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Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops

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A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 15 September 2026 | Viewed by 10053

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Special Issue Editors

Dr. Xing Huang

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Guest Editor

Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
Interests: plant development; plant biotechnology; plant; genetics

Dr. Qibin Wu

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Guest Editor

National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology/Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
Interests: sugarcane; sugarcane breeding; sugarcane smut

Special Issue Information

Dear Colleagues,

Tropical and subtropical climates cover over half of the world and create diverse plant species. Many of these have been planted for food supply and industrial applications, including rice, maize, rapeseed, cassava, sugarcane, rubber tree, banana, mango, coffee, pineapple, sisal, etc. However, global climate change has brought severe challenges for the plantation and production of tropical and subtropical crops. It is of great importance to explore adaptive traits in germplasms, with the aim of breeding excellent varieties for extreme weather. During the past decade, the research progress of tropical and subtropical crops has significantly accelerated, due to the rapid development of advanced technologies, such as omics and gene editing.

This Special Issue will focus on “Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops”. We welcome novel reviews, research, opinions, protocols, etc., covering all topics related to germplasm evaluation and conservation, including phenotyping, diversity, domestication, omics, in vitro propagation, and the physiological and biochemical characteristics of tropical and subtropical crops. In addition, the aim of this Special Issue is also to gather information concerning genetic improvement in relation to individual gene studies, cultivars exploited for commercial applications, breeding, and methods and applications of genetic transformation

Dr. Xing Huang
Dr. Qibin Wu
Guest Editors

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Keywords

tropical and subtropical crops
germplasm
genetic improvement
biotechnology
omics technology
adaptive traits
climate change

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Published Papers (8 papers)

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Research

25 pages, 4466 KB

Open AccessArticle

Integrated Multi-Omics Profiling Elucidates the Molecular Mechanisms of Salt Stress Adaptation in Tartary Buckwheat (Fagopyrum tataricum)

by Yi Yuan, Zilong Liu, Yunzhe He, Liming Men, Zhihui Chen, Guoqing Dong and Dengxiang Du

Agronomy 2026, 16(8), 771; https://doi.org/10.3390/agronomy16080771 - 8 Apr 2026

Viewed by 527

Abstract

Soil salinization is a major threat to global crop production. Tartary buckwheat (Fagopyrum tataricum), valued for its hardiness in marginal environments, provides an excellent system for studying plant salt tolerance. Using an integrated multi-omics approach, we deciphered the physiological, metabolic, and transcriptional responses of Tartary buckwheat to prolonged NaCl stress. Physiological profiling confirmed membrane damage alongside osmotic adjustment via proline accumulation and a phased antioxidant response. Metabolomics revealed extensive reprogramming, with dynamic enrichment in pathways of flavonoid biosynthesis, lipid metabolism, and the TCA cycle. Transcriptomics delineated a time-specific cascade from early signaling to late defense activation. Critical regulators within ABA and MAPK signaling pathways showed fine-tuned, divergent expression; for instance, SnRK2.3 was suppressed while specific PP2Cs were induced, and FtMAPK10 was dramatically up-regulated. Integrated analysis demonstrated coordinated induction of osmoprotectant synthesis (e.g., galactinol and betaine pathways) and a rewiring of central carbon metabolism. Our findings reveal a sophisticated, multi-layered adaptation strategy in Tartary buckwheat, integrating enhanced osmolyte production, antioxidant defense, membrane remodeling, and metabolic reprogramming, orchestrated by key signaling networks. This study provides a comprehensive molecular framework for salt tolerance and identifies valuable genetic targets for improving crop resilience. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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14 pages, 2116 KB

Open AccessArticle

Genetic Diversity and Population Structure of Platonia insignis Across Amazon–Cerrado Ecotones: Implications for Conservation and Germplasm Management of a Fruit Tree

by Thailson de Jesus Santos Silva, Gabriel Garcês Santos, Priscila Marlys Sá Rivas, Emily Gabrielle Cunha Mendes, Rômulo Nunes Sousa, Gabriel Campos Fernandes, Sérgio Heitor Sousa Felipe, Juliane Maciel Henschel, Thais Roseli Corrêa and José de Ribamar Silva Barros

Agronomy 2026, 16(6), 635; https://doi.org/10.3390/agronomy16060635 - 17 Mar 2026

Viewed by 539

Abstract

Platonia insignis Mart. (Clusiaceae) is a native fruit tree of great ecological and socioeconomic importance in the Brazilian Amazon and Cerrado. However, habitat loss is threatening its genetic variability. We investigated whether habitat fragmentation across the Amazon, Cerrado, and transition zones shapes the genetic diversity and population structure of five natural populations of P. insignis, using ISSR markers. Leaf samples from 13–15 individuals per population were collected, and DNA was extracted using the CTAB protocol. Twelve ISSR primers amplified 149 loci, used to estimate genetic parameters. AMOVA showed that 73.58% of genetic variation occurred within populations and 26.41% among populations (F_ST = 0.261). Amazonian populations exhibited the highest genetic diversity, while transition zone populations had the lowest values. The Cerrado population was genetically distinct and maintained moderate intrapopulation diversity. Bayesian clustering, PCoA, and UPGMA revealed three genetic groups corresponding to the sampled regions. Transitional populations showed high genetic admixture, indicating their role as potential corridors for gene flow. Our results highlight the need to preserve genetically diverse Amazonian populations, safeguard the Cerrado population as an evolutionarily significant unit, and maintain transitional populations to promote landscape connectivity. The study provides a genetic baseline to support conservation and management of P. insignis germplasm resources. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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32 pages, 5862 KB

Open AccessArticle

The Effects of Sugarcane Leaf Consumption by Chilo sacchariphagus (Lepidoptera, Crambidae) on Plant Defense Mechanisms: Transcriptomic and Metabolomic Analysis

by Yanqiong Liang, Chao Yan, Jiayu Han, Shibei Tan, Ying Lu, Bo Wang, Helong Chen, Chunping He, Xiaoli Hu, Weihuai Wu and Kexian Yi

Agronomy 2026, 16(5), 570; https://doi.org/10.3390/agronomy16050570 - 5 Mar 2026

Viewed by 528

Abstract

Sugarcane (Saccharum spp.) is a globally vital sugar crop, yet its productivity faces severe challenges from infestation by Chilo sacchariphagus. To decipher the plant’s molecular and metabolic defense mechanisms, this study applied an integrated transcriptomic and metabolomic analysis to three field-grown sugarcane cultivars (Zhongtang 4, 5, and 6) under natural borer stress. The transcriptomic analysis identified a total of 34,004 differentially expressed genes (DEGs), of which 18,674 were up-regulated, and 15,330 were down-regulated. The three cultivars exhibited distinct transcriptional regulatory patterns: Z4 and Z5 showed a global suppression-type response and a strong activation-type response, respectively, and Z6 presented a balanced-type response. A functional enrichment analysis revealed that the DEGs were significantly involved in metabolic processes, stress response, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interaction pathways. Metabolomic analysis detected 963 differentially accumulated metabolites (DAMs), primarily including flavonoids, phenolic acids, amino acids and their derivatives, and lipids. These metabolites were significantly enriched in pathways such as amino acid metabolism, biosynthesis of secondary metabolites, and glutathione metabolism. Integrated multi-omics analysis further revealed strong synergistic regulatory relationships between gene expression and metabolite accumulation, particularly in defense-related secondary metabolic pathways, such as phenylpropanoid and flavonoid biosynthesis. Several key regulatory hubs were identified, including novel transcripts and D-xylulose-5-phosphate. Sugarcane employs a genetic background-dependent, multi-layered transcriptional reprogramming and metabolic restructuring to cope with borer stress. Cultivars Z4 and Z6 tend to activate and accumulate defensive compounds, while Z5 exhibits a different pattern of metabolic resource allocation. This research provides a systematic elucidation of the molecular mechanisms underlying insect resistance in sugarcane and offers important candidate genes and metabolites for breeding resistant varieties. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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15 pages, 1190 KB

Open AccessArticle

Hydroponic and Soil-Based Screening for Salt Tolerance and Yield Potential in the Different Growth Stages of Thai Indigenous Lowland Rice Germplasm

by Wilai Khamnonin, Tanawat Wongsa, Monchita Ponsen, Jirawat Sanitchon, Sompong Chankaew and Tidarat Monkham

Agronomy 2025, 15(11), 2574; https://doi.org/10.3390/agronomy15112574 - 8 Nov 2025

Cited by 1 | Viewed by 965

Abstract

Salinity is one of the primary limiting factors in the rice production system in northeast Thailand due to the presence of underground salt rocks, and the situation is expected to deteriorate further in the future since rice is particularly susceptible to salinity. In this study, 382 indigenous lowland rice germplasms were evaluated for salt tolerance under hydroponic conditions at the seedling stage. The stress condition was induced by adding NaCl from 2 dS/m to 22 dS/m. Twenty-two varieties (group 1) were selected based on low leaf salinity scores in 2019 and 2020. Ten varieties, LLR050, LLR054, LLR106, LLR216, LLR309, LLR365, LLR377, LLR402, LLR441, and LLR449, were selected from leaf salt injury scores under hydroponic conditions in 2021 and 2022. The response of ten selected varieties was investigated under both hydroponic and soil media at the seedling stage, as well as soil culture at the tillering and flowering stages. The results revealed that LLR054, LLR365, and LLR216 exhibited low leaf injury scores (less than 4.0) at both the seedling and tillering stages. At the seedling stage, most varieties demonstrated high Na+ accumulation in the root, while high accumulation in the shoot was observed at the tillering stage. Varieties LLR054 and LLR441 displayed low leaf damage scores, root sodium accumulation at the seedling stage, and shoot sodium accumulation at the tillering stage, similar to the tolerant check variety Pokkali. Additionally, LLR365 and LLR216 showed high shoot sodium accumulation but low leaf damage scores at the tillering stage. At the flowering stage, LLR050 and LLR449 maintained high yields and filled seeds per panicle under salt stress. Therefore, early-stage LLR054, LLR441, LLR365, and LLR216 had high tolerance and LLR050 and LLR449 maintained high yields, and these varieties are potential sources of salt tolerance for future rice breeding programs. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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16 pages, 2776 KB

Open AccessArticle

Complete Chloroplast Genome Sequence Structure and Phylogenetic Analysis of Brassica juncea var. multiceps (Brassicaceae)

by Tingting Liu, Ziwei Hu, Li’ai Xu, Xiahong Luo, Lina Zou, Shaocui Li, Changli Chen and Xia An

Agronomy 2025, 15(11), 2501; https://doi.org/10.3390/agronomy15112501 - 28 Oct 2025

Viewed by 1069

Abstract

Brassica juncea var. multiceps (Xuelihong), a variety of B. juncea (L.) Czern., holds considerable nutritional and economic value. However, its complete chloroplast genome and the evolutionary relationships within Brassicaceae remain poorly characterized. Using Illumina NovaSeq 6000 high-throughput sequencing, we assembled and annotated the full chloroplast genome sequence of B. juncea var. multiceps. The genome is 153,483 bp in length, with 36.36% GC content, and encodes 132 genes. Codon usage analysis identified leucine (Leu) as the dominant amino acid. Thirty-one codons had relative synonymous codon usage (RSCU; a metric for codon preference) values greater than one, with 93.55% of these preferred codons ending in A/U. We detected 37 dispersed repeats (14 forward, 18 palindromic, 3 reverse, and 2 complementary) and 315 simple sequence repeats (SSRs), with mononucleotide SSRs dominating (72.70%). Analysis of the Ka/Ks ratio, a measure of selection pressure (where values greater than one indicate positive selection), indicated that ycf1, ycf2, and nadhF genes may have undergone positive selection. The nucleotide diversity analysis revealed five hypervariable hotspot-genomic regions with high mutation rates, which are critical for phylogenetic studies. Phylogenetic analysis of 26 Brassicaceae species revealed that B. juncea var. multiceps is closely related to B. juncea. Notably, this is the first complete chloroplast genome of B. juncea var. multiceps, with unique hypervariable regions not reported in other B. juncea varieties. These findings clarify evolutionary relationships in Brassicaceae, provide molecular markers for the genetic breeding of B. juncea var. multiceps, and enhance our understanding of chloroplast genome adaptation in Brassica. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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31 pages, 6233 KB

Open AccessArticle

Genome-Wide Identification of Flowering-Related Genes and Their Pleiotropic Roles in Regulating Flowering Time and Plant Height in Soybean

by Xiao Li, Hui Wang, Bei Liu, Yunhua Yang, Han Gou, Huan Du, Yuhao Chen, Huakun Yu, Mingqi Zhou, Jinming Zhao and Fengjie Yuan

Agronomy 2025, 15(9), 2204; https://doi.org/10.3390/agronomy15092204 - 17 Sep 2025

Viewed by 1911

Abstract

Soybean (Glycine max (L.) Merr.) flowering time and plant height are critical agronomic traits that significantly influence yield and environmental adaptability. To clarify the regulatory mechanisms of flowering-related genes and their associations with plant height, a genome-wide identification of such genes in soybean were performed. This analysis used Arabidopsis thaliana flowering genes as references, employing BLASTP searches and pathway classification. All of the identified flowering-related genes were classified into eight regulatory pathways, with the photoperiod pathway (Ph) being the most prominent. Evolutionary and expression analyses revealed that core regulators (e.g., GmFTs, GmSOC1s) are conserved across pathways and are preferentially expressed in shoot apical meristems (SAMs). Additionally, both flowering-related genes and key hormones (e.g., IAA, GA, ABA) exhibited rhythmic responses to light signals. CRISPR-Cas9-mediated validation confirmed that genes GmSAUR46b regulates both flowering time and plant height, as mutants of this gene showed early flowering and reduced height. Notably, a large proportion of previously mapped flowering genes overlapped with our identified ones, while some remained undetected, likely due to whole-genome duplication and adaptive evolution, which generate new regulatory networks. Most of the identified flowering-related genes, however, have not been mapped, which highlights substantial uncharacterized potential in soybean flowering and plant height regulation. This provides a valuable molecular framework to guide soybean molecular breeding for enhanced yield and environmental adaptability. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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16 pages, 2206 KB

Open AccessArticle

Identification and Characterization of SWEET Gene Family in Peanuts and the Role of AhSWEET50 in Sugar Accumulation

by Tiecheng Cai, Yijing Pan, Chong Zhang, Lang Chen, Biaojun Ji, Qiang Yang, Faqian Xiong and Weijian Zhuang

Agronomy 2025, 15(5), 1149; https://doi.org/10.3390/agronomy15051149 - 8 May 2025

Viewed by 1362

Abstract

The SWEET (sugars will eventually be exported transporter) gene family represents a novel class of sugar transporters capable of bidirectionally transporting sugars along the concentration gradient. In this study, we identified 50 SWEET genes from the peanut cultivar Shitouqi, which were phylogenetically classified into four clades. Promoter analysis revealed that the AhSWEET genes contain multiple cis-acting elements associated with stress responses, growth regulation, and hormone signaling, suggesting their potential roles in plant development and adaptation to environmental challenges. Transcriptome profiling highlighted AhSWEET50 as the most highly expressed member during early seed development stages in both low- and high-sucrose peanut cultivars and also highly expressed at the mature stage. Subcellular localization confirmed the presence of AhSWEET50 in both the plasma membrane and cytoplasm, with predominant expression observed in embryos. The heterologous overexpression of AhSWEET50 in Arabidopsis significantly increased soluble sugar accumulation when compared to wild-type plants. These results validate the functional role of AhSWEET50 in sugar transport and provide a foundation for understanding the mechanisms of sugar allocation in peanuts, which has implications for improving seed quality through metabolic engineering. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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11 pages, 3087 KB

Open AccessArticle

Population Structure and Genetic Diversity of Agave Germplasms in China

by Xiaoli Hu, Yubo Li, Shibei Tan, Lisha Chen, Dietram Samson Mkapa, Chen Lin, Qingqing Liu, Gang Jin, Tao Chen, Xu Qin, Kexian Yi and Xing Huang

Agronomy 2025, 15(3), 722; https://doi.org/10.3390/agronomy15030722 - 17 Mar 2025

Cited by 3 | Viewed by 1884

Abstract

Agave hybrid cultivar 11,648 has been planted for sisal fiber production in China since the 1960s. However, little is known about the population structure and genetic diversity of agave germplasms in China. Therefore, we developed a group of core SNP markers to evaluate the population structure and genetic diversity of 125 agave germplasms in China, including 20 cultivars, 14 breeding lines, and 89 transplanted resources from different areas. Cost-effective amplicon sequencing technology was used to identify genetic variants. The results grouped most cultivars and breeding lines together, which indicated that local agave breeding programs aimed to improve fiber and disease-resistance traits. These breeding programs have reduced genetic diversity, even with the gene flows from other Agave species. The neighbor-joining phylogenetic tree revealed the relationships between A. H11648 and its parents. The phylogenetic relationship between A. sisalana and A. amanuensis is doubtful, even if they are considered heterotypic synonyms. The 11 agave germplasms introduced from Mexico suggest the abundant diversity of agave germplasms in Mexico, which is also the source of agave germplasms in China. This study provides a sketch map for agave germplasms in China, which will benefit future studies related to population genetics and breeding works of agave. Full article

(This article belongs to the Special Issue Germplasm Conservation and Genetic Improvement in Tropical and Subtropical Crops)

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