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5Gs in Crop Genetic and Genomic Improvement: 2025–2026

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

Deadline for manuscript submissions: 20 July 2026 | Viewed by 6486

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Dr. Xinjie Shen

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Department of Horticulture, College of Agriculture, Guizhou University, Guiyang 550001, China
Interests: crop breeding; fruit development biology; plant flavonoid biosynthesis
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Dear Colleagues,

Global warming will lead to extreme weather, including floods, droughts, cold damage, high temperatures, and other disasters. Crop yields and quality will suffer greatly from these extreme weather events. In facing these threats, traditional breeding systems cannot create sufficient crop improvement to meet demands. So far, genetic and genomic research have entered 5G stages (1G: genome sequencing and assembly; 2G: germplasm characterized at genomic and agronomic levels; 3G: gene function analysis; 4G: genomic breeding strategies; 5G: gene editing technology). The recent advances in 5G, including crop sequencing, phenomics and multiple omics analysis, have greatly promoted crop breeding.

This Special Issue focuses on the 5G in crop genetic and genomic improvement including but not limited to crop gene functional analysis, crop proteome and metabolism research, crop GWAS analysis and epigenetics regulation in crop breeding. We welcome the submission of reviews and research articles. We especially encourage the submission of original papers that use gene editing technology for crop breeding.

Dr. Xinjie Shen
Guest Editor

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Keywords

crop gene functional analysis
crop protemics
crop metabonomics
new crop breeding methods
crop GWAS analysis
crop gene edit technology
crop gene epigenetic modification

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Published Papers (9 papers)

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Research

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14 pages, 2175 KB

Open AccessArticle

Genetic Characterization and Population Structure of Mozambique’s Sesame (Sesamum indicum L.) Accessions Using DArTseq-Derived SNP Markers

by Winfred Nthamo Muteti, Rogerio Marcos Chiulele and Wilfred Abincha

Genes 2026, 17(5), 528; https://doi.org/10.3390/genes17050528 - 29 Apr 2026

Viewed by 217

Abstract

Background/Objective: Sesame (Sesamum indicum L.) is a nutritionally and economically important oilseed crop that is grown predominantly by smallholder farmers in Mozambique. However, its breeding process is constrained by a limited understanding of the genetic diversity in sesame germplasm. Therefore, this study determined the genetic diversity and population structure of a panel of 109 sesame accessions from Instituto de Investigação Agrária de Mocambique (IIAM) using DArTseq SNPs. Methods: The generated 14,763 SNPs were filtered, retaining 11,502 high-quality SNPs for this study. Results: Overall genetic diversity was moderate (mean He = 0.30, Ho = 0.30, MAF = 0.21, PIC = 0.25). Population structure analysis using sparse non-negative matrix factorization identified eight subpopulations, consistent with principal component analysis implemented via the Latent factor mixed model. Discriminant analysis of principal components (DAPC) and Ward’s hierarchical clustering based on Nei’s distance resolved the same eight clusters, although DAPC revealed overlap among clusters, consistent with extensive admixture. Analysis of molecular variance showed that 85.85% of total molecular variation was within subpopulations and 14.15% among the subpopulations. Pairwise fixation indices (ranging from 0.02 to 0.10) identified divergent subpopulations 7 and 1 as suitable candidates for hybridization. Within subpopulations, observed heterozygosity exceeded expected heterozygosity, likely reflecting residual heterozygosity in sesame landraces, admixture, reverse Wahlund effect and scoring of paralogs as heterozygous SNPs. Conclusions: Overall, this study provided insights into sesame’s genetic diversity in Mozambique, contributing to germplasm conservation and informed parental selection. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

16 pages, 7290 KB

Open AccessArticle

Heterologous Overexpression of NtNACa from Narcissus tazetta L. var. chinensis ‘Yunxiang’ Enhances Drought and Salt Stress Resistance in Arabidopsis thaliana

by Peng-Fei Li, Yong Wu, Xiang-Yun Rui, Xiao-Jing Chen, Ming-Yue Wei and Huan Li

Genes 2026, 17(3), 316; https://doi.org/10.3390/genes17030316 - 13 Mar 2026

Viewed by 438

Abstract

Background/Objectives: NAC transcription factors are key regulators of stress responses, yet their roles in Narcissus tazetta L. var. chinensis remain uncharacterized. This study aimed to isolate and functionally analyze NtNACa, a NAC gene from the ‘Yunxiang’ narcissus variety, to evaluate its potential in enhancing abiotic stress tolerance. Methods: NtNACa was cloned and its expression pattern under heat, salt, and ABA treatments was assessed via qRT-PCR. Subcellular localization was determined using GFP fusion in tobacco. NtNACa was overexpressed in Arabidopsis thaliana through floral dip transformation, and transgenic lines were subjected to NaCl, ABA, and drought stress assays. Results: The results showed that NtNACa has high homology with monocot NAC family members and possesses typical NAC transcription factor features. Further analyses revealed that NtNACa localizes to the nucleus, and tissue-specific expression analysis indicated that it is highly expressed in leaves, followed by roots and bulbs. The transcriptional expression of NtNACa is differentially regulated in response to 100 mM NaCl, 100 μM ABA, and 50 °C temperature stress. Overexpression of NtNACa in A. thaliana produced transgenic lines with significantly higher germination rates under ABA and NaCl treatments. Soil-grown transgenic A. thaliana plants overexpressing NtNACa showed markedly increased drought stress. Moreover, NtNACa confers drought resilience by coordinately suppressing oxidative damage (via reduced O₂⁻· production rate and MDA accumulation and elevated AtCAT2 expression), enhancing osmotic adjustment (through AtP5CR-mediated proline biosynthesis), and activating core stress-signaling components such as AtRD29A and AtSnRK2.4. Conclusions: Taken together, these results indicate that heterologous overexpression of NtNACa from ‘Yunxiang’ (N. tazetta) confers enhanced drought and salt tolerance in A. thaliana. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

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17 pages, 4259 KB

Open AccessArticle

Condition-Specific Transcriptional and Metabolic Divergence in the Dual-Fungal Symbiosis of JinEr Mushroom Under Postharvest Low-Temperature Stress

by Yuntao Li, Hao Tang, Fuwei Wang, Chaotian Lv, Bin Zhang and Huan Li

Genes 2026, 17(3), 296; https://doi.org/10.3390/genes17030296 - 28 Feb 2026

Viewed by 515

Abstract

Background: The JinEr mushroom results from the heterogeneous symbiosis of Naematelia aurantialba and Stereum hirsutum, with low-temperature storage being key for postharvest quality preservation. However, the species-specific low-temperature response patterns remain unclear. Methods: An integrated approach combining metabolomics, transcriptomics (dual-genome alignment), and spatially resolved enzyme assays was used to dissect responses at 0 °C and 4 °C. Results: The two fungi displayed distinct stress response tendencies under the studied conditions. N. aurantialba showed enhanced stress defense (DNA repair, antioxidant pathways) with defense-related enzyme activities concentrated in its apical/middle enrichment regions. S. hirsutum was observed to maintain overall metabolic activity at the pathway level, and its metabolic enzyme activities were predominant in the basal region. The symbiotic system exhibited temperature-dependent plasticity stress responses. Storage at 0 °C induced a survival-oriented response with slower crude polysaccharide degradation. In contrast, storage at 4 °C supported active metabolic defense coordination but more pronounced polysaccharide loss. Conclusions: These observed defense- and metabolism-biased differential responses suggest a cold stress-specific coordination working model within the symbiotic system under postharvest cold stress. A temperature of 0 °C is more suitable for enabling JinEr mushroom postharvest storage to retain polysaccharides. This study advances our understanding of heterogeneous symbiotic fungi’s postharvest biology and provides a temperature-targeted theoretical basis for storage optimization. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

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16 pages, 1565 KB

Open AccessArticle

Genetic and Phenotypic Characterization of a Novel dull1 Allele Affecting Starch Accumulation in Maize

by Mingmin Zheng, Xiaowei Liu, Ziwen Shi, Xin Yuan, Yujiao Gao, Xian Zhao and Qiang Huang

Genes 2026, 17(2), 250; https://doi.org/10.3390/genes17020250 - 23 Feb 2026

Viewed by 450

Abstract

Background: Starch accumulation contributes substantially to maize grain yield and quality. Starch synthase III (SSIII) is a key component of the starch biosynthetic enzyme complex. However, its regulatory role in starch accumulation in maize endosperm remains incompletely understood. Methods: The du1-2018 mutant arose spontaneously during a conventional maize breeding program. Phenotypic characterization, storage compound contents, and starch structure were compared between the mutant and wild-type lines. BSA-seq, genetic linkage analysis, and transcriptomic analysis were employed to identify the candidate gene responsible for the mutant phenotype. Transcriptome sequencing was performed on developing kernels to evaluate the genome-wide effects of the du1-2018 mutation. Results: The du1-2018 mutant exhibited dull, glassy, and mildly shrunken kernels, with decreased starch levels and elevated soluble sugar and protein contents. The du1-2018 mutation disrupted starch accumulation, resulting in smaller, irregularly shaped starch granules and significant changes in starch composition and fine structure. This mutation was identified as a severe loss-of-function allele of the dull1 (du1) gene, evidenced by almost undetectable Du1 transcripts in developing kernels. Notably, transcriptomic analysis revealed that a substantial proportion of differentially expressed genes (DEGs) were involved in amino acid and protein metabolism. Conclusions: The novel du1 allelic variant, du1-2018, disrupts starch biosynthesis in maize endosperm, leading to reduced starch accumulation, altered starch structure, and transcriptional changes in nitrogen-related metabolic pathways. Our results provide new insights into the regulatory mechanisms underlying SSIII function in starch synthesis and endosperm development, and suggest potential links to carbon/nitrogen balance, with implications for future genetic improvement of maize grain quality. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

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31 pages, 25746 KB

Open AccessArticle

Integrated Physiological and Multi-Omics Analyses Reveal the Coordinated Regulation of Carbon and Nitrogen Metabolism in Rapeseed (Brassica napus L.) Tolerance to Saline-Alkaline Stress

by Li He, Weichao Wang, Chenhao Zhang and Fenghua Zhang

Genes 2026, 17(2), 147; https://doi.org/10.3390/genes17020147 - 28 Jan 2026

Viewed by 533

Abstract

Background/Objectives: Soil salinization and alkalization critically limit global agricultural production. This study aimed to investigate the differential response mechanisms of rapeseed (Brassica napus L.) varieties to saline and alkaline stresses at the seedling stage. Methods: Seedlings of a salt-tolerant variety, Huayouza 62 (H62), and a non-salt-tolerant variety, Xiangyou 15 (X15), were exposed to saline (NaCl:Na₂SO₄ = 1:1) and alkaline (Na₂CO₃:NaHCO₃ = 1:1) stresses. An integrated analysis combining physiology, biochemistry, transcriptomics, and metabolomics was conducted to systematically elucidate their differential stress responses. Results: (1) H62 maintained favorable photosynthetic and carbon–nitrogen homeostasis. Notably, under saline and alkaline stresses, the activity of glutamate dehydrogenase (GDH) in H62 showed a significant increasing trend, whereas it was inhibited in X15. (2) Alkaline stress triggered more differential genes than saline stress, with H62 exhibiting broader transcriptional up-regulation in carbon–nitrogen metabolism. (3) Metabolomic profiling showed that H62 accumulated more beneficial metabolites than X15 under both stresses, such as phenolic acids, amino acids, and their derivatives. (4) In multi-omics analysis, key genes in starch–sucrose and amino acid metabolism in H62 were up-regulated to accumulate osmolytes, enabling an efficient defense network. However, X15’s responses were disordered. Conclusions: H62 leverages robust transcriptional reprogramming to coordinate carbon–nitrogen metabolism, constituting a multidimensional defense network. This study provides potential physiological indicators, candidate genes, and metabolite markers associated with short-term saline–alkaline stress responses, laying a foundation for further exploration of stress response mechanisms. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

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21 pages, 3116 KB

Open AccessArticle

Integrated Transcriptomic and Metabolomic Analysis Reveals Metabolic Heterosis in Hybrid Tea Plants (Camellia sinensis)

by Yu Lei, Jihua Duan, Feiyi Huang, Ding Ding, Yankai Kang, Yi Luo, Yingyu Chen, Nianci Xie and Saijun Li

Genes 2025, 16(12), 1457; https://doi.org/10.3390/genes16121457 - 5 Dec 2025

Viewed by 808

Abstract

Background: Heterosis (hybrid vigor) is a fundamental phenomenon in plant breeding, but its molecular basis remains poorly understood in perennial crops such as tea (Camellia sinensis). This study aimed to elucidate the molecular mechanisms underlying heterosis in tea and its hybrids by performing integrated transcriptomic and metabolomic analyses of F₁ hybrids derived from two elite cultivars, Fuding Dabaicha (FD) and Baojing Huangjincha 1 (HJC). Methods: Comprehensive RNA sequencing and widely targeted metabolomic profiling were conducted on the parental lines and F₁ hybrids at the one-bud-one-leaf stage. Primary metabolites (including amino acids, nucleotides, saccharides, and fatty acids) were quantified, and gene expression profiles were obtained. Transcriptomic and metabolomic datasets were integrated using KEGG pathway enrichment and co-expression network analysis to identify coordinated molecular changes underlying heterosis. Results: Metabolomic profiling detected 977 primary metabolites, many of which displayed non-additive accumulation patterns. Notably, linoleic acid derivatives (9(S)-HODE, 13(S)-HODE) and nucleotides (guanosine, uridine) exhibited significant positive mid-parent heterosis. Transcriptomic analysis revealed extensive non-additive gene expression in F₁ hybrids, and upregulated genes were enriched in fatty acid metabolism, nucleotide biosynthesis, and stress signaling pathways. Integrated analysis demonstrated strong coordination between differential gene expression and metabolite accumulation, especially in linoleic acid metabolism, cutin/suberine biosynthesis, and pyrimidine metabolism. Positive correlations between elevated fatty acid levels and transcript abundance of lipid metabolism genes suggest that the transcriptional remodeling of lipid pathways contributes to heterosis. Conclusions: These findings provide novel insights into tea plant heterosis and identify potential molecular targets for breeding high-quality cultivars. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

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18 pages, 3198 KB

Open AccessArticle

Chloroplast Genome Features and Phylogeny of Two Nationally Protected Medicinal Plants, Euchresta tubulosa and Euchresta japonica: Molecular Resources for Identification and Conservation

by Dabao Yin, Xue Li, Zhongchun Xiao and Li Zhou

Genes 2025, 16(11), 1286; https://doi.org/10.3390/genes16111286 - 29 Oct 2025

Viewed by 1047

Abstract

[Objectives]: By performing genome assembly, annotation, comparative characterization, and phylogenetic analysis on the complete chloroplast genomes of E. tubulosa and E. japonica—two medicinal plants belonging to the genus Euchresta—this study aims to identify their differential genes, thereby providing fundamental research for screening candidate genes as DNA barcodes for species identification and facilitating the conservation of these endangered species. [Methods]: Illumina PE150 sequencing was performed. Chloroplast genomes (plastomes) were assembled and annotated with GetOrganelle/SPAdes. Comparative analyses assessed gene content, IR/LSC/SSC structure, repeat profiles, and codon-usage bias. Using related Fabaceae as references, we conducted mVISTA alignments and sliding-window nucleotide diversity (Pi) analyses to identify candidate DNA barcodes. Phylogenies from whole-plastome sequences were inferred with Maximum Likelihood, Bayesian Inference, and Maximum Parsimony. [Results]: The plastomes measured 153,960 bp (E. japonica) and 150,146 bp (E. tubulosa), with GC contents of 36.30% and 36.20%, respectively, each exhibiting a typical quadripartite structure. IR/SC boundaries were highly conserved without evident expansion or contraction. Repeat statistics were 20/30 palindromic repeats, 57/64 tandem repeats, and 156/159 simple sequence repeats (SSRs) in E. japonica/E. tubulosa, respectively. Leucine was the most frequently encoded amino acid, cysteine the least, and codon usage favored A/U at third positions. Five hypervariable loci—rps19, psbA, trnK, matK, and rps16 (Pi > 0.03)—were identified as candidate DNA barcodes. All trees consistently placed both species within Papilionoideae (Fabaceae) and recovered the closest relationship to Sophora macrocarpa. [Conclusions]: This study provides, for the first time, complete plastomes and candidate barcoding regions for two protected Euchresta species, supplying foundational resources for species identification, resource assessment, and conservation planning. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

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14 pages, 3627 KB

Open AccessArticle

Comparative Analysis of Chloroplast Genome Sequences and Phylogeny in Three Macadamia integrifolia Cultivars

by Jihua Guo, Zhuanmiao Kang, Zhongchun Xiao, Chunyan Zhong, Guidong Miao, Pei Zhang, Weiwei Zhao, Rongrong Su and Kecan Xia

Genes 2025, 16(11), 1248; https://doi.org/10.3390/genes16111248 - 22 Oct 2025

Cited by 2 | Viewed by 968

Abstract

Background/Objectives: Macadamia integrifolia is a valuable subtropical fruit tree, yet genomic studies on its cultivars are limited. This study aims to elucidate the chloroplast genome features, variations, and phylogenetic relationships of three main cultivars (‘Guilin No. 1’, ‘Nanya No. 1’, ‘Qian’ao No. 1’) to support germplasm identification and breeding. Methods: chloroplast genomes of three M. integrifolia cultivars from Guangxi, Guangdong, and Guizhou were sequenced using Illumina technology, followed by assembly, annotation, and comparative analyses of structure, repeats, and codon usage. Phylogenetic relationships were reconstructed using complete genome sequences. Results: The three chloroplast genomes displayed typical quadripartite structures, with lengths of 159,714 bp, 159,195 bp, and 159,508 bp, and GC contents of 38.12%, 38.16%, and 38.14%, respectively. Each encoded 135 genes. Codon usage was biased towards A/U-ending codons. We identified 81, 87, and 80 SSRs and 26, 21, and 20 long repeats, respectively. IR boundary regions were highly conserved. Phylogenetically, the cultivars showed close relationships with M. integrifolia, Macadamia tetraphylla, and Macadamiaternifolia, forming a sister clade to Platanus occidentalis. Conclusions: This study provides essential chloroplast genomic resources for three M. integrifolia cultivars, revealing conserved structures and specific variations. The findings offer crucial insights for the genus's genetic diversity, supporting future germplasm evaluation and phylogenetic research. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

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Review

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26 pages, 5140 KB

Open AccessReview

DNA Methylation Dynamics in Plant Abiotic Stress Response: Mechanisms, Memory, and Breeding Applications

by Huanqing Huang, Chenyu Guo, Shiping Cheng and Zhe Wang

Genes 2026, 17(3), 301; https://doi.org/10.3390/genes17030301 - 28 Feb 2026

Viewed by 725

Abstract

Abiotic stresses such as drought, salinity, extreme temperatures, and heavy metal contamination severely limit global crop productivity and threaten food security. Plants have evolved epigenetic strategies, particularly DNA methylation, to perceive, adapt to, and memorize environmental challenges. This review systematically elucidates the dynamic regulatory mechanisms of DNA methylation—including establishment via RNA-directed DNA methylation (RdDM), maintenance by methyltransferases (MET1, CMT), and active removal by demethylases (ROS1)—in plant responses to diverse abiotic stresses. We highlight how stress-induced methylation reprogramming modulates gene expression, chromatin states, and physiological adaptations, contributing to both somatic and transgenerational stress memory. Furthermore, we discuss advanced detection technologies for profiling methylation patterns and evaluate their applications in epigenetic breeding, such as exploiting heritable epialleles, RdDM-based gene silencing, and methylation markers for heterosis prediction. Despite significant progress, translating epigenetic insights into predictable breeding tools remains challenging. Future efforts should focus on establishing causal links between methylation changes and stress phenotypes, improving epigenome editing precision, and integrating multi-omics approaches for the development of climate-resilient crops. This work provides a comprehensive epigenetic perspective for enhancing crop adaptability and sustainable agriculture. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2025–2026)

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