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Development and Application of Advanced Genetics Methods to Orphan Crops
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Development and Application of Advanced Genetics Methods to Orphan Crops

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 October 2021) | Viewed by 8877

Special Issue Editors

Dr. Vicente Arbona

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Guest Editor
Departamento de Biología, Bioquímica i Ciències Naturals, Universitat Jaume I, Castelló de la Plana, Spain
Interests: abiotic stress; Arabidopsis; biochemistry; citrus; drought; flooding; metabolomics; plant physiology; tomato
Special Issues, Collections and Topics in MDPI journals
Dr. Héctor Candela

E-Mail Website
Guest Editor
Instituto de Bioingenieria, Universidad Miguel Hernandez de Elche, Elche, Spain
Interests: plant genetics; bioinformatics; plant development; adenosine methylation; Arabidopsis; maize; garlic; passion fruit
Dr. Jose V. Die

E-Mail Website
Guest Editor
Department of Genetics, University of Cordoba, Campus de Rabanales, C-5, 14071 Cordoba, Spain
Interests: bioinformatics; breeding; gene expression; genetics; NGS, qPCR
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The availability of optimized breeding methods (e.g., speed breeding) and affordable massively parallel sequencing technologies is enabling the rapid development of molecular toolkits for neglected cultivated plants, the so-called orphan crop species, which have only received minor attention in the past. The combination of high-throughput genomic approaches with advanced genetic analysis methods has paved the way to quickly identifying genetic variants underlying traits of agronomic interest in these species. Appropriate topics for this Special Issue might include the development and application of advanced genetic, genomic, and bioinformatic methods (e.g., de novo transcriptome or genome assemblies, mapping-by-sequencing, GWAS, speed breeding, and other related subjects), as well as studies of genes or gene families relevant to the domestication process and the development of agronomic traits in the species of interest. For this Special Issue, we welcome any original research or review articles that highlight recent advances in these areas.

Dr. Vicente Arbona
Dr. Héctor Candela
Dr. Jose V. Die
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

  • orphan crops
  • speed breeding
  • high-throughput approaches
  • advanced genetic analysis

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Published Papers (3 papers)

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Research

15 pages, 5555 KiB  
Article
Aldehyde Dehydrogenase 3 Is an Expanded Gene Family with Potential Adaptive Roles in Chickpea
by Rocío Carmona-Molero, Jose C. Jimenez-Lopez, Cristina Caballo, Juan Gil, Teresa Millán and Jose V. Die
Plants 2021, 10(11), 2429; https://doi.org/10.3390/plants10112429 - 10 Nov 2021
Cited by 6 | Viewed by 2374
Abstract
Legumes play an important role in ensuring food security, improving nutrition and enhancing ecosystem resilience. Chickpea is a globally important grain legume adapted to semi-arid regions under rain-fed conditions. A growing body of research shows that aldehyde dehydrogenases (ALDHs) represent a gene class [...] Read more.
Legumes play an important role in ensuring food security, improving nutrition and enhancing ecosystem resilience. Chickpea is a globally important grain legume adapted to semi-arid regions under rain-fed conditions. A growing body of research shows that aldehyde dehydrogenases (ALDHs) represent a gene class with promising potential for plant adaptation improvement. Aldehyde dehydrogenases constitute a superfamily of proteins with important functions as ‘aldehyde scavengers’ by detoxifying aldehydes molecules, and thus play important roles in stress responses. We performed a comprehensive study of the ALDH superfamily in the chickpea genome and identified 27 unique ALDH loci. Most chickpea ALDHs originated from duplication events and the ALDH3 gene family was noticeably expanded. Based on the physical locations of genes and sequence similarities, our results suggest that segmental duplication is a major driving force in the expansion of the ALDH family. Supported by expression data, the findings of this study offer new potential target genes for improving stress tolerance in chickpea that will be useful for breeding programs. Full article
(This article belongs to the Special Issue Development and Application of Advanced Genetics Methods to Orphan Crops)
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14 pages, 30826 KiB  
Article
Genome-Wide Analysis and Expression Profiles of the Dof Family in Cleistogenes songorica under Temperature, Salt and ABA Treatment
by Penglei Wang, Zhuanzhuan Yan, Xifang Zong, Qi Yan and Jiyu Zhang
Plants 2021, 10(5), 850; https://doi.org/10.3390/plants10050850 - 23 Apr 2021
Cited by 8 | Viewed by 2429
Abstract
The DNA-binding with one zinc finger (Dof) family of plant-specific transcription factors has a variety of important functions in gene transcriptional regulation, development, and stress responses. However, the structure and expression patterns of Dof family have not been identified in Cleistogenes [...] Read more.
The DNA-binding with one zinc finger (Dof) family of plant-specific transcription factors has a variety of important functions in gene transcriptional regulation, development, and stress responses. However, the structure and expression patterns of Dof family have not been identified in Cleistogenes songorica, which is an important xerophytic and perennial gramineous grass in desert grassland. In this study, 50 Dof genes were identified in C. songorica and could be classified into four groups. According to genome-wide analysis, 46 of 50 Dof genes were located on 20 chromosomes, and the gene structure and conserved protein motif of these proteins were analyzed. In addition, phylogenetic analysis of Dof genes in C. songorica, Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon estimated the evolutionary relationships, and these genes were grouped into seven clusters. Moreover, the expression profiles of these Dof genes in C. songorica were analyzed in response to high/low temperature, salinity, and ABA treatments. These results will provide valuable information for future studies on gene classification, cloning, and functional characterization of this family in C. songorica. Full article
(This article belongs to the Special Issue Development and Application of Advanced Genetics Methods to Orphan Crops)
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19 pages, 7498 KiB  
Article
NAC and MYB Families and Lignin Biosynthesis-Related Members Identification and Expression Analysis in Melilotus albus
by Lijun Chen, Fan Wu and Jiyu Zhang
Plants 2021, 10(2), 303; https://doi.org/10.3390/plants10020303 - 5 Feb 2021
Cited by 24 | Viewed by 3003
Abstract
Melilotus albus is an annual or biennial legume species that adapts to extreme environments via its high stress tolerance. NAC and MYB transcription factors (TFs) are involved in the regulation of lignin biosynthesis, which has not been studied in M. albus. A [...] Read more.
Melilotus albus is an annual or biennial legume species that adapts to extreme environments via its high stress tolerance. NAC and MYB transcription factors (TFs) are involved in the regulation of lignin biosynthesis, which has not been studied in M. albus. A total of 101 MaNAC and 299 MaMYB members were identified based on M. albus genome. Chromosome distribution and synteny analysis indicated that some genes underwent tandem duplication. Ka/Ks analysis suggested that MaNACs and MaMYBs underwent strong purifying selection. Stress-, hormone- and development-related cis-elements and MYB-binding sites were identified in the promoter regions of MaNACs and MaMYBs. Five MaNACs, two MaMYBs and ten lignin biosynthesis genes were identified as presenting coexpression relationships according to weighted gene coexpression network analysis (WGCNA). Eleven and thirteen candidate MaNAC and MaMYB genes related to lignin biosynthesis were identified, respectively, and a network comprising these genes was constructed which further confirmed the MaNAC and MaMYB relationship. These candidate genes had conserved gene structures and motifs and were highly expressed in the stems and roots, and qRT-PCR further verified the expression patterns. Overall, our results provide a reference for determining the precise role of NAC and MYB genes in M. albus and may facilitate efforts to breed low-lignin-content forage cultivars in the future. Full article
(This article belongs to the Special Issue Development and Application of Advanced Genetics Methods to Orphan Crops)
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