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Genetics and Genomics of the Brassicaceae
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Genetics and Genomics of the Brassicaceae

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 24198

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Ryo Fujimoto

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Guest Editor
Graduate School of Agricultural Science, Kobe University, Kobe 6578501, Japan
Interests: epigenetics; hybrid vigor; heterosis; vernalization; Brassica
Special Issues, Collections and Topics in MDPI journals
Dr. Yoshinobu Takada

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Guest Editor
Graduate School of Life-Science, Tohoku University, 9808577 Sendai, Japan
Interests: self-incompatibility; unilateral incompatibility; pollen–pistil recognition; Brassica
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Brassicaceae is a diverse family of angiosperms containing 338 genera and 3709 species, including the model plant Arabidopsis thaliana. The genus Brassica includes many economically important crops providing nutrition as well as health-promoting substances. Brassica rapa L. including Chinese cabbage, pak choi, and turnip, and Brassica oleracea L., including cabbage, broccoli, cauliflower, and kohlrabi, show extreme morphological divergence due to selection by the plant breeders. Most cultivars of the Brassica vegetables are F1 hybrids, and a breeding system was successfully established by effectively applying the phenomenon of heterosis/hybrid vigor, cytoplasmic male sterility, or self-incompatibility. Brassica napus comprises important oil seed crops, such as canola or rapeseed.

A famous diagram, Triangle of U, shows the genetic relationship between six species of the genus Brassica; three allotetraploid species, Brassica juncea L. (AABB), Brassica napus L. (AACC), and Brassica carinata L. (BBCC), were derived via hybridization between two diploid species, B. rapa (AA), Brassica nigra L. (BB), and B. oleracea (CC). Recently, whole genome sequences have been determined in some species of Brassicaceae, and the detailed genetic relationships in allotetraploids featured in the U’s triangle have been revealed. In addition, resequencing in more than a hundred lines has shown genetic variation within a species. Basic information based on the reference genome sequence has greatly contributed to the advances in genetic and epigenetic analyses regarding various traits. 

The forthcoming Special Issue aims to provide a comprehensive understanding of genomics and genetic analysis in Brassicaceae. There is particular interest in research on agronomically important traits.

Dr. Ryo Fujimoto
Dr. Yoshinobu Takada
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • comparative genome analysis
  • genetic analysis
  • epigenetics
  • phylogenetic analysis
  • agriculturally important traits
  • flowering time
  • vernalization
  • self-incompatibility
  • cytoplasmic male sterility
  • disease resistance
  • abiotic stress tolerance
  • secondary metabolite

Published Papers (7 papers)

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Research

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11 pages, 3445 KiB  
Article
Genetic Diversity of Genes Controlling Unilateral Incompatibility in Japanese Cultivars of Chinese Cabbage
by Yoshinobu Takada, Atsuki Mihara, Yuhui He, Haolin Xie, Yusuke Ozaki, Hikari Nishida, Seongmin Hong, Yong-Pyo Lim, Seiji Takayama, Go Suzuki and Masao Watanabe
Plants 2021, 10(11), 2467; https://doi.org/10.3390/plants10112467 - 15 Nov 2021
Cited by 4 | Viewed by 1746
Abstract
In recent years, unilateral incompatibility (UI), which is an incompatibility system for recognizing and rejecting foreign pollen that operates in one direction, has been shown to be closely related to self-incompatibility (SI) in Brassica rapa. The stigma- and pollen-side recognition factors ( [...] Read more.
In recent years, unilateral incompatibility (UI), which is an incompatibility system for recognizing and rejecting foreign pollen that operates in one direction, has been shown to be closely related to self-incompatibility (SI) in Brassica rapa. The stigma- and pollen-side recognition factors (SUI1 and PUI1, respectively) of this UI are similar to those of SI (stigma-side SRK and pollen-side SP11), indicating that SUI1 and PUI1 interact with each other and cause pollen-pistil incompatibility only when a specific genotype is pollinated. To clarify the genetic diversity of SUI1 and PUI1 in Japanese B. rapa, here we investigated the UI phenotype and the SUI1/PUI1 sequences in Japanese commercial varieties of Chinese cabbage. The present study showed that multiple copies of nonfunctional PUI1 were located within and in the vicinity of the UI locus region, and that the functional SUI1 was highly conserved in Chinese cabbage. In addition, we found a novel nonfunctional SUI1 allele with a dominant negative effect on the functional SUI1 allele in the heterozygote. Full article
(This article belongs to the Special Issue Genetics and Genomics of the Brassicaceae)
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12 pages, 1855 KiB  
Article
Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables
by Naomi Miyaji, Mst Arjina Akter, Chizuko Suzukamo, Hasan Mehraj, Tomoe Shindo, Takeru Itabashi, Keiichi Okazaki, Motoki Shimizu, Makoto Kaji, Masahiko Katsumata, Elizabeth S. Dennis and Ryo Fujimoto
Plants 2021, 10(6), 1082; https://doi.org/10.3390/plants10061082 - 27 May 2021
Cited by 4 | Viewed by 3170
Abstract
In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results [...] Read more.
In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F2 populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F2 populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed. Full article
(This article belongs to the Special Issue Genetics and Genomics of the Brassicaceae)
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12 pages, 1750 KiB  
Article
Mapping of Genetic Locus for Leaf Trichome Formation in Chinese Cabbage Based on Bulked Segregant Analysis
by Rujia Zhang, Yiming Ren, Huiyuan Wu, Yu Yang, Mengguo Yuan, Haonan Liang and Changwei Zhang
Plants 2021, 10(4), 771; https://doi.org/10.3390/plants10040771 - 14 Apr 2021
Cited by 5 | Viewed by 2220
Abstract
Chinese cabbage is a leafy vegetable, and its leaves are the main edible organs. The formation of trichomes on the leaves can significantly affect its taste, so studying this phenomenon is of great significance for improving the quality of Chinese cabbage. In this [...] Read more.
Chinese cabbage is a leafy vegetable, and its leaves are the main edible organs. The formation of trichomes on the leaves can significantly affect its taste, so studying this phenomenon is of great significance for improving the quality of Chinese cabbage. In this study, two varieties of Chinese cabbage, W30 with trichome leaves and 082 with glabrous leaves, were crossed to generate F1 and F1 plants, which were self-fertilized to develop segregating populations with trichome or glabrous morphotypes. The two bulks of the different segregating populations were used to conduct bulked segregant analysis (BSA). A total of 293.4 M clean reads were generated from the samples, and plants from the trichome leaves (AL) bulk and glabrous leaves (GL) bulk were identified. Between the two DNA pools generated from the trichome and glabrous plants, 55,048 SNPs and 272 indels were generated. In this study, three regions (on chromosomes 6, 10 and scaffold000100) were identified, and the annotation revealed three candidate genes that may participate in the formation of leaf trichomes. These findings suggest that the three genes—Bra025087 encoding a cyclin family protein, Bra035000 encoding an ATP-binding protein/kinase/protein kinase/protein serine/threonine kinase and Bra033370 encoding a WD-40 repeat family protein–influence the formation of trichomes by participating in trichome morphogenesis (GO: 0010090). These results demonstrate that BSA can be used to map genes associated with traits and provide new insights into the molecular mechanism of leafy trichome formation in Chinese cabbage. Full article
(This article belongs to the Special Issue Genetics and Genomics of the Brassicaceae)
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20 pages, 3798 KiB  
Article
Comparative Transcriptomic Analysis of Gene Expression Inheritance Patterns Associated with Cabbage Head Heterosis
by Shengjuan Li, Charitha P. A. Jayasinghege, Jia Guo, Enhui Zhang, Xingli Wang and Zhongmin Xu
Plants 2021, 10(2), 275; https://doi.org/10.3390/plants10020275 - 31 Jan 2021
Cited by 6 | Viewed by 3019
Abstract
The molecular mechanism of heterosis or hybrid vigor, where F1 hybrids of genetically diverse parents show superior traits compared to their parents, is not well understood. Here, we studied the molecular regulation of heterosis in four F1 cabbage hybrids that showed heterosis for [...] Read more.
The molecular mechanism of heterosis or hybrid vigor, where F1 hybrids of genetically diverse parents show superior traits compared to their parents, is not well understood. Here, we studied the molecular regulation of heterosis in four F1 cabbage hybrids that showed heterosis for several horticultural traits, including head size and weight. To examine the molecular mechanisms, we performed a global transcriptome profiling in the hybrids and their parents by RNA sequencing. The proportion of genetic variations detected as single nucleotide polymorphisms and small insertion–deletions as well as the numbers of differentially expressed genes indicated a larger role of the female parent than the male parent in the genetic divergence of the hybrids. More than 86% of hybrid gene expressions were non-additive. More than 81% of the genes showing divergent expressions showed dominant inheritance, and more than 56% of these exhibited maternal expression dominance. Gene expression regulation by cis-regulatory mechanisms appears to mediate most of the gene expression divergence in the hybrids; however, trans-regulatory factors appear to have a higher effect compared to cis-regulatory factors on parental expression divergence. These observations bring new insights into the molecular mechanisms of heterosis during the cabbage head development. Full article
(This article belongs to the Special Issue Genetics and Genomics of the Brassicaceae)
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14 pages, 1968 KiB  
Article
Genome-Wide Identification and Analysis of SRO Gene Family in Chinese Cabbage (Brassica rapa L.)
by Yali Qiao, Xueqin Gao, Zeci Liu, Yue Wu, Linli Hu and Jihua Yu
Plants 2020, 9(9), 1235; https://doi.org/10.3390/plants9091235 - 18 Sep 2020
Cited by 8 | Viewed by 2770
Abstract
Similar to radical-induced cell death 1 (SROs) is a family of small proteins unique to plants. SRO transcription factors play an important role in plants’ response to biotic and abiotic stresses. In this study, we identified 12 BrSRO genes in Chinese cabbage ( [...] Read more.
Similar to radical-induced cell death 1 (SROs) is a family of small proteins unique to plants. SRO transcription factors play an important role in plants’ response to biotic and abiotic stresses. In this study, we identified 12 BrSRO genes in Chinese cabbage (Brassica rapa L.). Among them, a comprehensive overview of the SRO gene family is presented, including physical and chemical characteristics, chromosome locations, phylogenetic analysis, gene structures, motif analysis, and cis-element analyses. The number of amino acids of BrSRO genes is between 77–779 aa, isoelectric point changed from 6.02 to 9.6. Of the 12 BrSRO genes, 11 were randomly distributed along the 7 chromosomes, while BrSRO12 was located along unassigned scaffolds. Phylogenetic analysis indicated that the SRO proteins from six species, including Arabidopsis, banana, rice, Solanum lycopersicum, Zea mays, and Chinese cabbage were divided into eleven groups. The exon-rich BrSRO6 and BrSRO12 containing 15 exons were clustered to group K. All 12 genes have motif 2, which indicate that motif 2 is a relatively conservative motif. There are many hormone and stress response elements in BrSRO genes. The relative expression levels of 12 BrSRO genes under high temperature, drought, salt, and low temperature conditions were analyzed by real-time fluorescence quantitative PCR. The results indicated the relative expression level of BrSRO8 was significantly up-regulated when plants were exposed to high temperature. The relative expression levels of BrSRO1, 3, 7, 8, and 9 were higher under low temperature treatment. The up-regulated genes response to drought and salt stresses were BrSRO1, 5, 9 and BrSRO1, 8, respectively. These results indicated that these genes have certain responses to different abiotic stresses. This work has provided a foundation for further functional analyses of SRO genes in Chinese cabbage. Full article
(This article belongs to the Special Issue Genetics and Genomics of the Brassicaceae)
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21 pages, 2766 KiB  
Article
Gibberellin Promotes Bolting and Flowering via the Floral Integrators RsFT and RsSOC1-1 under Marginal Vernalization in Radish
by Haemyeong Jung, Seung Hee Jo, Won Yong Jung, Hyun Ji Park, Areum Lee, Jae Sun Moon, So Yoon Seong, Ju-Kon Kim, Youn-Sung Kim and Hye Sun Cho
Plants 2020, 9(5), 594; https://doi.org/10.3390/plants9050594 - 07 May 2020
Cited by 14 | Viewed by 3969
Abstract
Gibberellic acid (GA) is one of the factors that promotes flowering in radish (Raphanus Sativus L.), although the mechanism mediating GA activation of flowering has not been determined. To identify this mechanism in radish, we compared the effects of GA treatment on [...] Read more.
Gibberellic acid (GA) is one of the factors that promotes flowering in radish (Raphanus Sativus L.), although the mechanism mediating GA activation of flowering has not been determined. To identify this mechanism in radish, we compared the effects of GA treatment on late-flowering (NH-JS1) and early-flowering (NH-JS2) radish lines. GA treatment promoted flowering in both lines, but not without vernalization. NH-JS2 plants displayed greater bolting and flowering pathway responses to GA treatment than NH-JS1. This variation was not due to differences in GA sensitivity in the two lines. We performed RNA-seq analysis to investigate GA-mediated changes in gene expression profiles in the two radish lines. We identified 313 upregulated, differentially expressed genes (DEGs) and 207 downregulated DEGs in NH-JS2 relative to NH-JS1 in response to GA. Of these, 21 and 8 genes were identified as flowering time and GA-responsive genes, respectively. The results of RNA-seq and quantitative PCR (qPCR) analyses indicated that RsFT and RsSOC1-1 expression levels increased after GA treatment in NH-JS2 plants but not in NH-JS1. These results identified the molecular mechanism underlying differences in the flowering-time genes of NH-JS1 and NH-JS2 after GA treatment under insufficient vernalization conditions. Full article
(This article belongs to the Special Issue Genetics and Genomics of the Brassicaceae)
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Review

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15 pages, 1115 KiB  
Review
Genetics of Clubroot and Fusarium Wilt Disease Resistance in Brassica Vegetables: The Application of Marker Assisted Breeding for Disease Resistance
by Hasan Mehraj, Ayasha Akter, Naomi Miyaji, Junji Miyazaki, Daniel J. Shea, Ryo Fujimoto and Md. Asad-ud Doullah
Plants 2020, 9(6), 726; https://doi.org/10.3390/plants9060726 - 09 Jun 2020
Cited by 29 | Viewed by 6005
Abstract
The genus Brassica contains important vegetable crops, which serve as a source of oil seed, condiments, and forages. However, their production is hampered by various diseases such as clubroot and Fusarium wilt, especially in Brassica vegetables. Soil-borne diseases are difficult to manage by [...] Read more.
The genus Brassica contains important vegetable crops, which serve as a source of oil seed, condiments, and forages. However, their production is hampered by various diseases such as clubroot and Fusarium wilt, especially in Brassica vegetables. Soil-borne diseases are difficult to manage by traditional methods. Host resistance is an important tool for minimizing disease and many types of resistance (R) genes have been identified. More than 20 major clubroot (CR) disease-related loci have been identified in Brassica vegetables and several CR-resistant genes have been isolated by map-based cloning. Fusarium wilt resistant genes in Brassica vegetables have also been isolated. These isolated R genes encode the toll-interleukin-1 receptor/nucleotide-binding site/leucine-rice-repeat (TIR-NBS-LRR) protein. DNA markers that are linked with disease resistance allele have been successfully applied to improve disease resistance through marker-assisted selection (MAS). In this review, we focused on the recent status of identifying clubroot and Fusarium wilt R genes and the feasibility of using MAS for developing disease resistance cultivars in Brassica vegetables. Full article
(This article belongs to the Special Issue Genetics and Genomics of the Brassicaceae)
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