysis and bioinformatics. This chapter demonstrates how interventions with NGS-enabled innovative strategies can be applied to increase genetic gain with insights from the Consortium of International

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QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber

Cited by 260 publications

References 36 publications

Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis

Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis

Next generation sequencing and omics in cucumber ( Cucumis sativus L.) breeding directed research

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

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