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Agriculture
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Crop Yield Improvement in Genetic and Biology Breeding
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Crop Yield Improvement in Genetic and Biology Breeding

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Genetics, Genomics and Breeding".

Deadline for manuscript submissions: closed (30 September 2025) | Viewed by 5586

Special Issue Editors

Dr. Zhiyong Li

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: plant genomics and genetics; molecular breeding; rice yield; carbon partitioning; seed development
Special Issues, Collections and Topics in MDPI journals
Dr. Jie Huang

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: rice (Oryza sativa L.); developmental biology; plant genetics; molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Food security is threatened, due to the burgeoning world population, increasing individual demands and degrading farmland. Additionally, over the past two decades, climate change is becoming more challenging in crop field improvement, especially given the incidences of elevated atmospheric CO2, as well as changing temperature and rainfall patterns. It is estimated that crop yields must double by 2050 to ensure food security all over the world. Crop breeding has been greatly accelerated by the enhanced knowledge of plant genomics and genetics, and the development of modern biotechnologies. However, crop yields have stabilized in recent years. To keep up with the future food demand, it is imperative to explore the genetic basis of plants and apply modern genetic engineering and breeding biotechnologies.

The goal of this Special Issue, “Crop Yield Improvement in Genetic and Biology Breeding”, in Agriculture is to present an overview of the latest fundamental discoveries in crop genomics, genetics and crop germplasm resources, as well as the potential utilization of biotechnologies in crop yield improvement. All original research papers and reviews are welcome for submission to this research topic, and we believe your contribution will have a significant influence on future crop breeding.

Dr. Zhiyong Li
Dr. Jie Huang
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agriculture is an international peer-reviewed open access semimonthly 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

  • crops yield
  • gene cloning and function
  • genome editing
  • genetic improvements
  • genetic engineering
  • regulatory mechanisms
  • germplasm enhancement
  • molecular breeding

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Published Papers (6 papers)

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Research

16 pages, 4333 KB  
Article
Integrated Transcriptomic and Metabolomic Analyses Implicate Key Genes and Metabolic Pathways in Maize Lodging Resistance
by Chunlei Xue, Haiyan Wu, Xuting Zhang, Fengcheng Sun, Sainan Zhang, Zhonghao Yu, Qi Dong, Yanan Liu, Hailong Zhang, Qing Ma and Liming Wang
Agriculture 2025, 15(23), 2416; https://doi.org/10.3390/agriculture15232416 - 24 Nov 2025
Viewed by 260
Abstract
Maize stalk lodging causes substantial yield losses worldwide. Although stalk strength is a genetically determined trait, its molecular mechanisms—particularly the dynamic changes during key developmental stages—remain inadequately characterized due to limitations of single-omics approaches. This study employed an integrated transcriptomic and metabolomic analysis [...] Read more.
Maize stalk lodging causes substantial yield losses worldwide. Although stalk strength is a genetically determined trait, its molecular mechanisms—particularly the dynamic changes during key developmental stages—remain inadequately characterized due to limitations of single-omics approaches. This study employed an integrated transcriptomic and metabolomic analysis strategy to compare stalk tissues from three maize genotypes with contrasting lodging resistance: the highly resistant inbred line PHB1M, the susceptible inbred line Chang 7-2, and their recombinant inbred line 23NWZ561 (abbreviated as P, C, and Z, respectively). Dynamic sampling of all three genotypes was conducted at both grain-filling and maturity stages, with simultaneous measurement of physiological traits related to stalk strength. Phenotypic analysis revealed that the resistant genotype PHB1M exhibited superior rind penetration strength, cell wall composition (cellulose, hemicellulose, and lignin) content, and vascular bundle development. Multi-omics analysis indicated that the molecular basis of lodging resistance is primarily established during the maturity stage. The transcriptomic and metabolomic profiles of the recombinant inbred line Z shifted from clustering with the susceptible parent C at the grain-filling stage to grouping with the resistant parent P at maturity. Key pathways including phenylpropanoid biosynthesis were significantly enriched specifically at maturity, accompanied by upregulation of related genes (PAL, HCT, CCR) and accumulation of metabolites such as lignin precursors in PHB1M. Integrated analysis identified a core co-expression network within the phenylpropanoid pathway comprising three genes and three metabolites. This study systematically demonstrates that lodging resistance in maize is regulated by transcriptional and metabolic reprogramming during late stalk developmental stages, particularly at maturity, where enhanced activation of the phenylpropanoid biosynthesis pathway plays a central role. These findings provide valuable candidate genes and metabolic markers for breeding lodging-resistant maize varieties. Full article
(This article belongs to the Special Issue Crop Yield Improvement in Genetic and Biology Breeding)
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21 pages, 4042 KB  
Article
Transcriptomic and Physiological Insights into the Role of Nano-Silicon Dioxide in Alleviating Salt Stress During Soybean Germination
by Seo-Young Shin, Won-Ho Lee, Byeong Hee Kang, Sreeparna Chowdhury, Da-Yeon Kim, Hyeon-Seok Lee and Bo-Keun Ha
Agriculture 2025, 15(22), 2320; https://doi.org/10.3390/agriculture15222320 - 7 Nov 2025
Viewed by 299
Abstract
Salt stress is a major form of abiotic stress that disrupts soybean germination and early seedling establishment. In this study, physiological, biochemical, and transcriptomic analyses—including germination index, antioxidant enzyme activity, and RNA-seq profiling—were conducted during soybean germination to elucidate early responses to salt [...] Read more.
Salt stress is a major form of abiotic stress that disrupts soybean germination and early seedling establishment. In this study, physiological, biochemical, and transcriptomic analyses—including germination index, antioxidant enzyme activity, and RNA-seq profiling—were conducted during soybean germination to elucidate early responses to salt stress and biostimulant treatment. A preliminary screening of six biostimulants (nanoparticle zinc oxide (NP-ZnO), nanoparticle silicon dioxide (NP-SiO2), silicon dioxide (SiO2), glucose, humic acid, and fulvic acid) revealed NP-SiO2 as the most effective in promoting germination under salt stress. Under 150 mM NaCl, NP-SiO2 increased the germination rate and length of the radicle compared with the control, also enhancing peroxidase and ascorbate peroxidase activities while reducing malondialdehyde accumulation, suggesting alleviation of oxidative stress. RNA sequencing revealed extensive transcriptional reprogramming under salt stress, identifying 4579 differentially expressed genes (DEGs) compared with non-stress conditions, while NP-SiO2 treatment reduced this number to 2734, indicating that NP-SiO2 mitigated the transcriptional disturbance caused by salt stress and stabilized gene expression networks. Cluster analysis showed that growth- and hormone-related genes suppressed by salt stress were restored under NP-SiO2 treatment, whereas stress-responsive genes that were induced by salt were attenuated. Hormone-related DEG analysis revealed that NP-SiO2 down-regulated the overactivation in the abscisic acid, jasmonic acid, and salicylic acid pathways while partially restoring gibberellin, auxin, cytokinin, and brassinosteroid signaling. Overall, NP-SiO2 at 100 mg/L mitigated salt-induced oxidative stress and promoted early soybean growth by fine-tuning physiological and transcriptional responses, representing a promising nano-based biostimulant for enhancing salt tolerance in plants. Full article
(This article belongs to the Special Issue Crop Yield Improvement in Genetic and Biology Breeding)
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26 pages, 1475 KB  
Article
Multi-Environment Evaluation of Soybean Variety Heike 88: Transgressive Segregation and Regional Adaptation in Northern China
by Dezhi Han, Xiaofei Yan, Wei Li, Hongchang Jia, Honglei Ren and Wencheng Lu
Agriculture 2025, 15(20), 2106; https://doi.org/10.3390/agriculture15202106 - 10 Oct 2025
Cited by 1 | Viewed by 507
Abstract
Heike 88, a new soybean variety developed through strategic hybridization of Heijiao 08-1611 × Heihe 43 followed by pedigree selection, was evaluated across seven locations in Heilongjiang Province from 2019 to 2022. The variety demonstrated stable performance with a 10.3% average yield advantage [...] Read more.
Heike 88, a new soybean variety developed through strategic hybridization of Heijiao 08-1611 × Heihe 43 followed by pedigree selection, was evaluated across seven locations in Heilongjiang Province from 2019 to 2022. The variety demonstrated stable performance with a 10.3% average yield advantage over regional check varieties and mean yields of 3188 kg ha−1. Principal component analysis revealed that genetic variation accounted for 43.4% and 32.6% of performance variance in the first two components, indicating successful transgressive segregation where the pure line exceeded both parental lines through complementary gene action. Performance relative to parental averages ranged from −20% to +40% across the temperature gradient, demonstrating strong genotype-environment interaction effects. Machine learning analysis identified year effect (13% importance), accumulated temperature (7.6% importance), and oil content (4% importance) as primary yield drivers. Complete resistance to soybean mosaic virous (SMV) and cyst nematode attack was observed across all locations, with excellent gray leaf spot resistance (grades 0–1) maintained under natural pathogen pressure. Seed quality parameters remained stable across environments, with protein content ranging from 41.69% to 42.25% and oil content from 19.74% to 20.13%, indicating minimal environmental effects on compositional traits. Yield stability improved progressively over the evaluation period, with the coefficient of variation decreasing from 18.7% in 2019 to 6.7% in 2022, while absolute yields increased from 2550 to 3200 kg ha−1. These results demonstrate successful exploitation of transgressive segregation for regional adaptation through strategic parent selection and pedigree breeding, supporting commercial deployment in northern China’s challenging production environments while providing methodological guidance for future breeding programs targeting environmental specificity. Full article
(This article belongs to the Special Issue Crop Yield Improvement in Genetic and Biology Breeding)
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23 pages, 5834 KB  
Article
Comparative Analysis of the Expression of Genes Involved in Fatty Acid Synthesis Across Camelina Varieties
by Elisa Gómez, Gregorio Hueros, David Mostaza-Colado, Aníbal Capuano, Mercedes Uscola and Pedro V. Mauri
Agriculture 2025, 15(12), 1305; https://doi.org/10.3390/agriculture15121305 - 17 Jun 2025
Viewed by 954
Abstract
Camelina sativa (L.) Crantz, a native European oilseed crop of the Brassicaceae family, is notable for its short life cycle, making it well-suited for crop rotation and diversification. Its seeds contain a high content of oil (36–47%) that is rich in polyunsaturated fatty [...] Read more.
Camelina sativa (L.) Crantz, a native European oilseed crop of the Brassicaceae family, is notable for its short life cycle, making it well-suited for crop rotation and diversification. Its seeds contain a high content of oil (36–47%) that is rich in polyunsaturated fatty acids (PUFAs) such as alpha-linolenic acid (ALA, C18:3, Ω-3) and linoleic acid (LA, C18:2, Ω-6). This oil has diverse industrial applications, including low-emission biofuels, animal feed, pharmaceuticals, biolubricants, bioplastics, and cosmetics. We analyzed the expression of seven key enzymes involved in fatty acid biosynthesis across nine C. sativa accessions at three stages of silique development using highly efficient qRT-PCR assays designed for the target genes and a normalizing control. Our detailed expression analysis revealed significant variation across varieties, with only the gene FAB2c exhibiting genotype-independent expression, indicating a constitutive and essential role in monounsaturated fatty acid (MUFA) biosynthesis. Other genes showed significant interactions between the variety and developmental stage, highlighting the combined influences of genetic background and silique maturation on gene regulation. V18 emerges as particularly promising, exhibiting elevated expression of genes linked to PUFA and VLCFA biosynthesis—traits of significance for food, biofuel, and industrial applications. These findings, together with the developed qRT-PCR assays, provide valuable tools for selecting Camelina varieties with optimized genetic profiles, highlighting the potential of harnessing natural transcriptional diversity for crop improvement. Full article
(This article belongs to the Special Issue Crop Yield Improvement in Genetic and Biology Breeding)
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20 pages, 6141 KB  
Article
Effect of Low Nighttime Temperature on Oil Accumulation of Rapeseed Seeds (Brassica napus L.) Based on RNA-Seq of Silique Wall Tissue
by Chao Mi, Yanning Zhao, Xuetao Yang, Liangbin Lin and Jinxiong Wang
Agriculture 2025, 15(6), 576; https://doi.org/10.3390/agriculture15060576 - 9 Mar 2025
Viewed by 1097
Abstract
This study investigated the impact of nighttime temperature and elevation on the oil and erucic acid content of rapeseed (Brassica napus L.) seeds, focusing on the role of sugar synthesis in the silique wall as a substrate for oil synthesis. Field experiments [...] Read more.
This study investigated the impact of nighttime temperature and elevation on the oil and erucic acid content of rapeseed (Brassica napus L.) seeds, focusing on the role of sugar synthesis in the silique wall as a substrate for oil synthesis. Field experiments across different altitudes and controlled low nighttime temperature (LNT) treatments (20/18 °C and 20/13 °C) were conducted. Transcriptome analysis of the silique walls was performed to explore gene expression changes. The results showed that higher altitudes and lower nighttime temperatures significantly increased seed oil and erucic acid content, particularly in strong temperature-sensitive line (STSL) seeds. LNT conditions promoted sucrose synthesis and transport in the silique wall by upregulating genes involved in sugar transport (SUT, SWEET, SUC1) and transcription factors (WRKY51, NAC104). This, in turn, enhanced the substrate availability for oil synthesis in the seeds. Furthermore, genes associated with oil biosynthesis (SAD, FAD2, KAS) were significantly upregulated under LNT, promoting oil accumulation. In conclusion, nighttime temperature is a critical factor influencing oil content in rapeseed seeds. Low nighttime temperatures enhance sucrose transport and gene expression in the silique wall, leading to increased oil synthesis. These findings provide insights for breeding strategies aimed at improving seed oil content under varying climatic conditions. Full article
(This article belongs to the Special Issue Crop Yield Improvement in Genetic and Biology Breeding)
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16 pages, 3170 KB  
Article
Stability of Early Maturing Soybean Genotypes in Poland
by Danuta Kurasiak-Popowska, Agnieszka Katańska-Kaczmarek, Przemysław Matysik, Piotr Stefański, Patrycja Przybył, Ewa Skotarczak and Jerzy Nawracała
Agriculture 2024, 14(12), 2202; https://doi.org/10.3390/agriculture14122202 - 2 Dec 2024
Cited by 1 | Viewed by 1618
Abstract
Poland is one of the northernmost countries in the world where soybean breeding is actively conducted. A large collection of soybean genotypes was analyzed in three locations in Poland during the 2022–2023 growing seasons. The objective of this research was to determine the [...] Read more.
Poland is one of the northernmost countries in the world where soybean breeding is actively conducted. A large collection of soybean genotypes was analyzed in three locations in Poland during the 2022–2023 growing seasons. The objective of this research was to determine the stability of yield, as well as the protein and fat content in the seeds of 280 genotypes. The phenotypic correlations across genotypes and environments were assessed using the Spearman coefficient. The statistical analysis was provided using the additive main effects and multiplicative interaction model. The stability of genotypes was assessed using the weighted average of absolute scores. The main factor differentiating the results between locations was the variation in weather conditions. The variety Karok, which ranks among the top 10% in genotype selection indices for yield and thousand-seed weight, is recommended based on studies conducted within the Post-Registration Variety Testing System in three voivodeships in Poland. Among the most stable genotypes, in terms of the traits analyzed in this paper, are many registered and currently grown soybean varieties such as Obelix Pompei, Coraline, Kapral, ES Mentor, NS Mercury, Pepita, Pollux, Silesia, and Heihe 45. The yield stability of soybean genotypes during the development of new varieties should be one of the factors analyzed by breeders. Full article
(This article belongs to the Special Issue Crop Yield Improvement in Genetic and Biology Breeding)
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