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5Gs in Crop Genetic and Genomic Improvement: 2nd Edition
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5Gs in Crop Genetic and Genomic Improvement: 2nd Edition

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

Deadline for manuscript submissions: 25 July 2025 | Viewed by 10289

Special Issue Editor

Dr. Xinjie Shen

E-Mail Website
Guest Editor
Department of Horticulture, College of Agriculture, Guizhou University, Guiyang 550001, China
Interests: crop breeding; fruit development biology; plant flavonoid biosynthesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Global warming will lead to extreme weather, including floods, droughts, cold damage, high temperature 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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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

  • 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 (10 papers)

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Research

18 pages, 10821 KiB  
Article
Combined Analysis of Transcriptomes and Metabolomes Reveals That MeJA-Mediated Flavonoid Biosynthesis Is Crucial for Pigment Deposition in Naturally Colored Green Cotton Fibers
by Shuangquan Xie, Kailu Chen, Rui Tang, Xuechi Li, Yuxin Wei, Yijie Cheng, Shouwu Tang, Wengang Chen, Quanliang Xie, Zhuang Meng, Asigul Ismayil, Xiang Jin, Fei Wang, Haifeng Liu and Hongbin Li
Genes 2025, 16(5), 599; https://doi.org/10.3390/genes16050599 (registering DOI) - 19 May 2025
Abstract
Background: Green cotton fibers (GCFs) are valued for their natural coloration and eco-friendly properties, but their pigmentation mechanisms remain unclear, limiting their wider application in the textile industry. This study aims to uncover the key regulatory genes and metabolic pathways involved in [...] Read more.
Background: Green cotton fibers (GCFs) are valued for their natural coloration and eco-friendly properties, but their pigmentation mechanisms remain unclear, limiting their wider application in the textile industry. This study aims to uncover the key regulatory genes and metabolic pathways involved in GCF coloration. Methods: We conducted transcriptome and metabolome profiling of green and white cotton fibers at different developmental stages to identify differences in gene expression and metabolite accumulation related to pigmentation. Results: Transcript analysis revealed significant enrichment in α-linolenic acid metabolism, flavonoid biosynthesis and phenylpropane metabolism pathways during late pigmentation stages. Key genes in methyl jasmonate (MeJA) biosynthesis and flavonoid biosynthesis (LOX, JMT, ANS, C4H, DFR, F3H) were upregulated. The MYB transcription factor showed the most significant increase during fiber development. Metabolomic analysis identified 12 metabolites that accumulated specifically in green fibers. MeJA treatment promoted the expression of MYB genes and flavonoid biosynthesis genes (DFRs, ANSs, F3H, C4H), as well as the accumulation of Luteolin, Gallocatechin, Cyanidin and Chrysanthemum metabolites. Conclusions: Our study demonstrates that MeJA-mediated flavonoid biosynthesis, regulated by MYB transcription factors, is the central pathway controlling pigment deposition in GCFs. These findings provide valuable insights for developing improved colored cotton materials. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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18 pages, 9166 KiB  
Article
Analysis of Multi-Target Synergistic Mechanism of Coix Seed Therapy for Herpes Zoster Based on Machine Learning and Network Pharmacology
by Zhiqin Song, Lin Yang, Jing He, Yuchao Li, Ningxian Yang, Min Yang and Mingkai Wu
Genes 2025, 16(5), 580; https://doi.org/10.3390/genes16050580 - 14 May 2025
Viewed by 145
Abstract
Objective: To explore the efficacy and mechanism of Coix seeds in treating herpes zoster (HZ) using an integrated computational approach. Methods: Network pharmacology, molecular docking, and machine learning were employed. Disease-related targets were collected from multiple databases, and intersection targets with Coix seed [...] Read more.
Objective: To explore the efficacy and mechanism of Coix seeds in treating herpes zoster (HZ) using an integrated computational approach. Methods: Network pharmacology, molecular docking, and machine learning were employed. Disease-related targets were collected from multiple databases, and intersection targets with Coix seed were analyzed via PPI, GO, and KEGG enrichment. A “TCM-Ingredient-Target” network was constructed using Cytoscape. Molecular docking and dynamics simulations were performed for validation. Results: Fifty-five overlapping targets were identified, with core targets including TNF, EGF, and GAPDH. Enrichment analysis revealed key pathways such as inflammation and immune regulation. Molecular docking confirmed strong binding affinity between active compounds and targets. Conclusions: This study demonstrates that Coix seed exerts anti-HZ effects through multi-target mechanisms, providing a theoretical basis for developing novel multi-pathway treatment strategies. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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22 pages, 12266 KiB  
Article
Physiological and Transcriptomic Analyses Unveil the Preservation Mechanism of Streptomyces albulus Ah11601 Fermentation Broth on ‘Shine Muscat’ Grapes
by Chao-Tian Lv, Huan Li and Ri-Mao Hua
Genes 2025, 16(4), 468; https://doi.org/10.3390/genes16040468 - 19 Apr 2025
Viewed by 349
Abstract
Background/Objectives: Grapes (Vitis vinifera), particularly ‘Shine Muscat’, are prone to postharvest quality loss mainly due to poor storage tolerance. Actinomycetes are microbial resources that produce secondary metabolites that exhibit notable functional properties. Methods: This study explored the use of Streptomyces albulus [...] Read more.
Background/Objectives: Grapes (Vitis vinifera), particularly ‘Shine Muscat’, are prone to postharvest quality loss mainly due to poor storage tolerance. Actinomycetes are microbial resources that produce secondary metabolites that exhibit notable functional properties. Methods: This study explored the use of Streptomyces albulus Ah11601 fermentation broth (SFB) as a postharvest treatment to preserve ‘Shine Muscat’ grape quality during 6 days of room temperature storage using physiological, transcriptomic, and bioinformatics analyses to elucidate the underlying regulatory mechanism. Results: The results demonstrated that, compared to the control group stored at room temperature (25 °C) for 6 days (6D), the SFB-treated group (T6D) presented a significant delay in the decrease in fruit hardness and vitamin C content. Further investigations revealed that the 6D treatment significantly elevated lipoxygenase activity, MDA content, O2− generation rate, and H2O2 levels. In addition, both the 6D and T6D treatments significantly increased the activities of SOD and APX. Functional enrichment analysis revealed that the upregulated DEGs in the 6D group were predominantly enriched in pathways such as phenylpropanoid biosynthesis; flavonoid biosynthesis; phenylalanine metabolism; and stilbenoid, diarylheptanoid, and gingerol biosynthesis. The downregulated DEGs were enriched primarily in the endoplasmic reticulum protein processing pathway. In the T6D group, the upregulated DEGs were predominantly enriched in the zeatin biosynthesis pathway. In addition, significant alterations in the expression of genes associated with the ethylene and abscisic acid signaling pathways were detected. Conclusions: In conclusion, SFB treatment effectively mitigated the deterioration of the postharvest quality of ‘Shine Muscat’ grapes by preserving the cellular redox balance, regulating cytokinin and ethylene biosynthesis, and optimizing the regulation of ethylene and abscisic acid signaling. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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15 pages, 6261 KiB  
Article
Metabolomics and WGCNA Analyses Reveal the Underlying Mechanisms of Resistance to Botrytis cinerea in Hazelnut
by Jun Sun, Liyuan Lu, Juanjuan Liu, Yanhong Cui, Hanqi Liu, Yue Zhang, Zeyang Zheng and Weicong Yang
Genes 2025, 16(1), 2; https://doi.org/10.3390/genes16010002 - 24 Dec 2024
Viewed by 880
Abstract
Background: Hazelnut (Corylus), a significant woody oil tree species in economic forests, faces production constraints due to biotic stresses, with Hazelnut Husk Brown Rot, caused by the pathogenic necrotrophic fungus Botrytis cinerea (B. cinerea), being the most severe. To [...] Read more.
Background: Hazelnut (Corylus), a significant woody oil tree species in economic forests, faces production constraints due to biotic stresses, with Hazelnut Husk Brown Rot, caused by the pathogenic necrotrophic fungus Botrytis cinerea (B. cinerea), being the most severe. To date, limited information is available regarding the resistance of hazelnuts to B. cinerea. To better understand the mechanisms of resistance to B. cinerea. in hazelnut, we conducted metabolomics and WGCNA analyses of a B. cinerea-resistant Ping’ou hybrid hazelnut variety (Dawei; DW) and a susceptible variety (Qiuxiang; QX). Methods: In this study, metabolomics and weighted gene co-expression network analysis (WGCNA, weighted correlation network analysis) were applied to elucidate the resistance mechanisms underlying different hazelnut varieties to B. cinerea. Our study focused on the metabolome profiles of DW and QX plants after 72 h of B. cinerea infection. Results: Venn analysis of QX_0 vs. DW_0 and QX_72 vs. DW_72 revealed 120 differential accumulation metabolites (DAMs) that were upregulated. Among these metabolites, the concentrations of flavonoids and phenolic acids in DW were significantly higher than those in QX, respectively, suggesting that the elevated levels of these compounds contribute substantially to the resistance of hazelnut against B. cinerea. 3,4-hydroxyphenyllactic acid and phloretin were significantly more abundant in accumulation in DW than in QX after infection by B. cinerea. Conclusions: This study provides that the elevated levels of these compounds (flavonoids and phenolic acids) contribute substantially to the resistance of hazelnut against B. cinerea. Furthermore, 3,4-hydroxyphenyllactic acid and phloretin were identified as pivotal metabolites in modulating the resistance of hazelnut to B. cinerea. Through WGCNA analyses, we identified four transcription factors (WRKY19, HSFC1, ERF071, and RAP2-1) that are most likely to regulate the synthesis of 3,4-dihydroxyphenyllactic acid and phloretin. This study provides crucial insights for further investigation into the regulatory network of metabolites associated with hazelnut resistance to B. cinerea. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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15 pages, 3556 KiB  
Article
The Characteristics and Expression Analysis of the Tomato KWL Gene Family Under Biotic Stress
by Mei Su, Xuejuan Ru, Yang Chen, Hongjuan Wang, Jia Luo and Hong Wu
Genes 2024, 15(12), 1555; https://doi.org/10.3390/genes15121555 - 29 Nov 2024
Viewed by 972
Abstract
Background: Tomatoes are renowned for their popularity and nutritional value across the globe, yet their production and quality face significant challenges from various biotic stresses in their growing environments. Kiwellin (KWL) has been implicated in plant disease resistance. However, our comprehension of this [...] Read more.
Background: Tomatoes are renowned for their popularity and nutritional value across the globe, yet their production and quality face significant challenges from various biotic stresses in their growing environments. Kiwellin (KWL) has been implicated in plant disease resistance. However, our comprehension of this gene family in plants is still remarkably insufficient. Methods: We conducted a comprehensive genomic analysis of the KWL gene family in tomatoes. The tertiary structures of SlKWLs were predicted by AlphaFold2. EMBOSS was used for codon analysis. RNA-seq and RT-qPCR analysis were performed to explore the expression profile of SlKWLs. Results: Our findings identified 12 distinct SlKWL members distributed across four chromosomes within the tomato genome. By examining their gene structure, conserved motifs, functional domains, and phylogenetic relationships, we elucidated the complex evolutionary relationships and potential functions of these genes. Notably, we identified numerous cis-regulatory elements within the promoter regions of the SlKWL genes which are associated with responses to both abiotic and biotic stresses, as well as hormone signaling pathways. This finding strongly implies that SlKWLs are integral to plant growth and adaptation to diverse stress conditions. Furthermore, RNA-seq and RT-qPCR analysis revealed an upregulation of five SlKWLs expressed subsequent to Phytophthora infestans infection. Particularly, SlKWL2 and SlKWL3 exhibited substantially elevated expression levels, underscoring their active involvement in biotic stress responses. Conclusions: Collectively, these findings advance our comprehension of the SlKWL gene family and provide a robust foundation for future investigations into the roles of SlKWL genes in tomato stress responses. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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15 pages, 4589 KiB  
Article
Unraveling the Anthocyanin Regulatory Mechanisms of White Mutation in Verbena stricta by Integrative Transcriptome and Metabolome Analysis
by Shengyue Chai, Jiaming Yang, Xiaofei Zhang, Xuwen Shang and Lixin Lang
Genes 2024, 15(12), 1496; https://doi.org/10.3390/genes15121496 - 21 Nov 2024
Viewed by 783
Abstract
Background: Verbena stricta is a perennial herb of the Verbenaceae family, known for its medicinal properties, wide adaptability, and high resistance. Methods: This research investigated the metabolic pathways of flower color change by combining transcriptome and metabolomics analyses. Results: In [...] Read more.
Background: Verbena stricta is a perennial herb of the Verbenaceae family, known for its medicinal properties, wide adaptability, and high resistance. Methods: This research investigated the metabolic pathways of flower color change by combining transcriptome and metabolomics analyses. Results: In purple flowers and white variants, a total of 118 differentially accumulated metabolites (DAMs), including 20 anthocyanins, and 7627 differentially expressed genes (DEGs) were found. The downregulation of delphinidin-3-O-galactoside, delphinidin-3-O-glucoside, and delphinidin-3-O-(6″-O-p-coumaroyl) glucoside, along with the absence of petunidin and malvidin derivatives, may explain the loss of pigmentation in the white-flower mutant. Fourteen candidate genes involved in anthocyanin biosynthesis were identified, among which the expression of Flavonoid 3′, 5′-hydroxylase (F3′5′H) was significantly downregulated, notably limiting flux through the delphinidin pathway and reducing delphinidin accumulation. This limitation in upstream reactions, coupled with the multi-shunt process in downstream reactions, completely blocked the production of petunidin and malvidin. Conclusions: These findings offer new opinions on the anthocyanin metabolites and key genes responsible for the floral pigmentation in V. stricta. Additionally, the white variant provides a valuable platform for future research into the ornamental flower color of the Verbenaceae family. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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11 pages, 4786 KiB  
Article
Effect of Supplemental Light for Leaves Development and Seed Oil Content in Brassica napus
by Xingying Yan, Wenqin Bai and Taocui Huang
Genes 2024, 15(11), 1371; https://doi.org/10.3390/genes15111371 - 24 Oct 2024
Viewed by 1162
Abstract
Rapeseed is an important commercial crop globally, used for both animal fodder and human consumption. Varied insolation duration and intensity are among the main factors affecting the seed yield and quality of Brassica napus (B. napus) worldwide. In this study, the [...] Read more.
Rapeseed is an important commercial crop globally, used for both animal fodder and human consumption. Varied insolation duration and intensity are among the main factors affecting the seed yield and quality of Brassica napus (B. napus) worldwide. In this study, the high-oil-content rapeseed cultivar “Qingyou 3” was subjected to a light supplementation trial during both the vegetative growth period and the seed productive stage. Different light intensity conditions were stimulated using light-emitting diodes (LEDs). The main plot factor was land condition, with LED treatment (Treatment) and without LED treatment (Control) under natural conditions. The results showed that the leaf size and thickness, photosynthesis efficiency, and seed oil content of B. napus increased significantly after light supplementation. Then, 18 cDNA libraries were constructed from leaf segments (30 days after transplanting—DAT) and seeds 30 and 40 days after pollination (DPA) for RNA transcriptome sequencing. It was found that genes encoding lipid transfer protein, phenylpropanoid biosynthesis, photosynthesis, and plant hormone signal transduction were enriched in differentially expressed genes (DEGs). The qRT-PCR analysis showed that eight key genes had significant variations, a finding also consistent with the RNA-seq results. The aim of this study was to identify the DEGs and signaling pathways in the leaves and seeds of B. napus during the vegetative and seed productive stages under different light intensities. The results provide insight into how sufficient light plays a critical role in promoting photosynthesis and serves as the foundation for material accumulation and yield formation. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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18 pages, 8420 KiB  
Article
Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses
by Hao-Zhi Zheng, Wei Dai, Meng-Han Xu, Yu-Ye Lin, Xing-Li Zhu, Hui Long, Li-Li Tong and Xiao-Gang Xu
Genes 2024, 15(7), 940; https://doi.org/10.3390/genes15070940 - 18 Jul 2024
Cited by 4 | Viewed by 1181
Abstract
Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. [...] Read more.
Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914–157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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26 pages, 4586 KiB  
Article
Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl
by Xinchun Mo, Ling Wang, Chenghua Yu and Can Kou
Genes 2024, 15(7), 828; https://doi.org/10.3390/genes15070828 - 22 Jun 2024
Cited by 1 | Viewed by 1680
Abstract
Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of [...] Read more.
Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of Polygonatum kingianum Coll.et Hemsl. were studied to explore the secondary metabolite expression and flavonoid biosynthesis mechanisms using transcriptomics and metabolomics. Metabolic analysis identified that the differentially accumulated metabolites (DAMs) in the fibrous root and taproot were predominantly flavonoids, steroids, alkaloids, and phenolic acids. Overall, 200 flavonoids were identified in P. kingianum Coll.et Hemsl., with 170 exhibiting variances between the fibrous root and taproot. The transcriptome analysis revealed that a total of 289 unigenes encoding 32 enzymes were annotated into four flavonoid biosynthesis pathways, which include phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, isoflavonoid biosynthesis pathway, and flavone and flavonol biosynthesis pathway. The integration of transcriptomic and metabolomic data elucidated that the 76 differentially expressed genes (DEGs) encoding 13 enzyme genes (HCT, CCOMT, C4H, C3′H, CHI, PGT1, FLS, F3′H, CHS, ANR, DFR, F3′5′H, and LAR) and 15 DAMs preferred to be regulated in the flavonoid biosynthesis pathway. The expression of 10 DEGs was validated by qRT-PCR, agreeing with the same results by RNA-Seq. These findings shed light into the biosynthesis of secondary metabolites in P. kingianum Coll.et Hemsl., offering valuable information for the sustainable utilization and enhancement of this plant species. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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17 pages, 4282 KiB  
Article
Soil Microbial Community Characteristics and Their Effect on Tea Quality under Different Fertilization Treatments in Two Tea Plantations
by Yu Lei, Ding Ding, Jihua Duan, Yi Luo, Feiyi Huang, Yankai Kang, Yingyu Chen and Saijun Li
Genes 2024, 15(5), 610; https://doi.org/10.3390/genes15050610 - 11 May 2024
Cited by 4 | Viewed by 2203
Abstract
Fertilization is an essential aspect of tea plantation management that supports a sustainable tea production and drastically influences soil microbial communities. However, few research studies have focused on the differences of microbial communities and the variation in tea quality in response to different [...] Read more.
Fertilization is an essential aspect of tea plantation management that supports a sustainable tea production and drastically influences soil microbial communities. However, few research studies have focused on the differences of microbial communities and the variation in tea quality in response to different fertilization treatments. In this work, the soil fertility, tea quality, and soil microbial communities were investigated in two domestic tea plantations following the application of chemical and organic fertilizers. We determined the content of mineral elements in the soil, including nitrogen, phosphorus, and potassium, and found that the supplementation of chemical fertilizer directly increased the content of mineral elements. However, the application of organic fertilizer significantly improved the accumulation of tea polyphenols and reduced the content of caffeine. Furthermore, amplicon sequencing results showed that the different ways of applying fertilizer have limited effect on the alpha diversity of the microbial community in the soil while the beta diversity was remarkably influenced. This work also suggests that the bacterial community structure and abundance were also relatively constant while the fungal community structure and abundance were dramatically influenced; for example, Chaetomiaceae at the family level, Hypocreaceae at the order level, Trichoderma at the genus level, and Fusarium oxysporum at the species level were predominantly enriched in the tea plantation applying organic fertilizer. Moreover, the bacterial and fungal biomarkers were also analyzed and it was found that Proteobacteria and Gammaproteobacteria (bacteria) and Tremellomycetes (fungi) were potentially characterized as biomarkers in the plantation under organic fertilization. These results provide a valuable basis for the application of organic fertilizer to improve the soil of tea plantations in the future. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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