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Power Up Plant Genetic Research with Genomic Data

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 January 2023) | Viewed by 16132

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Special Issue Editors

Prof. Dr. Hon-Ming Lam

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Guest Editor

1. School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
2. Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
Interests: climate-smart and sustainable agriculture; plant and agricultural biotechnology; genomic studies on crop–environment interaction
Special Issues, Collections and Topics in MDPI journals

Dr. Sachiko Isobe

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Guest Editor

Lab of Plant Genetics and Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
Interests: molecular genetics; breeding, whole genome sequencing; digital phenotyping
Special Issues, Collections and Topics in MDPI journals

Dr. Man-Wah Li

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Guest Editor

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
Interests: genome; domestication; quantitative trait locus; flowering; agriculture; soybean
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Developments in plant genetics and genomics research usually lags behind those in mammals and human due to the complexity of the plant genome and the limitations of research resources. Regardless, with the advances in sequencing technology, the building of high-quality genomes and the sequencing of huge populations of plants are no longer technologically challenging, nor resource intensive. Epigenomics, transcriptomics, proteomics, metabolomics, and phenomics have also made significant advances in recently years, creating more opportunities in plant genomic research. Although the generation of genome sequencing data is no longer a limitation, there are a vast volume of genomic data deposited in public databases. Diving into the sea of genomic data to generate new knowledge has become the next challenge in the genomic era. Each plant genome is made up of hundreds of millions to trillions of bases, which each contain tens of thousands of genes and numerous non-coding elements. Currently, only a tiny fraction of the plant genome is being characterized, even in the model plant Arabidopsis. In this Special Issue, we would like to invite dedicated scientists to submit their recent research and review articles on plant genomics and genetics with the support of molecular biology and biotechnology.

Prof. Dr. Hon-Ming Lam
Dr. Sachiko Isobe
Dr. Man-Wah Li
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

genome sequencing
optical mapping
genome editing
population genomics
genome-wide association mapping
functional genomics
epigenomics
genetic interaction
chromatin
biodiversity

Published Papers (9 papers)

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Editorial

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3 pages, 189 KiB

Open AccessEditorial

Power Up Plant Genetic Research with Genomic Data

by Man-Wah Li, Sachiko Isobe and Hon-Ming Lam

Int. J. Mol. Sci. 2023, 24(8), 6876; https://doi.org/10.3390/ijms24086876 - 07 Apr 2023

Viewed by 901

Abstract

The official debut of the reference genome of Arabidopsis thaliana in 2000 [...] Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

Research

Jump to: Editorial

17 pages, 10326 KiB

Open AccessArticle

Changes in the Histology of Walnut (Juglans regia L.) Infected with Phomopsis capsici and Transcriptome and Metabolome Analysis

by Leming Zhou, Tianhui Zhu, Shan Han, Shujiang Li, Yinggao Liu, Tiantian Lin and Tianmin Qiao

Int. J. Mol. Sci. 2023, 24(5), 4879; https://doi.org/10.3390/ijms24054879 - 02 Mar 2023

Cited by 4 | Viewed by 1416

Abstract

Phomopsis capsici (P. capsici) causes branch blight of walnuts, which leads to significant economic loss. The molecular mechanism behind the response of walnuts remains unknown. Paraffin sectioning and transcriptome and metabolome analyses were performed to explore the changes in tissue structure, gene expression, and metabolic processes in walnut after infection with P. capsici. We found that P. capsici caused serious damage to xylem vessels during the infestation of walnut branches, destroying the structure and function of the vessels and creating obstacles to the transport of nutrients and water to the branches. The transcriptome results showed that differentially expressed genes (DEGs) were mainly annotated in carbon metabolism and ribosomes. Further metabolome analyses verified the specific induction of carbohydrate and amino acid biosynthesis by P. capsici. Finally, association analysis was performed for DEGs and differentially expressed metabolites (DEMs), which focused on the synthesis and metabolic pathways of amino acids, carbon metabolism, and secondary metabolites and cofactors. Three significant metabolites were identified: succinic semialdehyde acid, fumaric acid, and phosphoenolpyruvic acid. In conclusion, this study provides data reference on the pathogenesis of walnut branch blight and direction for breeding walnut to enhance its disease resistance. Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

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19 pages, 10636 KiB

Open AccessArticle

Dual Transcriptome Analysis Reveals That ChATG8 Is Required for Fungal Development, Melanization and Pathogenicity during the Interaction between Colletotrichum higginsianum and Arabidopsis thaliana

by Yiming Zhu, Lingtao Duan, Chengqi Zhu, Li Wang, Zhenrui He, Mei Yang and Erxun Zhou

Int. J. Mol. Sci. 2023, 24(5), 4376; https://doi.org/10.3390/ijms24054376 - 22 Feb 2023

Cited by 2 | Viewed by 1492

Abstract

Anthracnose disease of cruciferous plants caused by Colletotrichum higginsianum is a serious fungal disease that affects cruciferous crops such as Chinese cabbage, Chinese flowering cabbage, broccoli, mustard plant, as well as the model plant Arabidopsis thaliana. Dual transcriptome analysis is commonly used to identify the potential mechanisms of interaction between host and pathogen. In order to identify differentially expressed genes (DEGs) in both the pathogen and host, the conidia of wild-type (ChWT) and Chatg8 mutant (Chatg8Δ) strains were inoculated onto leaves of A. thaliana, and the infected leaves of A. thaliana at 8, 22, 40, and 60 h post-inoculation (hpi) were subjected to dual RNA-seq analysis. The results showed that comparison of gene expression between the ‘ChWT’ and ‘Chatg8Δ’ samples detected 900 DEGs (306 upregulated and 594 down-regulated) at 8 hpi, 692 DEGs (283 upregulated and 409 down-regulated) at 22 hpi, 496 DEGs (220 upregulated and 276 down-regulated) at 40 hpi, and 3159 DEGs (1544 upregulated and 1615 down-regulated) at 60 hpi. GO and KEGG analyses found that the DEGs were mainly involved in fungal development, biosynthesis of secondary metabolites, plant–fungal interactions, and phytohormone signaling. The regulatory network of key genes annotated in the Pathogen–Host Interactions database (PHI-base) and Plant Resistance Genes database (PRGdb), as well as a number of key genes highly correlated with the 8, 22, 40, and 60 hpi, were identified during the infection. Among the key genes, the most significant enrichment was in the gene encoding the trihydroxynaphthalene reductase (THR1) in the melanin biosynthesis pathway. Both Chatg8Δ and Chthr1Δ strains showed varying degrees of reduction of melanin in appressoria and colonies. The pathogenicity of the Chthr1Δ strain was lost. In addition, six DEGs from C. higginsianum and six DEGs from A. thaliana were selected for real-time quantitative PCR (RT-qPCR) to confirm the RNA-seq results. The information gathered from this study enriches the resources available for research into the role of the gene ChATG8 during the infection of A. thaliana by C. higginsianum, such as potential links between melanin biosynthesis and autophagy, and the response of A. thaliana to different fungal strains, thereby providing a theoretical basis for the breeding of cruciferous green leaf vegetable cultivars with resistance to anthracnose disease. Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

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16 pages, 3692 KiB

Open AccessArticle

Genome-Wide Identification and Transcriptional Analysis of the MYB Gene Family in Pearl Millet (Pennisetum glaucum)

by Miaohong Lin, Zhuoyan Dong, Hongkai Zhou, Guanyu Wu, Liang Xu, Sheng Ying and Miao Chen

Int. J. Mol. Sci. 2023, 24(3), 2484; https://doi.org/10.3390/ijms24032484 - 27 Jan 2023

Cited by 6 | Viewed by 2186

Abstract

The MYB gene family widely exists in the plant kingdom and participates in the regulation of plant development and stress response. Pearl millet (Pennisetum glaucum (L.) R. Br.), as one of the most important cereals, is not only considered a good source of protein and nutrients but also has excellent tolerances to various abiotic stresses (e.g., salinity, water deficit, etc.). Although the genome sequence of pearl millet was recently published, bioinformatics and expression pattern analysis of the MYB gene family are limited. Here, we identified 208 PgMYB genes in the pearl millet genome and employed 193 high-confidence candidates for downstream analysis. Phylogenetic and structural analysis classified these PgMYBs into four subgroups. Eighteen pairs of segmental duplications of the PgMYB gene were found using synteny analysis. Collinear analysis revealed pearl millet had the closest evolutionary relationship with foxtail millet. Nucleotide substitution analysis (Ka/Ks) revealed PgMYB genes were under purifying positive selection pressure. Reverse transcription-quantitative PCR analysis of eleven R2R3-type PgMYB genes revealed they were preferentially expressed in shoots and seeds and actively responded to various environment stimuli. Current results provide insightful information regarding the molecular features of the MYB family in pearl millet to support further functional characterizations. Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

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17 pages, 5010 KiB

Open AccessArticle

Genome-Wide Analysis of Snf2 Gene Family Reveals Potential Role in Regulation of Spike Development in Barley

by Gang Chen, Kohei Mishina, Hongjing Zhu, Shinji Kikuchi, Hidenori Sassa, Youko Oono and Takao Komatsuda

Int. J. Mol. Sci. 2023, 24(1), 457; https://doi.org/10.3390/ijms24010457 - 27 Dec 2022

Cited by 7 | Viewed by 2597

Abstract

Sucrose nonfermenting 2 (Snf2) family proteins, as the catalytic core of ATP-dependent chromatin remodeling complexes, play important roles in nuclear processes as diverse as DNA replication, transcriptional regulation, and DNA repair and recombination. The Snf2 gene family has been characterized in several plant species; some of its members regulate flower development in Arabidopsis. However, little is known about the members of the family in barley (Hordeum vulgare). Here, 38 Snf2 genes unevenly distributed among seven chromosomes were identified from the barley (cv. Morex) genome. Phylogenetic analysis categorized them into 18 subfamilies. They contained combinations of 21 domains and consisted of 3 to 34 exons. Evolution analysis revealed that segmental duplication contributed predominantly to the expansion of the family in barley, and the duplicated gene pairs have undergone purifying selection. About eight hundred Snf2 family genes were identified from 20 barley accessions, ranging from 38 to 41 genes in each. Most of these genes were subjected to purification selection during barley domestication. Most were expressed abundantly during spike development. This study provides a comprehensive characterization of barley Snf2 family members, which should help to improve our understanding of their potential regulatory roles in barley spike development. Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

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16 pages, 2655 KiB

Open AccessArticle

An Integration of Linkage Mapping and GWAS Reveals the Key Genes for Ear Shank Length in Maize

by Zhenjuan Liang, Na Xi, Hao Liu, Peng Liu, Chenchaoyang Xiang, Chen Zhang, Chaoying Zou, Xuyujuan Cheng, Hong Yu, Minyan Zhang, Zhong Chen, Guangtang Pan, Guangsheng Yuan, Shibin Gao, Langlang Ma and Yaou Shen

Int. J. Mol. Sci. 2022, 23(23), 15073; https://doi.org/10.3390/ijms232315073 - 01 Dec 2022

Cited by 2 | Viewed by 1338

Abstract

Ear shank length (ESL) has significant effects on grain yield and kernel dehydration rate in maize. Herein, linkage mapping and genome-wide association study were combined to reveal the genetic architecture of maize ESL. Sixteen quantitative trait loci (QTL) were identified in the segregation population, among which five were repeatedly detected across multiple environments. Meanwhile, 23 single nucleotide polymorphisms were associated with the ESL in the association panel, of which four were located in the QTL identified by linkage mapping and were designated as the population-common loci. A total of 42 genes residing in the linkage disequilibrium regions of these common variants and 12 of them were responsive to ear shank elongation. Of the 12 genes, five encode leucine-rich repeat receptor-like protein kinases, proline-rich proteins, and cyclin11, respectively, which were previously shown to regulate cell division, expansion, and elongation. Gene-based association analyses revealed that the variant located in Cyclin11 promoter affected the ESL among different lines. Cyclin11 showed the highest expression in the ear shank 15 days after silking among diverse tissues of maize, suggesting its role in modulating ESL. Our study contributes to the understanding of the genetic mechanism underlying maize ESL and genetic modification of maize dehydration rate and kernel yield. Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

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29 pages, 4579 KiB

Open AccessArticle

Membrane Proteomic Profiling of Soybean Leaf and Root Tissues Uncovers Salt-Stress-Responsive Membrane Proteins

by Hafiz Mamoon Rehman, Shengjie Chen, Shoudong Zhang, Memoona Khalid, Muhammad Uzair, Phillip A. Wilmarth, Shakeel Ahmad and Hon-Ming Lam

Int. J. Mol. Sci. 2022, 23(21), 13270; https://doi.org/10.3390/ijms232113270 - 31 Oct 2022

Cited by 7 | Viewed by 1955

Abstract

Cultivated soybean (Glycine max (L.)), the world’s most important legume crop, has high-to-moderate salt sensitivity. Being the frontier for sensing and controlling solute transport, membrane proteins could be involved in cell signaling, osmoregulation, and stress-sensing mechanisms, but their roles in abiotic stresses are still largely unknown. By analyzing salt-induced membrane proteomic changes in the roots and leaves of salt-sensitive soybean cultivar (C08) seedlings germinated under NaCl, we detected 972 membrane proteins, with those present in both leaves and roots annotated as receptor kinases, calcium-sensing proteins, abscisic acid receptors, cation and anion channel proteins, proton pumps, amide and peptide transporters, and vesicle transport-related proteins etc. Endocytosis, linoleic acid metabolism, and fatty acid biosynthesis pathway-related proteins were enriched in roots whereas phagosome, spliceosome and soluble NSF attachment protein receptor (SNARE) interaction-related proteins were enriched in leaves. Using label-free quantitation, 129 differentially expressed membrane proteins were found in both tissues upon NaCl treatment. Additionally, the 140 NaCl-induced proteins identified in roots and 57 in leaves are vesicle-, mitochondrial-, and chloroplast-associated membrane proteins and those with functions related to ion transport, protein transport, ATP hydrolysis, protein folding, and receptor kinases, etc. Our proteomic results were verified against corresponding gene expression patterns from published C08 RNA-seq data, demonstrating the importance of solute transport and sensing in salt stress responses. Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

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16 pages, 1777 KiB

Open AccessArticle

Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant

by Wenxiang Guan, Changjiao Ke, Weiqi Tang, Jialong Jiang, Jing Xia, Xiaofang Xie, Mei Yang, Chenfeng Duan, Weiren Wu and Yan Zheng

Int. J. Mol. Sci. 2022, 23(18), 10258; https://doi.org/10.3390/ijms231810258 - 06 Sep 2022

Cited by 3 | Viewed by 1555

Abstract

High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F₂ plants from an interspecific cross (Solanum melongena × S. incanum) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F_2:3 lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL. Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

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21 pages, 2971 KiB

Open AccessArticle

Metatranscriptomic Analysis Reveals Rich Mycoviral Diversity in Three Major Fungal Pathogens of Rice

by Zhenrui He, Xiaotong Huang, Yu Fan, Mei Yang and Erxun Zhou

Int. J. Mol. Sci. 2022, 23(16), 9192; https://doi.org/10.3390/ijms23169192 - 16 Aug 2022

Cited by 9 | Viewed by 1596

Abstract

In recent years, three major fungal diseases of rice, i.e., rice blast, rice false smut, and rice-sheath blight, have caused serious worldwide rice-yield reductions and are threatening global food security. Mycoviruses are ubiquitous in almost all major groups of filamentous fungi, oomycetes, and yeasts. To reveal the mycoviral diversity in three major fungal pathogens of rice, we performed a metatranscriptomic analysis of 343 strains, representing the three major fungal pathogens of rice, Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, sampled in southern China. The analysis identified 682 contigs representing the partial or complete genomes of 68 mycoviruses, with 42 described for the first time. These mycoviruses showed affinity with eight distinct lineages: Botourmiaviridae, Partitiviridae, Totiviridae, Chrysoviridae, Hypoviridae, Mitoviridae, Narnaviridae, and Polymycoviridae. More than half (36/68, 52.9%) of the viral sequences were predicted to be members of the families Narnaviridae and Botourmiaviridae. The members of the family Polymycoviridae were also identified for the first time in the three major fungal pathogens of rice. These findings are of great significance for understanding the diversity, origin, and evolution of, as well as the relationship between, genome structures and functions of mycoviruses in three major fungal pathogens of rice. Full article

(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data)

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