Submit to Genes Review for Genes Propose a Special Issue

Journal Browser

► Journal Browser

Plant Genetics and Breeding Improvement

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 October 2022) | Viewed by 18580

Share This Special Issue

Special Issue Editor

Dr. Wuwei Ye

E-Mail Website
Guest Editor

1. Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang 455008, China
2. School of Agricultural Science, Zhengzhou University, Zhengzhou 450001, China
Interests: plant; cotton; functional genome; stress; germplasm; genetic improvement

Special Issue Information

Dear Colleagues,

In the current context of continuous climatic change, abiotic stresses—especially drought and salinity stress—pose significant threats to both agricultural crop production and plant biodiversity. The need to improve staple crops, develop new crops, and to investigate new agricultural systems is clear.

This Special Issue invites contributions focused on the evaluation of crop genetic diversity (and associated trait diversity), with a focus on utilizing the available diversity in crop improvement programmes to improve existing germplasm resources by means of innovative molecular breeding and conventional breeding. Topics include—but are not limited to—the following:

Gene identification;
Plant breeding;
Salinity
Drought

Dr. Wuwei Ye
Guest Editor

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. Genes is an international peer-reviewed open access monthly 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 2600 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

gene identification
plant breeding
salinity
drought

Published Papers (9 papers)

Download All Papers

Research

17 pages, 2602 KiB

Open AccessArticle

Screening Spring Wheat Genotypes for TaDreb-B1 and Fehw3 Genes under Severe Drought Stress at the Germination Stage Using KASP Technology

by Elsayed A. Mohamed, Asmaa A. M. Ahmed, Matías Schierenbeck, Mohamed Y. Hussein, P. Stephen Baenziger, Andreas Börner and Ahmed Sallam

Genes 2023, 14(2), 373; https://doi.org/10.3390/genes14020373 - 31 Jan 2023

Cited by 3 | Viewed by 2136

Abstract

Drought stress is a major yield-limiting factor throughout the world in wheat (Triticum aestivum L.), causing losses of up to 80% of the total yield. The identification of factors affecting drought stress tolerance in the seedling stage is especially important to increase adaptation and accelerate the grain yield potential. In the current study, 41 spring wheat genotypes were tested for their tolerance to drought at the germination stage under two different polyethylene glycol concentrations (PEG) of 25% and 30%. For this purpose, twenty seedlings from each genotype were evaluated in triplicate with a randomized complete block design (RCBD) in a controlled growth chamber. The following nine parameters were recorded: germination pace (GP), germination percentage (G%), number of roots (NR), shoot length (SL), root length (RL), shoot–root length ratio (SRR), fresh biomass weight (FBW), dry biomass weight (DBW), and water content (WC). An analysis of variance (ANOVA) revealed highly significant differences (p < 0.01) among the genotypes, treatments (PEG25%, PEG30%) and genotypes × treatment interaction, for all traits. The broad-sense heritability (H²) estimates were very high in both concentrations. They ranged from 89.4 to 98.9% under PEG25% and from 70.8 to 98.7% under PEG30%. Citr15314 (Afghanistan) was among the best performing genotypes under both concentrations for most of the germination traits. Two KASP markers for TaDreb-B1 and Fehw3 genes were used to screen all genotypes and to study the effect of these on drought tolerance at the germination stage. All genotypes with Fehw3 (only) showed a better performance for most traits under both concentrations compared to other genotypes having TaDreb-B1 or having both genes. To our knowledge, this work is the first report showing the effect of the two genes on germination traits under severe drought stress conditions. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Figure 1

21 pages, 5728 KiB

Open AccessArticle

Wild Vicia Species Possess a Drought Tolerance System for Faba Bean Improvement

by Irfanul Haq, Dalal Nasser Binjawhar, Zahid Ullah, Ahmad Ali, Hassan Sher and Iftikhar Ali

Genes 2022, 13(10), 1877; https://doi.org/10.3390/genes13101877 - 17 Oct 2022

Cited by 6 | Viewed by 1619

Abstract

Faba bean (Vicia faba L.), a drought-sensitive crop, is drastically affected by drought stresses compromising its growth and yield. However, wild relatives of faba bean are considered a reservoir of potential genetic resources for tolerance against abiotic stresses. This study was conducted to characterize wild relatives of faba bean for identification of a specific tolerance system required for its improvement against drought stress. The study focused on physiological, biochemical, and anatomical responses of wild Vicia species under drought stress conditions. The experiment was carried out under various levels of drought stress imposed through different field capacities (FC) which included 80% FC ie (well-watered condition), 55% FC (moderate stress), and 30% FC (severe stress). When compared to plants grown in a control environment, drought stress significantly reduced the studied physiological attributes including soluble sugars (21.3% and 15.8%), protein contents (14.7 and 14.6%), and chlorophyll (8.4 and 28.6%) under moderate (55% FC) and severe drought stress (30% FC), respectively. However, proline content increased by 20.5% and 27.6%, peroxidase activity by 48.5% and 57.1%, and superoxide dismutase activity by 72.6% and 64.8% under moderate and severe stress, respectively. The studied anatomical attributes were also affected under drought stress treatments, including diameter of stem xylem vessels (9.1% and 13.7%), leaf lower epidermal thickness (8.05% and 13.34%), and leaf phloem width (5.3% and 10.1%) under moderate and severe stress, respectively. Wild Vicia spp. showed better tolerance to water-deficit conditions as compared to cultivated Vicia L. The observed potential diversity for drought tolerance in wild Vicia spp. may assist in improvement of faba bean and may also help in understanding the mechanisms of adaptations in drought-prone environments. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Figure 1

16 pages, 3841 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of the CCT Gene Family in Foxtail Millet (Setaria italica) Response to Diurnal Rhythm and Abiotic Stress

by Yuntong Li, Shumin Yu, Qiyuan Zhang, Ziwei Wang, Meiling Liu, Ao Zhang, Xiaomei Dong, Jinjuan Fan, Yanshu Zhu, Yanye Ruan and Cong Li

Genes 2022, 13(10), 1829; https://doi.org/10.3390/genes13101829 - 10 Oct 2022

Cited by 6 | Viewed by 1705

Abstract

The CCT gene family plays important roles in diurnal rhythm and abiotic stress response, affecting crop growth and development, and thus yield. However, little information is available on the CCT family in foxtail millet (Setaria italica). In the present study, we identified 37 putative SiCCT genes from the foxtail millet genome. A phylogenetic tree was constructed from the predicted full-length SiCCT amino acid sequences, together with CCT proteins from rice and Arabidopsis as representatives of monocotyledonous and dicotyledonous plants, respectively. Based on the conserved structure and phylogenetic relationships, 13, 5, and 19 SiCCT proteins were classified in the COL, PRR, and CMF subfamilies, respectively. The gene structure and protein conserved motifs analysis exhibited highly similar compositions within the same subfamily. Whole-genome duplication analysis indicated that segmental duplication events played an important role in the expansion of the CCT gene family in foxtail millet. Analysis of transcriptome data showed that 16 SiCCT genes had significant diurnal rhythm oscillations. Under abiotic stress and exogenous hormonal treatment, the expression of many CMF subfamily genes was significantly changed. Especially after drought treatment, the expression of CMF subfamily genes except SiCCT32 was significantly up-regulated. This work provides valuable information for further study of the molecular mechanism of diurnal rhythm regulation, abiotic stress responses, and the identification of candidate genes for foxtail millet molecular breeding. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Figure 1

16 pages, 3049 KiB

Open AccessArticle

Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

by Yan Liu, Xiaoyan Xiao, Guangzhu Li, Chenglei Zhu, Kebin Yang, Xiaohu Feng, Yongfeng Lou and Zhimin Gao

Genes 2022, 13(9), 1518; https://doi.org/10.3390/genes13091518 - 24 Aug 2022

Cited by 4 | Viewed by 1693

Abstract

Simple sequence repeats (SSRs) are one of the most important molecular markers, which are widespread in plants. Bamboos are important forest resources worldwide. Here, the comprehensive identification and comparative analysis of SSRs were performed in three woody and two herbaceous bamboo species. Altogether 567,175 perfect SSRs and 71,141 compound SSRs were identified from 5737.8 Mb genome sequences of five bamboo species. Di-nucleotide SSRs were the most predominant type, with an average of ~50,152.2 per species. Most SSRs were located in intergenic regions, while those located in genic regions were relatively less. Moreover, the results of annotation distribution indicated that terms with P450, peroxidase and ATP-binding cassette transporter related to lignin biosynthesis might play important roles in woody and herbaceous bamboos under the mediation of SSRs. Furthermore, the peroxidase gene family consisted of a large number of genes containing SSRs was selected for the evolutionary relationship analysis and SSR markers development. Fifteen SSR markers derived from peroxidase family genes of Phyllostachys edulis were identified as polymorphic in 34 accessions belonging to seven genera in Bambusoideae. These results provided a comprehensive insight of SSR markers into bamboo genomes, which would facilitate bamboo research related to comparative genomics, evolution and marker-assisted selection. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Figure 1

12 pages, 2101 KiB

Open AccessArticle

The New Variation in the Promoter Region of FLOWERING LOCUS T Is Involved in Flowering in Brassica rapa

by Qingzhen Wei, Tianhua Hu, Xinfeng Xu, Zhen Tian, Chonglai Bao, Jinglei Wang, Hongtao Pang, Haijiao Hu, Yaqin Yan, Tongkun Liu and Wuhong Wang

Genes 2022, 13(7), 1162; https://doi.org/10.3390/genes13071162 - 27 Jun 2022

Cited by 4 | Viewed by 1691

Abstract

Flowering time is an important agronomic trait in Brassica rapa and has a wide range of variation. The change from vegetative to reproductive development is a major transition period, especially in flowering vegetable crops. In this study, two non-heading Chinese cabbage varieties with significantly different flowering times, Pak-choi (B. rapa var. communis Tesn et Lee) and Caitai (B. rapa var. tsaitai Hort.), were used to construct segregated F₂ populations. The bulk-segregant approach coupled with whole genome re-sequencing was used for QTL sequencing (QTL-seq) analysis to map flowering time traits. The candidate genes controlling flowering time in B. rapa were predicted by homologous gene alignment and function annotation. The major-effect QTL ft7.1 was detected on chromosome A07 of B. rapa, and the FT family gene BrFT was predicted as the candidate gene. Moreover, a new promoter regional difference of 1577 bp was revealed by analyzing the sequence of the BrFT gene. The promoter region activity analysis and divergent gene expression levels indicated that the difference in the promoter region may contribute to different flowering times. These findings provide insights into the mechanisms underlying the flowering time in Brassica and the candidate genes regulating flowering in production. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Figure 1

14 pages, 5289 KiB

Open AccessArticle

The Genetic Diversity of Bletilla spp. Based on SLAF-seq and Oligo-FISH

by Jie Huan, Zhoujian He, Yuting Lei, Wenjun Li, Liqiong Jiang and Xiaomei Luo

Genes 2022, 13(7), 1118; https://doi.org/10.3390/genes13071118 - 22 Jun 2022

Cited by 1 | Viewed by 1727

Abstract

Bletilla spp. Rchb. F. is a traditional Chinese medicinal material. In this study, Bletilla striata (Thunb. ex A. Murray) Rchb F, Bletilla formosana (Hayata) Schltr, and Bletilla ochracea Schltr were collected to analyze the genetic diversity of 16 materials using specific site-amplified fragment sequencing (SLAF-seq) and fluorescence in situ hybridization (FISH). The results showed that the phylogenetic tree of the single-nucleotide polymorphism (SNP) data rendering system was correlated with the shape and geographical distribution of the material. The results of the population structural analysis showed that all the materials containing yellow labellum came from the same ancestor. The results of the principal component analysis were able to preliminarily judge the genetic distance and provided a reference for the selection of hybrid parents. The FISH analysis showed that the chromosomes of B. striata were 2n = 32 and the chromosomes of the B. striata (safflower) mutant were 2n = 34 and the chromosomes of B. ochracea and B. formosana were 2n = 34–36. The (AG₃T₃)₃ non-terminal signal was different from the 5S rDNA signal. These results revealed that the 16 materials had rich genetic diversity, which can provide molecular and cytogenetic data for the study of the genus and its relatives and serve as a reference for the breeding of new genus varieties and improve breeding efficiency and cost. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Figure 1

15 pages, 2695 KiB

Open AccessArticle

Identification of Putative SNP Markers Associated with Resistance to Egyptian Loose Smut Race(s) in Spring Barley

by Kamal A. M. Abo-Elyousr, Amira M. I. Mourad, P. Stephen Baenziger, Abdelaal H. A. Shehata, Peter E. Eckstein, Aaron D. Beattie and Ahmed Sallam

Genes 2022, 13(6), 1075; https://doi.org/10.3390/genes13061075 - 16 Jun 2022

Cited by 5 | Viewed by 2210

Abstract

Loose smut (LS) disease is a serious problem that affects barley yield. Breeding of resistant cultivars and identifying new genes controlling LS has received very little attention. Therefore, it is important to understand the genetic basis of LS control in order to genetically improve LS resistance. To address this challenge, a set of 57 highly diverse barley genotypes were inoculated with Egyptian loose smut race(s) and the infected seeds/plants were evaluated in two growing seasons. Loose smut resistance (%) was scored on each genotype. High genetic variation was found among all tested genotypes indicating considerable differences in LS resistance that can be used for breeding. The broad-sense heritability (H²) of LS (0.95) was found. Moreover, genotyping-by-sequencing (GBS) was performed on all genotypes and generated in 16,966 SNP markers which were used for genetic association analysis using single-marker analysis. The analysis identified 27 significant SNPs distributed across all seven chromosomes that were associated with LS resistance. One SNP (S6_17854595) was located within the HORVU6Hr1G010050 gene model that encodes a protein kinase domain-containing protein (similar to the Un8 LS resistance gene, which contains two kinase domains). A TaqMan marker (0751D06 F6/R6) for the Un8 gene was tested in the diverse collection. The results indicated that none of the Egyptian genotypes had the Un8 gene. The result of this study provided new information on the genetic control of LS resistance. Moreover, good resistance genotypes were identified and can be used for breeding cultivars with improved resistance to Egyptian LS. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Figure 1

21 pages, 2634 KiB

Open AccessArticle

Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks

by Shengmei Li, Shiwei Geng, Bo Pang, Jieyin Zhao, Yajie Huang, Cun Rui, Jinxin Cui, Yang Jiao, Ru Zhang and Wenwei Gao

Genes 2022, 13(6), 954; https://doi.org/10.3390/genes13060954 - 26 May 2022

Cited by 4 | Viewed by 2324

Abstract

Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Graphical abstract

10 pages, 2013 KiB

Open AccessArticle

Five Fabaceae Karyotype and Phylogenetic Relationship Analysis Based on Oligo-FISH for 5S rDNA and (AG₃T₃)₃

by Zhoujian He, Wei Zhang, Xiaomei Luo and Jie Huan

Genes 2022, 13(5), 768; https://doi.org/10.3390/genes13050768 - 26 Apr 2022

Cited by 4 | Viewed by 2624

Abstract

Most Fabaceae have nitrogen fixation abilities and are valuable forage and medicinal resources. However, cytogenetic data of many Fabaceae species are unclear. Karyotypes reveal cytological characteristics and are crucial to understanding the organization and evolution of chromosomes in species. Oligo-FISH can reveal genetic composition and karyotype variation patterns with rapid and efficient results. Karyotype analysis of five Fabaceae species by oligonucleotide probes showed that: Robinia pseudoacacia, karyotype formula 2n = 2x = 20m + 2sm, cytotype 2B, arm ratio 3.4821, eight chromosomes distributed 5S rDNA signal. The karyotype formula of Robinia pseudoacacia ‘idaho’ was 2n = 2x = 20m + 2sm, cytotype 1A, arm ratio 1.8997, and 5S rDNA signal was distributed on six chromosomes. Karyotype of Robinia pseudoacacia f. decaisneana 2n = 2x = 20m + 2sm, cytotype 1B, arm ratio 2.0787, the distribution of eight chromosomes with 5S rDNA signal. Karyotype formula of Styphnolobium japonicum 2n = 2x = 14m + 12sm + 2st, cytotype 2B, arm ratio 2.6847, two chromosomes have 5S rDNA signal. Amorpha fruticose karyotype 2n = 2x = 38m + 2sm, cytotype 1B, arm ratio 3.2058, four chromosomes possessed 5S rDNA signal. Both ends of all species’ chromosomes have (AG₃T₃)₃ signals. The results of this study provide chromosome numbers and a physical map, contributing to the construction of the Oligo-FISH barcode and providing molecular cytogenetics data for Fabaceae. Full article

(This article belongs to the Special Issue Plant Genetics and Breeding Improvement)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Plant Genetics and Breeding Improvement

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (9 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI