Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis

Chen, Jianrong; Rao, Jing; Wang, Yanzhou; Zeng, Zheng; Liu, Fang; Tang, Yuxuan; Chen, Xiaorong; Lee, Chan; Liu, Touming

doi:10.3390/genes10110842

Cited by 5 publications

(3 citation statements)

References 33 publications

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“…However, none of these genes were confirmed to be involved in fibre development. Recent genetic studies identified some genetic loci associated with fibre traits (Chen et al, 2019;Liu et al, 2014cLiu et al, , 2017Zeng et al, 2019); however, these loci showed limited benefits for breeding improvement based on marker-assisted selection because the examined population originates from only a few parent individuals, which provided only a limited number of excellent alleles.…”

Section: Introductionmentioning

confidence: 99%

Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits

Zeng

Zhu

Wang

et al. 2021

Plant Biotechnology Journal

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Summary Ramie is an important fibre‐producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fibre yield‐related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fibre abundance, providing the first evidence for the role of pectin methylesterase in fibre growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focussed on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin‐signalling‐repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fibre yield traits in ramie. Moreover, the identification of fibre yield‐related genetic loci and large‐scale genomic variation represent valuable resources for genomics‐assisted breeding of this crop.

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Section: Introductionmentioning

confidence: 99%

Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits

Zeng

Zhu

Wang

et al. 2021

Plant Biotechnology Journal

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“…Unfortunately, the information on QTL mapping in ramie is negligible, which needs urgent studies to screen the population for Cd tolerance and identify the QTL to be used in the QTL pyramiding program [36,126]. Researchers have identified QTL in ramie, which were mainly related to fiber yield-related traits, lignin biosynthesis, and flowering time [126][127][128][129]. Choosing an ideal mapping population is critical in identifying dominant regions controlling Cd tolerance [125].…”

Section: Qtl Mapping For CD Tolerance In Ramiementioning

confidence: 99%

A Systematic Review on the Improvement of Cd Stress Tolerance in Ramie Crop, Limitations and Future Prospective

Rasheed,

Jie,

et al. 2023

Agronomy

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Cadmium (Cd) is a non-essential, highly phytotoxic metal and damages ramie plant growth and development even at low concentrations. Ramie is one of the most significant crops in China, with excellent fiber quality and immense industrial importance. Planting Cd-tolerant ramie cultivars can prevent yield loss on contaminated soil. Previously, significant efforts have been made to develop Cd tolerance in ramie. However, the Cd tolerance mechanism is still not fully understood; hence, breeding industrial crops is critical to tackling the ongoing challenges. Cd tolerance is a complex genetic mechanism requiring high-level molecular studies to clarify the genes network. Genetic studies have identified several Cd-tolerant genes in ramie, which led to the development of several ramie cultivars suitable to grow on toxic soils; however, due to the continuous rise in Cd toxicity, potent molecular tools are critical in modern-day breeding programs. Genetic engineering, and transcriptome analysis have been used to develop abiotic stress tolerance in ramie, but QTL mapping and clustered regularly interspaced short palindromic repeats (CRISPR) are rarely studied. However, studies are still limited in addressing this issue. This review critically elaborated on using QTL mapping, transcriptomes, transcription factors, CRISPR/Cas9, and genetic engineering to enhance Cd tolerance in ramie. These genes/QTL should be transferred or edited into sensitive cultivars using genetic engineering or CRISPR/Cas9. CRISPR/Cas9 is highly recommended because it provides targeted gene editing in ramie, its use is limited and can address the research gaps, and it would revolutionize the field of agriculture. Limitations, gaps, and future potential are briefly discussed. This review paper presents new clues to help future researchers comprehensively understand Cd tolerance in ramie and develop tolerant cultivars for industrial purposes.

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“…The rapid development of next-generation sequencing technology has recently led to the identification of large-scale single-nucleotide polymorphisms (SNPs) in ramie, resulting in several high-density genetic maps ( Liu et al, 2017 ; Zeng et al, 2019 ). Consequently, the genetic architecture of many agronomic traits, such as fiber yield, quality, and flowering time, has been systematically characterized using linkage mapping and genome-wide association mapping ( Zhu et al, 2016 ; Liu et al, 2017 ; Chen et al, 2018 , 2019 ; Zeng et al, 2019 , 2022 ; Huang et al, 2021 ; Wang et al, 2021 ), and several candidates across various loci have been documented ( Liu et al, 2017 ; Wang et al, 2021 ; Zeng et al, 2022 ). Recently, ramie feeding traits have also been researched, and the genetic basis of six forage yield-related traits was characterized, resulting in 78 significant association signals from 43 genomic regions ( Bai et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic insights into the crude protein and fiber content of ramie leaves

Zeng

Yang

et al. 2022

Front. Plant Sci.

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Ramie (Boehmeria nivea L.) is a perennial plant with vigorously vegetative growth and high nutritive value that is an excellent source of green feed in China. Crude protein and fiber content are the most important traits associated with ramie forage quality; however, their genetic basis remains largely unknown. In this study, we investigated the genetic architecture of these two traits using an F2 population derived from cultivated Zhongsizhu 1 (ZSZ1) and wild Boehmeria nivea var. tenacissima (tenacissima). Linkage mapping identified eight quantitative trait loci (QTLs) in crude fiber and one QTL in crude protein. Of these, five were further validated by association analysis. Then, two major QTLs for crude fiber content, CF7 and CF13, were further identified using bulked segregant analysis (BSA) sequencing, and their exact physical intervals were determined via genotype analysis of F2 progenies with extremely low crude fiber content. In total, 10 genes in the CF7 and CF13 regions showed differential expression in ZSZ1 and tenacissima leaves, including an MYB gene whole_GLEAN_10016511 from the CF13 region. Wide variation was observed in the promoter regions of whole_GLEAN_10016511, likely responsible for its downregulated expression in tenacissima. Interestingly, more fiber cells were observed in Arabidopsis with overexpression of whole_GLEAN_10016511, indicating that the downregulated expression of this gene could have an association with the relatively low fiber content in wild tenacissima. These results provided evidence that whole_GLEAN_10016511 is a logical candidate for CF13. This study provides important insights into the genetic basis underlying ramie crude protein and fiber content, and it presents genetic loci for improving the forage quality of ramie using marker-assisted selection.

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Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis

Cited by 5 publications

References 33 publications

Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits

Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits

A Systematic Review on the Improvement of Cd Stress Tolerance in Ramie Crop, Limitations and Future Prospective

Genetic insights into the crude protein and fiber content of ramie leaves

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