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Plant Genetic Diversity and Genomics
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Plant Genetic Diversity and Genomics

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

Deadline for manuscript submissions: closed (27 May 2022) | Viewed by 14023

Special Issue Editors

Dr. Wenpan Dong

E-Mail Website
Guest Editor
Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
Interests: chloroplast genome evolution; DNA barcoding; plant genetic diversity; plant phylogenomics; Oleaceae; medicinal plants; biogeography; molecular evolution
Special Issues, Collections and Topics in MDPI journals
Dr. Shiliang Zhou

E-Mail Website
Guest Editor
State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
Interests: DNA barcoding; phylogeography; genomics; population genetics; speciation; conservation genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetic diversity is an important component of biodiversity and genetic resources which are the basis for food security, sources of energy, animal feed, fiber, as well as other ecosystem services. Owing to their great importance, understanding the genetic diversity and structure of germplasm resources is critically necessary for their rational development and the utilization on the premise of effective protection. Advances in sequencing technology and computational power in the past decade have paved the way for dramatic progress in our understanding of plant genetic diversity. In particular, next-generation sequencing technology has enabled cost-effective production of genomic data for large population samples. With more than 300 plant nuclear genomes and 6000 organelle genomes now sequenced, the stage is set for gleaning rich and new insights into genetic structure of natural populations, mechanisms, and drivers of gene flow and its fluctuation in response to environmental heterogeneity and other forces.

This Special Issue welcomes manuscripts that advance knowledge and understanding of plant genetic diversity at the genomic level. Topics covered by this issue include but are not limited to:

  • Genetic structure of natural populations
  • Plant evolutionary genetics 
  • Phylogenomics
  • Plant speciation
  • Phylogeography and biogeography
  • Genotype–phenotype relationships

Dr. Wenpan Dong
Dr. Shiliang Zhou
Guest Editors

Manuscript Submission Information

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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

  • plant genetic diversity
  • speciation
  • phylogeography
  • evolutionary genetics
  • phylogenomics

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Published Papers (4 papers)

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Research

21 pages, 11074 KiB  
Article
Whole Genome Analysis of SLs Pathway Genes and Functional Characterization of DlSMXL6 in Longan Early Somatic Embryo Development
by Xueying Zhang, Chunwang Lai, Mengyu Liu, Xiaodong Xue, Shuting Zhang, Yan Chen, Xuechen Xiao, Zihao Zhang, Yukun Chen, Zhongxiong Lai and Yuling Lin
Int. J. Mol. Sci. 2022, 23(22), 14047; https://doi.org/10.3390/ijms232214047 - 14 Nov 2022
Cited by 4 | Viewed by 2927
Abstract
Strigolactones (SLs), a new class of plant hormones, are implicated in the regulation of various biological processes. However, the related family members and functions are not identified in longan (Dimocarpus longan Lour.). In this study, 23 genes in the CCD, D27, and [...] Read more.
Strigolactones (SLs), a new class of plant hormones, are implicated in the regulation of various biological processes. However, the related family members and functions are not identified in longan (Dimocarpus longan Lour.). In this study, 23 genes in the CCD, D27, and SMXL family were identified in the longan genome. The phylogenetic relationships, gene structure, conserved motifs, promoter elements, and transcription factor-binding site predictions were comprehensively analysed. The expression profiles indicated that these genes may play important roles in longan organ development and abiotic stress responses, especially during early somatic embryogenesis (SE). Furthermore, GR24 (synthetic SL analogue) and Tis108 (SL biosynthesis inhibitor) could affect longan early SE by regulating the levels of endogenous IAA (indole-3-acetic acid), JA (jasmonic acid), GA (gibberellin), and ABA (abscisic acid). Overexpression of SMXL6 resulted in inhibition of longan SE by regulating the synthesis of SLs, carotenoids, and IAA levels. This study establishes a foundation for further investigation of SL genes and provides novel insights into their biological functions. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Genomics)
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17 pages, 8762 KiB  
Article
Chromosome Number and Genome Size Evolution in Brasolia and Sobralia (Sobralieae, Orchidaceae)
by Przemysław Baranow, Joanna Rojek, Magdalena Dudek, Dariusz Szlachetko, Jerzy Bohdanowicz, Małgorzata Kapusta, Iwona Jedrzejczyk, Monika Rewers and Ana Paula Moraes
Int. J. Mol. Sci. 2022, 23(7), 3948; https://doi.org/10.3390/ijms23073948 - 1 Apr 2022
Cited by 3 | Viewed by 3324
Abstract
Despite the clear circumscription of tribe Sobralieae (Orchidaceae), its internal relationships are still dubious. The recently delimited genus Brasolia, based on previous Sobralia species, is now assumed to be paraphyletic, with a third genus, Elleanthus, nested in it. The morphology of [...] Read more.
Despite the clear circumscription of tribe Sobralieae (Orchidaceae), its internal relationships are still dubious. The recently delimited genus Brasolia, based on previous Sobralia species, is now assumed to be paraphyletic, with a third genus, Elleanthus, nested in it. The morphology of these three genera is significantly different, indicating the necessity of new data for a better genera delimitation. Though morphology and molecular data are available, cytogenetics data for Sobralieae is restricted to two Sobralia and one Elleanthus species. Aiming to evaluate the potential of cytogenetic data for Brasolia-Elleanthus-Sobralia genera delimitation, we present chromosome number and genome size data for 21 and 20 species, respectively, and used such data to infer the pattern of karyotype evolution in these genera. The analysis allowed us to infer x = 24 as the base chromosome number and genome size of average 1C-value of 5.0 pg for the common ancestor of Brasolia-Elleanthus-Sobralia. The recurrent descending dysploidy in Sobralieae and the punctual genome upsize suggest a recent diversification in Sobralieae but did not allow differing between Brasolia and Sobralia. However, the basal position of tribe Sobralieae in the subfamily Epidendroideae makes this tribe of interest to further studies clarifying the internal delimitation and pattern of karyotype evolution. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Genomics)
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15 pages, 15321 KiB  
Article
Genome-Wide Association Study Reveals Marker Trait Associations (MTA) for Waterlogging-Triggered Adventitious Roots and Aerenchyma Formation in Barley
by S. M. Nuruzzaman Manik, Md Quamruzzaman, Chenchen Zhao, Peter Johnson, Ian Hunt, Sergey Shabala and Meixue Zhou
Int. J. Mol. Sci. 2022, 23(6), 3341; https://doi.org/10.3390/ijms23063341 - 19 Mar 2022
Cited by 8 | Viewed by 3821
Abstract
Waterlogging is an environmental stress, which severely affects barley growth and development. Limited availability of oxygen in the root zone negatively affects the metabolism of the whole plant. Adventitious roots (AR) and root cortical aerenchyma (RCA) formation are the most important adaptive traits [...] Read more.
Waterlogging is an environmental stress, which severely affects barley growth and development. Limited availability of oxygen in the root zone negatively affects the metabolism of the whole plant. Adventitious roots (AR) and root cortical aerenchyma (RCA) formation are the most important adaptive traits that contribute to a plant’s ability to survive in waterlogged soil conditions. This study used a genome-wide association (GWAS) approach using 18,132 single nucleotide polymorphisms (SNPs) in a panel of 697 barley genotypes to reveal marker trait associations (MTA) conferring the above adaptive traits. Experiments were conducted over two consecutive years in tanks filled with soil and then validated in field experiments. GWAS analysis was conducted using general linear models (GLM), mixed linear models (MLM), and fixed and random model circulating probability unification models (FarmCPU model), with the FarmCPU showing to be the best suited model. Six and five significant (approximately −log10 (p) ≥ 5.5) MTA were identified for AR and RCA formation under waterlogged conditions, respectively. The highest −log10 (p) MTA for adventitious root and aerenchyma formation were approximately 9 and 8 on chromosome 2H and 4H, respectively. The combination of different MTA showed to be more effective in forming RCA and producing more AR under waterlogging stress. Genes from major facilitator superfamily (MFS) transporter and leucine-rich repeat (LRR) families for AR formation, and ethylene responsive factor (ERF) family genes and potassium transporter family genes for RCA formation were the potential candidate genes involved under waterlogging conditions. Several genotypes, which performed consistently well under different conditions, can be used in breeding programs to develop waterlogging-tolerant varieties. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Genomics)
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14 pages, 3497 KiB  
Article
Genome-Wide Survey Indicates Diverse Physiological Roles of Dendrobium officinale Calcium-Dependent Protein Kinase Genes
by Xingyu Yang, Zhiyu Chen, Xin Yin, Yuhua Wang, Yunqiang Yang and Yongping Yang
Int. J. Mol. Sci. 2022, 23(3), 1298; https://doi.org/10.3390/ijms23031298 - 24 Jan 2022
Cited by 10 | Viewed by 2986
Abstract
Calcium-dependent protein kinases (CDPKs) are crucial calcium ions (Ca2+) sensors in plants with important roles in signal transduction, plant growth, development, and stress responses. Here, we identified 24 genes encoding CDPKs in Dendrobium officinale using genome-wide analysis. The phylogenetic analysis [...] Read more.
Calcium-dependent protein kinases (CDPKs) are crucial calcium ions (Ca2+) sensors in plants with important roles in signal transduction, plant growth, development, and stress responses. Here, we identified 24 genes encoding CDPKs in Dendrobium officinale using genome-wide analysis. The phylogenetic analysis revealed that these genes formed four groups, with similar structures in the same group. The gene expression patterns following hormone treatments and yeast two-hybrid of homologous CDPK gene pairs with Rbohs showed differences, indicating functional divergence between homologous genes. In addition, the rapid accumulation of hydrogen peroxide (H2O2) and stomatal closure was observed in response to salicylic acid (SA)/jasmonic acid (JA) stress. Our data showed that CDPK9-2 and CDPK20-4 interacted with Rboh D and Rboh H, respectively, and were implicated in the generation of H2O2 and regulation of the stomatal aperture in response to salicylic acid/jasmonic acid treatment. We believe these results can provide a foundation for the functional divergence of homologous genes in D. officinale. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Genomics)
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