Submit to Plants Review for Plants Propose a Special Issue

Journal Menu

Journal Browser

Plant Chromosome Biology and Genomics for Breeding

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

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 August 2023) | Viewed by 24848

Share This Special Issue

Special Issue Editors

Prof. Dr. Fangpu Han

E-Mail Website
Guest Editor

Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
Interests: chromosome; centromere; wheat; maize; breeding

Prof. Dr. Handong Su

E-Mail Website
Guest Editor

College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
Interests: chromosome biology; synthetic genomics

Prof. Dr. Xiaojun Hu

E-Mail Website
Guest Editor

College of Life Sciences, Linyi University, Linyi 276000, China
Interests: crop breeding; molecular biology; stress biology

Prof. Dr. Bao Liu

E-Mail Website
Guest Editor

School of Life Sciences, Northeast Normal University, Changchun 430079, China
Interests: plant genomics; chromosome biology

Special Issue Information

Dear Colleagues,

Given the challenges of feeding the rapidly growing population, the effects of climate change, and resource depletion, there is increasing demand for novel solutions to improve crop yield and quality. With the rapidly advancing set of genomics tools available, a suite of genetic and (epi)genomic resources are now the key approach for basic research and breeding in the crop community. Knowledge of model plant species can be applied rapidly in crops, and the molecular mechanisms regulating agronomically important can will be performed directly in the crops. The elucidation of further functions of individual genes, pathways, networks, and ultimately entire genomes, as well as their manipulation, is critical for improving crops.

This Special Issue aims to collect a wide body of research studies dealing with functional genomics in crops that have relevance in multi-omics, gene function, gene expression regulation and important traits, and biotechnological techniques in crops.

Prof. Dr. Fangpu Han
Prof. Dr. Handong Su
Prof. Dr. Xiaojun Hu
Prof. Dr. Bao Liu
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

genomics
transcriptomics
epigenetics
omics
gene function and regulation
crop
CRISPR
chromosome

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (9 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review, Other

15 pages, 1784 KiB

Open AccessArticle

Effects of Allopolyploidization and Homoeologous Chromosomal Segment Exchange on Homoeolog Expression in a Synthetic Allotetraploid Wheat under Variable Environmental Conditions

by Zhibin Zhang, Ruili Lv, Bin Wang, Hongwei Xun, Bao Liu and Chunming Xu

Plants 2023, 12(17), 3111; https://doi.org/10.3390/plants12173111 - 30 Aug 2023

Cited by 1 | Viewed by 1467

Abstract

Allopolyploidy through the combination of divergent genomes into a common nucleus at doubled dosage is known as a potent genetic and evolutionary force. As a macromutation, a striking feature of allopolyploidy in comparison with other mutational processes is that ‘genome shock’ can be evoked, thereby generating rapid and saltational biological consequences. A major manifestation of genome shock is genome-wide gene expression rewiring, which previously remained to be fully elucidated. Here, using a large set of RNAseq-based transcriptomic data of a synthetic allotetraploid wheat (genome AADD) and its parental species, we performed in-depth analyses of changes in the genome-wide gene expression under diverse environmental conditions at the subgenome (homoeolog) level and investigated the additional effects of homoeologous chromosomal segment exchanges (abbreviated HEs). We show that allopolyploidy caused large-scale changes in gene expression that were variable across the conditions and exacerbated by both stresses and HEs. Moreover, although both subgenomes (A and D) showed clear commonality in the changes, they responded differentially under variable conditions. The subgenome- and condition-dependent differentially expressed genes were enriched for different gene ontology terms implicating different biological functions. Our results provide new insights into the direct impacts of allopolyploidy on condition-dependent changes in subgenome expression and the additional effects of HEs in nascent allopolyploidy. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Figure 1

15 pages, 1853 KiB

Open AccessArticle

Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut

by Yang Liu, Congyang Yi, Qian Liu, Chunhui Wang, Wenpeng Wang, Fangpu Han and Xiaojun Hu

Plants 2022, 11(23), 3276; https://doi.org/10.3390/plants11233276 - 28 Nov 2022

Cited by 2 | Viewed by 1739

Abstract

Seed size is the major yield component and a key target trait that is selected during peanut breeding. However, the mechanisms that regulate peanut seed size are unknown. Two peanut mutants with bigger seed size were isolated in this study by ⁶⁰Co treatment of a common peanut landrace, Huayu 22, and were designated as the “big seed” mutant lines (hybs). The length and weight of the seed in hybs were about 118% and 170% of those in wild-type (WT), respectively. We adopted a multi-omics approach to identify the genomic locus underlying the hybs mutants. We performed whole genome sequencing (WGS) of WT and hybs mutants and identified thousands of large-effect variants (SNPs and indels) that occurred in about four hundred genes in hybs mutants. Seeds from both WT and hybs lines were sampled 20 days after flowering (DAF) and were used for RNA-Seq analysis; the results revealed about one thousand highly differentially expressed genes (DEGs) in hybs compared to WT. Using a method that combined large-effect variants with DEGs, we identified 45 potential candidate genes that shared gene product mutations and expression level changes in hybs compared to WT. Among the genes, two candidate genes encoding cytochrome P450 superfamily protein and NAC transcription factors may be associated with the increased seed size in hybs. The present findings provide new information on the identification and functional research into candidate genes responsible for the seed size phenotype in peanut. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Figure 1

18 pages, 2736 KiB

Open AccessArticle

Autotetraploidization Gives Rise to Differential Gene Expression in Response to Saline Stress in Rice

by Ningning Wang, Shiyan Wang, Fan Qi, Yingkai Wang, Yujie Lin, Yiming Zhou, Weilong Meng, Chunying Zhang, Yunpeng Wang and Jian Ma

Plants 2022, 11(22), 3114; https://doi.org/10.3390/plants11223114 - 15 Nov 2022

Cited by 7 | Viewed by 2264

Abstract

Plant polyploidization represents an effective means for plants to perpetuate their adaptive advantage in the face of environmental variation. Numerous studies have identified differential responsiveness to environmental cues between polyploids and their related diploids, and polyploids might better adapt to changing environments. However, the mechanism that underlies polyploidization contribution during abiotic stress remains hitherto obscure and needs more comprehensive assessment. In this study, we profile morphological and physiological characteristics, and genome-wide gene expression between an autotetraploid rice and its diploid donor plant following saline stress. The results show that the autotetraploid rice is more tolerant to saline stress than its diploid precursor. The physiological characteristics were rapidly responsive to saline stress in the first 24 h, during which the elevations in sodium ion, superoxide dismutase, peroxidase, and 1-aminocyclopropane-1-carboxylic acid were all significantly higher in the autotetraploid than in the diploid rice. Meanwhile, the genome-wide gene expression analysis revealed that the genes related to ionic transport, peroxidase activity, and phytohormone metabolism were differentially expressed in a significant manner between the autotetraploid and the diploid rice in response to saline stress. These findings support the hypothesis that diverse mechanisms exist between the autotetraploid rice and its diploid donor plant in response to saline stress, providing vital information for improving our understanding on the enhanced performance of polyploid plants in response to salt stress. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Figure 1

10 pages, 1319 KiB

Open AccessArticle

Location of Tandem Repeats on Wheat Chromosome 5B and the Breakpoint on the 5BS Arm in Wheat Translocation T7BS.7BL-5BS Using Single-Copy FISH Analysis

by Wei Zhang, Zongxiang Tang, Jie Luo, Guangrong Li, Zujun Yang, Manyu Yang, Ennian Yang and Shulan Fu

Plants 2022, 11(18), 2394; https://doi.org/10.3390/plants11182394 - 14 Sep 2022

Cited by 2 | Viewed by 1597

Abstract

Wheat (Triticum aestivum L.) is rich in tandem repeats, and this is helpful in studying its karyotypic evolution. Some tandem repeats have not been assembled into the wheat genome sequence. Alignment using the blastn tool in the B2DSC web server indicated that the genomic sequence of 5B chromosome (IWGSC RefSeq v2.1) does not contain the tandem repeat pTa-275, and the tandem repeat (GA)₂₆ distributed throughout the whole 5B chromosome. The nondenaturing fluorescence in situ hybridization (ND-FISH) using the oligonucleotide (oligo) probes derived from pTa-275 and (GA)₂₆ indicated that one signal band of pTa-275 and two signal bands of (GA)₂₆ appeared on the 5B chromosome of Chinese Spring wheat, indicating the aggregative distribution patterns of the two kinds of tandem repeats. Single-copy FISH indicated that the clustering region of pTa-275 and the two clustering regions of (GA)₂₆ were located in ~160–201 Mb, ~153–157 Mb, and ~201–234 Mb intervals, respectively. Using ND-FISH and single-copy FISH technologies, the translocation breakpoint on the 5BS portion of the translocation T7BS.7BL-5BS, which exists widely in north-western European wheat cultivars, was located in the region from 157,749,421 bp to 158,555,080 bp (~0.8 Mb), and this region mainly contains retrotransposons, and no gene was found. The clustering regions of two kinds of tandem repeats on wheat chromosome 5B were determined and this will be helpful to improve the future sequence assembly of this chromosome. The sequence characteristics of the translocation breakpoint on the translocation T7BS.7BL-5BS obtained in this study are helpful to understand the mechanism of wheat chromosome translocation. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Figure 1

10 pages, 5263 KiB

Open AccessCommunication

Distribution, Polymorphism and Function Characteristics of the GST-Encoding Fhb7 in Triticeae

by Xianrui Guo, Mian Wang, Houyang Kang, Yonghong Zhou and Fangpu Han

Plants 2022, 11(16), 2074; https://doi.org/10.3390/plants11162074 - 9 Aug 2022

Cited by 11 | Viewed by 3511

Abstract

Encoding a glutathione S-transferase (GST) and conferring resistance to Fusarium head blight (FHB), Fhb7 was successfully isolated from the newly assembled Thinopyrum elongatum genome by researchers, with blasting searches revealing that Thinopyrum gained Fhb7 through horizontal gene transfer from an endophytic Epichloë species. On the contrary, our molecular evidence reveals that the homologs of Fhb7 are distributed commonly in Triticeae. Other than Thinopyrum, the Fhb7 homologs were also detected in four other genera, Elymus, Leymus, Roegneria and Pseudoroegneria, respectively. Sequence comparisons revealed that the protein sequences were at least 94% identical across all of the Fhb7 homologs in Triticeae plants, which in turn suggested that the horizontal gene transfer of the Fhb7 might have occurred before Triticeae differentiation instead of Thinopyrum. The multiple Fhb7 homologs detected in some Triticeae accessions and wheat-Thinopyrum derivatives might be attributed to the alloploid nature and gene duplication during evolution. In addition, we discovered that some wheat-Thinopyrum derivatives carrying the Fhb7 homologs had a completely different reaction to Fusarium head blight, which made us question the ability of the GST-encoding Fhb7 to resist FHB. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Figure 1

16 pages, 3176 KiB

Open AccessArticle

Molecular Cytogenetic Identification of the Wheat–Dasypyrum villosum T3DL·3V#3S Translocation Line with Resistance against Stripe Rust

by Jie Zhang, Shuyao Tang, Tao Lang, Ying Wang, Hai Long, Guangbing Deng, Qian Chen, Yuanlin Guo, Pu Xuan, Jun Xiao and Yun Jiang

Plants 2022, 11(10), 1329; https://doi.org/10.3390/plants11101329 - 18 May 2022

Cited by 4 | Viewed by 2053

Abstract

The annual species Dasypyrum villosum possesses several potentially valuable genes for the improvement of common wheat. Previously, we identified a new stripe rust-resistant line, the Chinese Spring (CS)–D. villosum 3V#3 (3D) substitution line (named CD-3), and mapped its potential rust resistance gene (designated as YrCD-3) on the 3V#3 chromosome originating from D. villosum. The objective of the present study was to further narrow down the YrCD-3 locus to a physical region and develop wheat-3V#3 introgression lines with strong stripe rust resistance. By treating CD-3 seeds with ⁶⁰Co γ-irradiation, two CS-3V#3 translocation lines, T3V#3S.3DL and T3DS.3V#3L (termed 22-12 and 24-20, respectively), were identified from the M₄ generation through a combination of non-denaturing fluorescence in situ hybridization (ND-FISH) and functional molecular markers. Stripe rust resistance tests showed that the line 22-12 exhibited strong stripe rust resistance similarly to CD-3, whereas 24-20 was susceptible to stripe rust similarly to CS, indicating that YrCD-3 is located on the short arm of 3V#3. The line 22-12 can potentially be used for further wheat improvement. Additionally, to trace 3V#3 in the wheat genetic background, we produced 30 3V#3-specific sequence tag (EST) markers, among which, 11 markers could identify 3V#3S. These markers could be valuable in fine-mapping YrCD-3. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Figure 1

17 pages, 4388 KiB

Open AccessArticle

Identification of Peanut Aux/IAA Genes and Functional Prediction during Seed Development and Maturation

by Xiurong Zhang, Kun Zhang, Lu Luo, Yuying Lv, Yuying Li, Suqing Zhu, Bing Luo, Yongshan Wan, Xiansheng Zhang and Fengzhen Liu

Plants 2022, 11(4), 472; https://doi.org/10.3390/plants11040472 - 9 Feb 2022

Cited by 6 | Viewed by 1906

Abstract

Auxin-responsive genes AUX/IAA are important during plant growth and development, but there are few relevant reports in peanut. In this study, 44 AhIAA genes were identified from cultivated peanut, of which 31 genes were expressed in seed at varying degrees. AhIAA-3A, AhIAA-16A and AhIAA-15B were up-regulated, while AhIAA-11A, AhIAA-5B and AhIAA-14B were down-regulated with seed development and maturation. The expression patterns of seven genes, AhIAA-1A, AhIAA-4A, AhIAA-10A, AhIAA-20A, AhIAA-1B, AhIAA-4B and AhIAA-19B, were consistent with the change trend of auxin, and expression in late-maturing variety LM was significantly higher than that in early-maturing EM. Furthermore, allelic polymorphism analysis of AhIAA-1A and AhIAA-1B, which were specifically expressed in seeds, showed that three SNP loci in 3′UTR of AhIAA-1A could effectively distinguish the EM- and LM- type germplasm, providing a basis for breeding markers development. Our results offered a comprehensive understanding of Aux/IAA genes in peanut and provided valuable clues for further investigation of the auxin signal transduction pathway and auxin regulation mechanism in peanut. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Figure 1

Review

Jump to: Research, Other

19 pages, 1166 KiB

Open AccessReview

Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding

by Junming Zhou, Xinchao Luan, Yixuan Liu, Lixue Wang, Jiaxin Wang, Songnan Yang, Shuying Liu, Jun Zhang, Huijing Liu and Dan Yao

Plants 2023, 12(7), 1478; https://doi.org/10.3390/plants12071478 - 28 Mar 2023

Cited by 9 | Viewed by 6423

Abstract

Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Figure 1

Other

Jump to: Research, Review

10 pages, 2910 KiB

Open AccessBrief Report

Centromere-Specific Single-Copy Sequences of Secale Species

by Zijin Pan, Jie Luo, Zongxiang Tang and Shulan Fu

Plants 2022, 11(16), 2117; https://doi.org/10.3390/plants11162117 - 15 Aug 2022

Cited by 1 | Viewed by 2031

Abstract

Single-copy FISH analysis is a useful tool to physically locate a given sequence on chromosome. Centromeric single-copy sequences can be used to locate the position of centromere and disclose the subtle differences among different centromeres. Nine centromeric single-copy sequences 1R1, 3R1, 4R1, 4R2, 5R1, 5R2, 6R2, 6R3, and 7R1 were cloned from Kustro (Secale cereale L.). FISH analysis using these sequences as probes indicated that the signals of 1R1, 3R1, 4R1, 4R2, 5R1, 5R2, 6R1, 6R2, and 7R1 were located in the centromeric regions of rye 1R, 3R, 4R, 4R, 5R, 5R, 6R, 6R, and 7R chromosomes, respectively. In addition, for each of the centromeric single-copy sequences, high sequence similarity was observed among different Secale species. Combined with rye genomic sequence, single-copy FISH analysis indicated that the 1BL.1RS translocations in wheat cultivar CN17 and wheat line 20T363-4 contained the centromeric segment of 1R chromosome from 349,498,361 to 349,501,266 bp, and the 1BL.1RS translocations in the other two wheat cultivars did not contain this segment. The nine sequences are useful in determining the centromere location on rye chromosomes, and they have the potential to disclose the accurate structural differences of centromeres among the wheat-rye centric fusion translocation chromosomes; therefore, more centromeric single-copy sequences are needed. Full article

(This article belongs to the Special Issue Plant Chromosome Biology and Genomics for Breeding)

► Show Figures

Journal Menu

Journal Browser

Plant Chromosome Biology and Genomics for Breeding

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (9 papers)

Research

Review

Other

Further Information

Guidelines

MDPI Initiatives

Follow MDPI