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Agronomy
Special Issues
Genomics and Genetic Improvement of Bast Fiber Plants
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Genomics and Genetic Improvement of Bast Fiber Plants

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 31 May 2024 | Viewed by 4567

Special Issue Editors

Prof. Dr. Siyuan Zhu

E-Mail Website
Guest Editor
Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
Interests: bast fiber crop; genomics; genetic improvement; molecular breeding
Prof. Dr. Mingbao Luan

E-Mail Website
Guest Editor
Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
Interests: bast fiber crop; genomics; genetic improvement; molecular breeding

Special Issue Information

Dear Colleagues,

Bast fiber is one of the most important fibers, and it is typically extracted from the stem barks and leaves of crops including jute, flax, ramie, hemp, kenaf, and sisal. In the past decades, with the development of sequencing technology, reference genomes for major bast fiber crops including jute, kenaf, ramie, hemp, and flax have been released. Based on the reference genome and transcriptome sequencing, a large number of candidate genes related to fiber development and specific traits have been mined, which provides the possibility for the genetic improvement of bast fiber crops based on omics. The molecular basis of the formation of agronomic traits such as fiber yield, fiber quality, disease resistance, and resistance has been systematically analyzed, contributing to the establishment of a high-throughput genotype–phenotype database, where excellent genetic resources and new germplasms have been mined to breed new varieties of bast fiber crops with high yield and high quality to meet the market demand.

The objective of this Special Issue entitled “Genomics and Genetic Improvement of Bast Fiber Plants” is to gather and disseminate some of the most significant and recent contributions on the latest developments and advances in the application of the genomics and genetic breeding of bast fiber crops.  Accordingly, we cordially invite authors to contribute original research papers and reviews.

The topics include, but are not limited to, the following: gathering and disseminating some of the most significant and recent contributions on the latest developments and advances in the application of the genomics and genetic breeding of bast fiber crops. Accordingly, we cordially invite authors to contribute original research papers and reviews.

Prof. Dr. Siyuan Zhu
Prof. Dr. Mingbao Luan
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bast fiber crop
  • genomics
  • genetic improvement
  • molecular breeding

Published Papers (4 papers)

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Research

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15 pages, 3385 KiB  
Article
Development of Expressed Sequence Tag–Simple Sequence Repeat Markers Related to the Salt-Stress Response of Kenaf (Hibiscus cannabinus)
by Xia An, Qin Liu, Jinyao Ying, Jiqian Wei, Guoyun Dong, Xiahong Luo, Wenlue Li, Tingting Liu, Huaping Zhou, Lina Zou and Changli Chen
Agronomy 2023, 13(7), 1946; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13071946 - 23 Jul 2023
Viewed by 930
Abstract
Kenaf is one of the most important natural cannabis plants. Molecular marker-assisted breeding is vital for accelerating the breeding process of kenaf. However, the number of kenaf markers is insufficient for molecular marker-assisted breeding. Using transcriptome sequencing data for salt-stressed kenaf plants, the [...] Read more.
Kenaf is one of the most important natural cannabis plants. Molecular marker-assisted breeding is vital for accelerating the breeding process of kenaf. However, the number of kenaf markers is insufficient for molecular marker-assisted breeding. Using transcriptome sequencing data for salt-stressed kenaf plants, the number and distribution of simple sequence repeats (SSRs) and single nucleotide variations (SNVs) in the expressed sequences were determined. The objectives of this study were to elucidate the sequence variations in kenaf genes expressed in response to salt stress and to identify stable and dependable molecular markers. Primers were designed for SSR loci and then EST-SSR molecular markers were generated. The subsequent analyses revealed that 30.50% of the unigenes contained SSR motifs, most of which were single nucleotides followed by trinucleotides and dinucleotides. The unigenes containing SSRs were mostly associated with kenaf salt tolerance. Additionally, 10,483 SNVs were detected in contig sequences. Of the 3995 differentially expressed genes encoding interacting proteins, 1297 contained SSRs. Most of these genes were associated with metabolic pathways (e.g., 03000 transcription factors, B09132 signal transduction, and 04122 sulfur relay system). We designed 20 pairs of EST-SSR primers to genotype 30 kenaf varieties (lines), of which 9 primer pairs were ideal for genotyping (e.g., 1 highly polymorphic marker and 2 moderately polymorphic markers). The primer pairs designed for the EST-SSR markers in the kenaf genome may be useful SSR molecular markers for future research on kenaf. The verified polymorphic markers may be applicable to the molecular marker-assisted breeding of salt-tolerant kenaf varieties. Full article
(This article belongs to the Special Issue Genomics and Genetic Improvement of Bast Fiber Plants)
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17 pages, 9287 KiB  
Article
Genome-Wide Identification and Expression Pattern Analysis of the F5H Gene Family in Flax (Linum usitatissimum L.)
by Dandan Liu, Hongmei Yuan, Yubo Yao, Lili Cheng, Lili Tang, Qinghua Kang, Xixia Song, Si Chen and Guangwen Wu
Agronomy 2023, 13(4), 1108; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13041108 - 13 Apr 2023
Cited by 1 | Viewed by 1267
Abstract
Ferulate 5-hydroxylase (F5H) is a cytochrome P450-dependent monooxygenase that plays a key role in the biosynthesis of syringyl (S) lignin. In this study, mining of flax (Linum usitatissimum) genomic data enabled the identification of nine LuF5H genes. Bioinformatics analysis revealed the [...] Read more.
Ferulate 5-hydroxylase (F5H) is a cytochrome P450-dependent monooxygenase that plays a key role in the biosynthesis of syringyl (S) lignin. In this study, mining of flax (Linum usitatissimum) genomic data enabled the identification of nine LuF5H genes. Bioinformatics analysis revealed the physicochemical properties, gene structures, conserved motifs, phylogenetic evolutionary features and promoter cis-acting elements related to these genes and their encoded proteins. Based on the gene structural and phylogenetic features, the nine LuF5Hs were assigned to two subclasses. The expression levels of the nine LuF5Hs was analyzed by the RNA-seq technique, and the RNA-seq data were verified by qRT-PCR. The results of the RNA-seq analysis showed that LuF5H genes belonging to the same subclass exhibited similar expression patterns. Notably, the transcripts of the LuF5H3 and LuF5H7 subclass 1 genes accumulated at high levels in stem tissues, thus indicating that LuF5H3 and LuF5H7 are the main LuF5H genes involved in flax lignin biosynthesis. Furthermore, the expression levels of LuF5H1, LuF5H3, LuF5H4 and LuF5H7 were upregulated 1.2–1.9-fold under drought, NaCl stress and brassinosteroid treatment conditions. This first comprehensive study of the flax F5H gene family provides valuable data for use in gene function analysis toward improving flax fiber quality and reducing flax manufacturing costs and associated environmental pollution. Full article
(This article belongs to the Special Issue Genomics and Genetic Improvement of Bast Fiber Plants)
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Other

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11 pages, 4593 KiB  
Brief Report
Genome-Wide Investigation of Knotted Related Homeobox Genes and Identification of a Fiber-Growth-Repressed Knotted Related Homeobox Gene in Ramie
by Jianrong Chen, Xueyu Zhang, Fang Liu, Chan Liu, Yinghong Tang, Chunyan Li, Yuan Gong, Xiaojiang Xu, Yanzhou Wang and Touming Liu
Agronomy 2023, 13(9), 2297; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13092297 - 31 Aug 2023
Viewed by 660
Abstract
The KNOX transcription factor plays crucial roles in regulating fiber growth in plants. Although the genome of ramie, an important fiber crop in China, is available, knotted related homeobox (KNOX) genes have not been systematically explored in this crop. In this study, [...] Read more.
The KNOX transcription factor plays crucial roles in regulating fiber growth in plants. Although the genome of ramie, an important fiber crop in China, is available, knotted related homeobox (KNOX) genes have not been systematically explored in this crop. In this study, seven members of the KNOX gene from the ramie genome were identified and assigned to two groups, Class I and II. The intron–exon structure, conserved domain architecture, cis-regulating elements, and expression pattern showed distinct differences among the seven KNOX regulators. One of the genes, Bnt07G011994, encodes an ortholog of Arabidopsis fiber-growth-related KNAT7, and is differentially expressed among barks undergoing different stages of fiber growth. The overexpression of Bnt07G011994 dramatically decreases the fiber number in transgenic Arabidopsis, indicating a negative role played by this gene in modulating fiber growth. Further transcriptome analysis of transgenic Arabidopsis revealed that the overexpression of Bnt07G011994 resulted in an expression change in 14 pectin biosynthesis-/metabolism-related genes. These findings provide a useful foundation for further investigating the function of KNOX genes in ramie, and provide an important insight into the involvement of the ramie KNOX gene in fiber growth. Full article
(This article belongs to the Special Issue Genomics and Genetic Improvement of Bast Fiber Plants)
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9 pages, 2248 KiB  
Brief Report
Genome-Wide Identification of NAC Genes Associated with Bast Fiber Growth in Ramie (Boehmeria nivea L.)
by Zheng Zeng, Chan Liu, Xueyu Zhang, Siyuan Zhu, Yanzhou Wang and Touming Liu
Agronomy 2023, 13(5), 1311; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13051311 - 06 May 2023
Viewed by 1119
Abstract
NAM, ATAF, and CUC (NAC) proteins are plant-specific transcription factors that play crucial roles in fiber growth by regulating the secondary wall thickening. In this study, a systematical investigation of NAC genes was performed in the genome of ramie, an important fiber crop, [...] Read more.
NAM, ATAF, and CUC (NAC) proteins are plant-specific transcription factors that play crucial roles in fiber growth by regulating the secondary wall thickening. In this study, a systematical investigation of NAC genes was performed in the genome of ramie, an important fiber crop, resulting in a total of 60 ramie NAC genes identified. Phylogenetic analysis of these 60 NAC members in conjunction with 111 Arabidopsis NAC proteins identified 11 subfamilies, three of which showed considerable contraction in the ramie genome. Ten ramie NAC genes were identified to encode the orthologs of Arabidopsis NAC regulators involved in the control of secondary wall biosynthesis. Of these ten genes, most showed relatively high expression in the stems, and eight displayed a differential expression between the barks from the top and middle section of the stems where fiber growth is under different stages. Furthermore, the overexpression of three of these ten NAC genes significantly promoted fiber growth in transgenic Arabidopsis. These results indicated that these ten NAC genes were associated with the fiber growth of ramie. This study provided an important basis for researching the regulatory mechanism of fiber growth. Full article
(This article belongs to the Special Issue Genomics and Genetic Improvement of Bast Fiber Plants)
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