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Genes
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Genetic Research and Plant Breeding 2.0
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Genetic Research and Plant Breeding 2.0

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

Deadline for manuscript submissions: closed (25 June 2024) | Viewed by 10220

Special Issue Editors

Prof. Dr. Yong-Gu Cho

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Guest Editor
Department of Crop Science, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
Interests: marker-assisted breeding (MAS); genome editing; functional genomics; GWAS; functional analysis of genes; plant biotechnology; molecular breeding in rice
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Kwon-Kyoo Kang

E-Mail Website
Guest Editor
Division of Horticultural Biotechnology, Hankyung National University, Anseong 17579, Republic of Korea
Interests: functional analysis of genes via CRISPR/Cas9; functional genomics; MABc (marker-assisted backcross); transcriptomics; plant biotechnology; molecular breeding in plants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the last two decades, molecular biology has improved markedly with regard to QTL and functional analysis, as well as gene identification and cloning of plant species. In parallel, innovation in molecular technologies has been exponential in the areas of genetics and genomics.

Functional genomics has become one of the most promising scientific areas in the characterization of gene (and protein) functions and interactions, using vast genetics and various omics data. In addition, various advanced tools and methodologies have been developed that allow the effective and efficient validation of gene functions when used in lab settings, such as transcriptome analysis, metabolomics, overexpression, knock-out, RNAi and gene editing, and when advanced computational methodologies, such as machine learning and deep learning, are applied.

This Special Issue welcomes original research articles and reviews that explore agronomic trait characterization, gene discovery, and function and expression control analysis, using both wet lab technologies and computational biology, which could accelerate plant breeding programs.

Prof. Dr. Yong-Gu Cho
Prof. Dr. Kwon-Kyoo Kang
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. 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

  • transcriptomics
  • metabolomics
  • function of genes
  • transcription factors
  • plant gene regulation
  • gene silencing and miRNAs
  • molecular genetics
  • molecular marker
  • genetic mapping
  • marker-assisted selection
  • genomic selection
  • genetic engineering
  • molecular design breeding
  • plant breeding

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Related Special Issue

Published Papers (6 papers)

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Research

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17 pages, 6409 KiB  
Article
Knockout of the Chlorophyll a Oxygenase Gene OsCAO1 Reduces Chilling Tolerance in Rice Seedlings
by Jiayi Xiong, Genping Wen, Jin Song, Xiaoyi Liu, Qiuhong Chen, Guilian Zhang, Yunhua Xiao, Xiong Liu, Huabing Deng, Wenbang Tang, Feng Wang and Xuedan Lu
Genes 2024, 15(6), 721; https://doi.org/10.3390/genes15060721 - 2 Jun 2024
Viewed by 1223
Abstract
Chilling stress is one of the main abiotic factors affecting rice growth and yield. In rice, chlorophyllide a oxygenase encoded by OsCAO1 is responsible for converting chlorophyllide a to chlorophyllide b, playing a crucial role in photosynthesis and thus rice growth. However, [...] Read more.
Chilling stress is one of the main abiotic factors affecting rice growth and yield. In rice, chlorophyllide a oxygenase encoded by OsCAO1 is responsible for converting chlorophyllide a to chlorophyllide b, playing a crucial role in photosynthesis and thus rice growth. However, little is known about the function of OsCAO1 in chilling stress responses. The presence of the cis-acting element involved in low-temperature responsiveness (LTR) in the OsCAO1 promoter implied that OsCAO1 probably is a cold-responsive gene. The gene expression level of OsCAO1 was usually inhibited by low temperatures during the day and promoted by low temperatures at night. The OsCAO1 knockout mutants generated by the CRISPR-Cas9 technology in rice (Oryza sativa L.) exhibited significantly weakened chilling tolerance at the seedling stage. OsCAO1 dysfunction led to the accumulation of reactive oxygen species and malondialdehyde, an increase in relative electrolyte leakage, and a reduction in antioxidant gene expression under chilling stress. In addition, the functional deficiency of OsCAO1 resulted in more severe damage to chloroplast morphology, such as abnormal grana thylakoid stacking, caused by low temperatures. Moreover, the rice yield was reduced in OsCAO1 knockout mutants. Therefore, the elevated expression of OsCAO1 probably has the potential to increase both rice yield and chilling tolerance simultaneously, providing a strategy to cultivate chilling-tolerant rice varieties with high yields. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding 2.0)
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16 pages, 2271 KiB  
Article
Molecular Evaluation of the Effects of FLC Homologs and Coordinating Regulators on the Flowering Responses to Vernalization in Cabbage (Brassica oleracea var. capitata) Genotypes
by Ju-Young Ahn, Saminathan Subburaj, Fanzhuang Yan, Jian Yao, Ajithan Chandrasekaran, Kyoung-Gu Ahn and Geung-Joo Lee
Genes 2024, 15(2), 154; https://doi.org/10.3390/genes15020154 - 24 Jan 2024
Viewed by 1569
Abstract
The flowering loci of cabbage must be understood to boost their productivity. In this study, to clarify the flowering mechanisms of cabbage, we examined the three flowering repressors BoFLC1, 2 and 3, and the flowering regulators BoGI, BoCOOLAIR, and [...] Read more.
The flowering loci of cabbage must be understood to boost their productivity. In this study, to clarify the flowering mechanisms of cabbage, we examined the three flowering repressors BoFLC1, 2 and 3, and the flowering regulators BoGI, BoCOOLAIR, and BoVIN3 of early (CAB1), middle (CAB3), and late (CAB5) flowering cabbage genotypes. Analysis of allele-specifically amplified genomic DNA and various sequence alignments demonstrated that maximal insertions and deletions influenced cabbage flowering behavior, notably in CAB3 and CAB5. Phylogenetic studies showed that BoFLC1, 2, and 3 in the CAB1, 3, and 5 genotypes had the highest homologies to other Brassica species, with CAB3 and 5 the most similar. Although CAB3 and CAB5 have comparable genetic patterns, flowering repressors and flowering regulators were investigated individually with and without vernalization to determine their minor flowering differences. The expression investigation revealed that vernalized CAB5 downregulated all BoFLC genes compared to CAB3 and, in contrast, CAB3 exhibited upregulated BoCOOLAIR. We hypothesized that the CAB3 BoFLC locus’ additional insertions may have led to BoCOOLAIR overexpression and BoFLC downregulation. This study sheds light on cabbage genotypes—particularly those of CAB1 and CAB5—and suggests that structural variations in BoFLC2 and 3 bind flowering regulators, such as COOLAIR, which may affect cabbage flowering time. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding 2.0)
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11 pages, 1741 KiB  
Article
β-Aminobutyric Acid and Powdery Mildew Infection Enhanced the Activation of Defense-Related Genes and Salicylic Acid in Cucumber (Cucumis sativus L.)
by Ja-Yoon Kim and Hee-Wan Kang
Genes 2023, 14(11), 2087; https://doi.org/10.3390/genes14112087 - 17 Nov 2023
Cited by 2 | Viewed by 1548
Abstract
Powdery mildew disease, caused by Sphaerotheca fusca, is a major disease affecting cucumbers cultivated in greenhouses. This study was conducted to find defense genes induced by β-aminobutyric acid (BABA) and powdery mildew in cucumber. Disease severities of 25% and 5% were exhibited [...] Read more.
Powdery mildew disease, caused by Sphaerotheca fusca, is a major disease affecting cucumbers cultivated in greenhouses. This study was conducted to find defense genes induced by β-aminobutyric acid (BABA) and powdery mildew in cucumber. Disease severities of 25% and 5% were exhibited by the 2000 and 5000 mg/L BABA-treated cucumber, respectively. BABA did not affect the spore germination of the powdery mildew pathogen, showing that BABA is not an antifungal agent against the pathogen. In quantitative real-time PCR analysis, BABA-treated cucumber upregulated the transcriptional levels of the defense genes CsPAL, CsPR3, CsPR1, CsLOX1, CsLOX23, Cs LecRK6.1, CsWRKY20, and Cupi4 in cucumber to maximum levels at 48 h, whereas CsLecRK6.1 reached maximum expression after 24 h, and further, salicylic acid (SA) levels were significantly increased in BABA-treated cucumber plants. In addition, the cucumber infected with powdery mildew underwent a 1.6- to 47.3-fold enhancement in the defense genes PAL, PR3, PR1, Lox1, Lox 23, LecRK6.1, WRKY20, and Cupi4 compared to heathy cucumber. These results suggest that the BABA-induced defense response is associated with SA signaling pathway-dependent systemic acquired resistance (SAR) in cucumber, which is involved in plant resistance mechanisms. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding 2.0)
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18 pages, 6831 KiB  
Article
Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea
by Zhen Li, Tian Wang, Lan Yun, Xiaomin Ren, Yong Wang and Fengling Shi
Genes 2023, 14(10), 1970; https://doi.org/10.3390/genes14101970 - 21 Oct 2023
Cited by 1 | Viewed by 1399
Abstract
Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation [...] Read more.
Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon’s information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker–trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding 2.0)
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14 pages, 3028 KiB  
Article
QTL Mapping of Tiller Number in Korean Japonica Rice Varieties
by Dong-Kyung Yoon, Inchan Choi, Yong Jae Won, Yunji Shin, Kyeong-Seong Cheon, Hyoja Oh, Chaewon Lee, Seoyeon Lee, Mi Hyun Cho, Soojin Jun, Yeongtae Kim, Song Lim Kim, Jeongho Baek, HwangWeon Jeong, Jae Il Lyu, Gang-Seob Lee, Kyung-Hwan Kim and Hyeonso Ji
Genes 2023, 14(8), 1593; https://doi.org/10.3390/genes14081593 - 6 Aug 2023
Cited by 1 | Viewed by 1639
Abstract
Tiller number is an important trait associated with yield in rice. Tiller number in Korean japonica rice was analyzed under greenhouse conditions in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae and Unbong40 to identify quantitative [...] Read more.
Tiller number is an important trait associated with yield in rice. Tiller number in Korean japonica rice was analyzed under greenhouse conditions in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae and Unbong40 to identify quantitative trait loci (QTLs). A genetic map comprising 239 kompetitive allele-specific PCR (KASP) and 57 cleaved amplified polymorphic sequence markers was constructed. qTN3, a major QTL for tiller number, was identified at 132.4 cm on chromosome 3. This QTL was also detected under field conditions in a backcross population; thus, qTN3 was stable across generations and environments. qTN3 co-located with QTLs associated with panicle number per plant and culm diameter, indicating it had pleiotropic effects. The qTN3 regions of Odae and Unbong40 differed in a known functional variant (4 bp TGTG insertion/deletion) in the 5ʹ UTR of OsTB1, a gene underlying variation in tiller number and culm strength. Investigation of variation in genotype and tiller number revealed that varieties with the insertion genotype had lower tiller numbers than those with the reference genotype. A high-resolution melting marker was developed to enable efficient marker-assisted selection. The QTL qTN3 will therefore be useful in breeding programs developing japonica varieties with optimal tiller numbers for increased yield. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding 2.0)
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Review

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23 pages, 2783 KiB  
Review
Stone Pine (Pinus pinea L.) High-Added-Value Genetics: An Overview
by Ana Sofia B. Simões, Margarida Machado Borges, Liliana Grazina and João Nunes
Genes 2024, 15(1), 84; https://doi.org/10.3390/genes15010084 - 10 Jan 2024
Cited by 1 | Viewed by 1955
Abstract
Stone pine (Pinus pinea L.) has received limited attention in terms of genetic research. However, genomic techniques hold promise for decoding the stone pine genome and contributing to developing a more resilient bioeconomy. Retrotransposon and specific genetic markers are effective tools for [...] Read more.
Stone pine (Pinus pinea L.) has received limited attention in terms of genetic research. However, genomic techniques hold promise for decoding the stone pine genome and contributing to developing a more resilient bioeconomy. Retrotransposon and specific genetic markers are effective tools for determining population-specific genomic diversity. Studies on the transcriptome and proteome have identified differentially expressed genes PAS1, CLV1, ATAF1, and ACBF involved in shoot bud formation. The stone pine proteome shows variation among populations and shows the industrial potential of the enzyme pinosylvin. Microsatellite studies have revealed low levels of polymorphism and a unique genetic diversity in stone pine, which may contribute to its environmental adaptation. Transcriptomic and proteomic analyses uncover the genetic and molecular responses of stone pine to fungal infections and nematode infestations, elucidating the defense activation, gene regulation, and the potential role of terpenes in pathogen resistance. Transcriptomics associated with carbohydrate metabolism, dehydrins, and transcription factors show promise as targets for improving stone pine’s drought stress response and water retention capabilities. Stone pine presents itself as an important model tree for studying climate change adaptation due to its characteristics. While knowledge gaps exist, stone pine’s genetic resources hold significant potential, and ongoing advancements in techniques offer prospects for future exploration. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding 2.0)
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