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Life
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Plant Functional Genomics and Breeding
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Plant Functional Genomics and Breeding

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 6755

Special Issue Editor

Dr. Yifeng Wang

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: seed developmental biology; seed dormancy; germination; phytohormone; molecular mechanism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The main goals of breeders are improving plant yield, resistance, and quality. The study of plant functional genomics is a crucial approach in biological breeding. Understanding plant functional genomics sheds insights into the genetic and molecular mechanisms regulating crucial traits, such as yield, and resistance to biotic and abiotic stresses, such as diseases, pests, and environmental stresses. This knowledge is instrumental in developing enhanced quantity and quality of elite plant varieties, guaranteeing an adequate and stable food supply. The goal of this Special Issue, “Plant Functional Genomics and Breeding” in Life, is to provide an overview of the latest research and discoveries in the functional genomics of plants, including cloning novel genes involved in yield, resistance, and quality. The study encompasses the functional analysis of these genes and investigates their applications in biological breeding. We welcome all types of submissions, including original research, reviews, and methodologies in this field, including (but not limited to) research covering:

  • Mining genes involved in plant development;
  • Uncovering the genetic and molecular mechanisms of plant development;
  • Genetic improvement plant growth via biotechnologies.

Dr. Yifeng Wang
Guest Editor

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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. Life 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

  • functional genomics
  • biological breeding
  • gene cloning
  • molecular network
  • genetic improvement

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Published Papers (7 papers)

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Research

26 pages, 6539 KiB  
Article
Genetic and Epigenetic Changes in Arabidopsis thaliana Exposed to Ultraviolet-C Radiation Stress for 25 Generations
by Andres Lopez Virgen, Narendra Singh Yadav, Boseon Byeon, Yaroslav Ilnytskyy and Igor Kovalchuk
Life 2025, 15(3), 502; https://doi.org/10.3390/life15030502 - 20 Mar 2025
Viewed by 542
Abstract
Continuous exposure to stress contributes to species diversity and drives microevolutionary processes. It is still unclear, however, whether epigenetic changes, in the form of epimutations such as, for example, differential DNA methylation, are the pre-requisite to speciation events. We hypothesized that continuous stress [...] Read more.
Continuous exposure to stress contributes to species diversity and drives microevolutionary processes. It is still unclear, however, whether epigenetic changes, in the form of epimutations such as, for example, differential DNA methylation, are the pre-requisite to speciation events. We hypothesized that continuous stress exposure would increase epigenetic diversity to a higher extent than genetic diversity. In this work, we have analyzed the effect of 25 consecutive generations of UV-C-stress exposure on the Arabidopsis thaliana genome and epigenome. We found no evidence of increased tolerance to UV-C in the progeny of UV-C-stressed plants (F25UV) as compared to the progeny of control plants (F25C). Genetic analysis showed an increased number of single nucleotide polymorphisms (SNPs) and deletions in F25UV plants. Most common SNPs were mutations in cytosines, C to T, C to A, and C to G. Analysis of cytosine methylation showed a significant increase in the percentage of methylated cytosines at CG context in F25UV as compared to F25C or F2C (parental control). The most significant differences between F25UV and either control group were observed in CHG and CHH contexts; the number of hypomethylated cytosines at CHH contexts was over 10 times higher in the F25UC group. F25UV plants clustered separately from other groups in both genomic and epigenomic analyses. GO term analysis of differentially methylated genes revealed enrichments in “DNA or RNA metabolism”, “response to stress”, “response to biotic and abiotic stimulus”, and “signal transduction”. Our work thus demonstrates that continuous exposure to UV-C increases genomic and epigenomic diversity in the progeny, with epigenetic changes occurring in many stress-responsive pathways. Full article
(This article belongs to the Special Issue Plant Functional Genomics and Breeding)
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18 pages, 1309 KiB  
Article
Accumulation Potential of Lead and Cadmium Metals in Maize (Zea mays L.) and Effects on Physiological-Morphological Characteristics
by Ümit Elik and Zeynep Gül
Life 2025, 15(2), 310; https://doi.org/10.3390/life15020310 - 17 Feb 2025
Cited by 1 | Viewed by 688
Abstract
Phytoremediation stands at the forefront of modern environmental science, offering an innovative and cost-effective solution for the remediation of heavy-metal-contaminated soils through the natural capabilities of plants. This study aims to investigate the effects of lead (Pb) and cadmium (Cd) metals on plant [...] Read more.
Phytoremediation stands at the forefront of modern environmental science, offering an innovative and cost-effective solution for the remediation of heavy-metal-contaminated soils through the natural capabilities of plants. This study aims to investigate the effects of lead (Pb) and cadmium (Cd) metals on plant growth (e.g., seedling height, stem diameter, fresh and dry weight), physiological properties (e.g., tissue relative water content, tissue electrical conductivity), and biochemical parameters (e.g., chlorophyll content, superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) enzyme activities) of maize compared to the control group under greenhouse conditions at the Atatürk University Plant Production Application and Research Center. The results show that plant height decreased by 20% in the lead (Pb3000) application and by 42% in the cadmium (Cd300) application compared to the control group. The highest Pb dose (Pb3000) caused a 15% weight loss compared to the control, while the highest Cd dose (Cd300) caused a weight loss of 63%. The accumulation rates of heavy metals in soil, roots, and aboveground parts of plants indicated that maize absorbed and accumulated more Cd compared to Pb. Full article
(This article belongs to the Special Issue Plant Functional Genomics and Breeding)
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26 pages, 4580 KiB  
Article
Physiological and Transcriptome Analysis Reveal the Underlying Mechanism of Salicylic Acid-Alleviated Drought Stress in Kenaf (Hibiscus cannabinus L.)
by Hui Zhang, Guofeng Xu, Samavia Mubeen, Rujian Wei, Muzammal Rehman, Shan Cao, Caijin Wang, Jiao Yue, Jiao Pan, Gang Jin, Ru Li, Tao Chen and Peng Chen
Life 2025, 15(2), 281; https://doi.org/10.3390/life15020281 - 12 Feb 2025
Viewed by 755
Abstract
Salicylic acid (SA) plays a crucial role in alleviating drought stress in plants. However, little is known about the molecular mechanisms underlying exogenous SA on the drought tolerance of kenaf. In this study, the kenaf seedlings were subjected to physiological and transcriptomic analysis [...] Read more.
Salicylic acid (SA) plays a crucial role in alleviating drought stress in plants. However, little is known about the molecular mechanisms underlying exogenous SA on the drought tolerance of kenaf. In this study, the kenaf seedlings were subjected to physiological and transcriptomic analysis under control (CK), moderate drought stress (D), and moderate drought stress with 1 mM SA (D_SA). Under drought conditions, SA significantly improved the plant biomass, leaf area, antioxidant enzyme activities (SOD, POD, and CAT), soluble sugars, starch and proline contents, and photosynthesis, while the contents of MDA, H2O2, and O2− were significantly decreased. A total of 3430 (1118 up-regulated and 2312 down-regulated) genes were differentially expressed in group D, compared with group CK. At the same time, 92 (56 up-regulated and 36 down-regulated) genes were differentially expressed in group D_SA compared with group D. GO and KEGG analysis showed that the differentially expressed genes (DEGs) were enriched in various metabolic pathways, such as carbohydrate metabolism, lipid metabolism, and the metabolism of terpenoids and polyketides. Results showed that the genes related to the antioxidant system, sucrose and starch synthesis, osmoregulation, ABA signal regulation, and differentially expressed transcription factors, such as AP2/ERF4 and NF-Y1, were involved in the increased drought tolerance of kenaf under exogenous SA. Virus-induced gene silencing (VIGS)-mediated silencing of salicylate binding protein 2 gene (HcSABP2) decreased the drought resistance of kenaf seedlings. Thus, the present study provides valuable insights into the regulatory mechanism of exogenous SA in alleviating drought stress in kenaf. Full article
(This article belongs to the Special Issue Plant Functional Genomics and Breeding)
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19 pages, 6058 KiB  
Article
Influence of Nutrient Medium Components on In Vitro Tuberization of Solanum tuberosum L. and Subsequent Minituber Production in Aeroponic and Greenhouse Conditions
by Gayane Hrant Melyan, Yuri Tsatur Martirosyan, Aghvan Jumshud Sahakyan, Hovik Yakshibek Sayadyan, Andreas Shmavon Melikyan, Andranik Hakob Barseghyan, Arayik Sajan Vardanyan, Hamlet Sargis Martirosyan, Margarita Gurgen Harutyunyan, Anzhela Liparit Mkrtchyan, Inna Lendrush Hakobjanyan, Kima Seryozha Dangyan, Khachik Harut Terteryan, Kamo Atam Khazaryan and Meruzhan Haykaram Galstyan
Life 2025, 15(2), 241; https://doi.org/10.3390/life15020241 - 5 Feb 2025
Cited by 1 | Viewed by 867
Abstract
Potatoes, a vital global food crop, have shown remarkable adaptability, significantly contributing to food security. Technological advancements now enable their cultivation from soil-based systems to liquid synthetic nutrient media, even in artificial closed environments without natural light or fertile soil. This study examined [...] Read more.
Potatoes, a vital global food crop, have shown remarkable adaptability, significantly contributing to food security. Technological advancements now enable their cultivation from soil-based systems to liquid synthetic nutrient media, even in artificial closed environments without natural light or fertile soil. This study examined the effects of Benzylaminopurine (BAP) and Kinetin (Kin) at concentrations ranging from 0 to 5 mg/L and sucrose concentrations ranging from 20 to 120 g/L on in vitro tuberization, focusing on microtuber size, weight, and tuberization rate. Nodal segments from virus-free ‘Red Scarlet’ in vitro potato plantlets were used as explants. These explants were cultured on Murashige and Skoog (MS) medium solidified with 0.5% agar. The study also compared minituber production efficiency under soil-based greenhouse and aeroponic conditions. The highest in vitro potato tuberization rate (90%) was achieved with 80 g/L sucrose and 3.0 mg/L BAP. After induction, virus-free microtubers were transferred to both greenhouse conditions and aeroponic systems for further assessment of minituber production and biochemical composition. These findings demonstrate the potential of aeroponics as a superior method for producing high-quality, pathogen-free minitubers. Aeroponics resulted in significantly higher minituber yields compared to soil-based greenhouse systems, offering a scalable and efficient solution for seed production. Full article
(This article belongs to the Special Issue Plant Functional Genomics and Breeding)
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28 pages, 5610 KiB  
Article
Reproductive Performance of the Alpine Plant Species Ranunculus kuepferi in a Climatic Elevation Gradient: Apomictic Tetraploids Do Not Show a General Fitness Advantage over Sexual Diploids
by Ursula Ladinig, Elvira Hörandl, Simone Klatt and Johanna Wagner
Life 2024, 14(9), 1202; https://doi.org/10.3390/life14091202 - 22 Sep 2024
Viewed by 1093
Abstract
Previous studies on the mountain plant Ranunculus kuepferi concluded that apomictic self-compatible tetraploids have experienced a niche shift toward a colder climate during the Holocene, which suggests a fitness advantage over the sexual, self-sterile diploid parents under cold and stressful high-mountain conditions. However, [...] Read more.
Previous studies on the mountain plant Ranunculus kuepferi concluded that apomictic self-compatible tetraploids have experienced a niche shift toward a colder climate during the Holocene, which suggests a fitness advantage over the sexual, self-sterile diploid parents under cold and stressful high-mountain conditions. However, there is still a lack of information on whether reproductive development would be advantageous for tetraploids. Here, we report on microsporogenesis, megagametogenesis, the dynamics of flower and seed development, and the consequences for reproductive success in a common garden experiment along a 1000 m climatic elevation gradient and in natural populations. Flower buds were initiated in the year preceding anthesis and passed winter in a pre-meiotic stage. Flower morphology differed in the known cytotype-specific way in that tetraploid flowers produced about twice as many carpels and fewer petals, stamens, and pollen grains than diploid flowers. Tetraploids developed precociously aposporous embryo sacs and showed a high rate of developmental disturbances. Sexual seed formation prevailed in diploids and pseudogamous apomixis in tetraploids. Along the elevation gradient, stigma pollen load, pollen performance, and seed output decreased. Combinations of reproductive traits, namely, bypass of meiosis irregularities and uniparental reproduction, might have promoted the vast expansion of apomictic R. kuepferi lines across the European Alps. Full article
(This article belongs to the Special Issue Plant Functional Genomics and Breeding)
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14 pages, 3400 KiB  
Article
Detection of Quantitative Trait Loci Associated with Alkaline Tolerance Using Recombinant Inbred Line Population Derived from Longdao5 × Zhongyouzao8 at Seedling Stage
by Xijuan Zhang, Kai Liu, Chuanming Yang, Benfu Hou, Xianli Yang, Lizhi Wang, Shize Cui, Yongcai Lai, Zhugang Li and Shukun Jiang
Life 2024, 14(9), 1151; https://doi.org/10.3390/life14091151 - 11 Sep 2024
Viewed by 913
Abstract
Salt–alkaline stress is one of the most stressful occurrences, causing negative effects on plant development and agricultural yield. Identifying and utilizing genes that affect alkaline tolerance is an excellent approach to accelerate breeding processes and meet the needs for remediating saline–alkaline soil. Here, [...] Read more.
Salt–alkaline stress is one of the most stressful occurrences, causing negative effects on plant development and agricultural yield. Identifying and utilizing genes that affect alkaline tolerance is an excellent approach to accelerate breeding processes and meet the needs for remediating saline–alkaline soil. Here, we employed a mapping population of 176 recombinant inbred lines (RILs) produced from a cross between alkali-tolerant Longdao5 and alkali-sensitive Zhongyouzao8 to identify the quantitative trait loci (QTLs) determining alkali tolerance at the seedling stage. For the evaluation of alkali tolerance, the recovered seedling’s average alkali tolerance index (ATI), root number (RN), root length (RL), seedling dry weight (SW), root dry weight (RW), and seedling height (SH) were assessed, together with their relative alkaline damage rate. Under alkaline stress, the ATI was substantially negative connected with the root number, seedling height, seedling dry weight, and root dry weight; however, it was considerably positive correlated with the relative alkaline damage rate of the root number and root dry weight. A total of 13 QTLs for the root number, root length, seedling height, seedling dry weight, root dry weight, and alkali tolerance index under alkaline stress were identified, which were distributed across chromosomes 1, 2, 3, 4, 5, 7, and 8. All of these QTLs formed two QTL clusters for alkali tolerance on chromosome 5 and chromosome 7, designated AT5 and AT7, respectively. Nine QTLs were identified for the relative alkaline damage rate of the root number, root length, seedling height, seedling dry weight, and root dry weight under alkali stress. These QTLs were located on chromosome 2, 4, 6, 7, 8, 9, and 12. In conclusion, these findings further strengthen our knowledge about rice’s genetic mechanisms for alkaline tolerance. This research offers clues to accelerate breeding programs for new alkaline-tolerance rice varieties. Full article
(This article belongs to the Special Issue Plant Functional Genomics and Breeding)
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15 pages, 2520 KiB  
Article
Cataloging the Genetic Response: Unveiling Drought-Responsive Gene Expression in Oil Tea Camellia (Camellia oleifera Abel.) through Transcriptomics
by Zhen Zhang, Yanming Xu, Caixia Liu, Longsheng Chen, Ying Zhang, Zhilong He, Rui Wang, Chengfeng Xun, Yushen Ma, Xiaokang Yuan, Xiangnan Wang, Yongzhong Chen and Xiaohu Yang
Life 2024, 14(8), 989; https://doi.org/10.3390/life14080989 - 8 Aug 2024
Cited by 1 | Viewed by 1200
Abstract
Drought stress is a critical environmental factor that significantly impacts plant growth and productivity. However, the transcriptome analysis of differentially expressed genes in response to drought stress in Camellia oleifera Abel. is still unclear. This study analyzed the transcriptome sequencing data of C. [...] Read more.
Drought stress is a critical environmental factor that significantly impacts plant growth and productivity. However, the transcriptome analysis of differentially expressed genes in response to drought stress in Camellia oleifera Abel. is still unclear. This study analyzed the transcriptome sequencing data of C. oleifera under drought treatments. A total of 20,674 differentially expressed genes (DEGs) were identified under drought stress, with the number of DEGs increasing with the duration of drought. Specifically, 11,793 and 18,046 DEGs were detected after 8 and 15 days of drought treatment, respectively, including numerous upregulated and downregulated genes. Gene Ontology (GO) enrichment analysis showed that the DEGs were primarily involved in various biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that carbon metabolism, glyoxylate and dicarboxylate metabolism, proteasome, glycine, serine, and threonine metabolism were the main affected pathways. Among the DEGs, 376 protein kinases, 42 proteases, 168 transcription factor (TF) genes, and 152 other potential functional genes were identified, which may play significant roles in the drought response of C. oleifera. The expression of relevant functional genes was further validated using quantitative real-time PCR (qRT-PCR). These findings contribute to the comprehension of drought tolerance mechanisms in C. oleifera and bolster the identification of drought-resistant genes for molecular breeding purposes. Full article
(This article belongs to the Special Issue Plant Functional Genomics and Breeding)
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