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Agronomy
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From Phenotype to Gene: A Holistic Approach to Improving Crop...
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From Phenotype to Gene: A Holistic Approach to Improving Crop Agronomic Traits

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 1375

Special Issue Editors

Dr. Zifeng Guo

E-Mail Website
Guest Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: molecular breeding; disease-resistant breeding in maize
Dr. Hongwei Zhang

E-Mail Website
Guest Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: genomic-enhanced breeding; breeding tool development
Special Issues, Collections and Topics in MDPI journals
Dr. Yinglun Li

E-Mail Website
Guest Editor Assistant
Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Interests: multidimensional plant phenotyping based on deep learning

Special Issue Information

Dear Colleagues,

Most agronomically important crop traits are quantitative in nature. These traits exhibit continuous variation due to polygenic control and complex genetic architectures, making their dissection at the population level particularly challenging. Recent breakthroughs in high-throughput phenomics, third-generation sequencing, and AI-driven analytics are revolutionizing our ability to study these traits. These technologies enable more precise quantitative trait dissection and predictive modeling, paving the way for data-driven molecular breeding strategies. As these tools continue to evolve, they will play an increasingly pivotal role in accelerating crop design breeding programs.

This Special Issue seeks to showcase cutting-edge strategies for high-throughput phenotyping, as well as the genetic dissection and genomic prediction of crop quantitative traits, with an emphasis on novel methodologies and their applications. In particular, we welcome papers on how high-throughput and time-series phenotyping technologies can improve trait measurement and how these data can be synergized with genomic approaches to identify the key loci governing quantitative traits. Ultimately, this knowledge can be translated into molecular design breeding strategies for trait enhancement.

We invite submissions in the form of original research, reviews, perspectives, and opinion articles on topics including, but not limited to, the following:

  1. Advanced phenotyping techniques for crop quantitative traits, including agronomic performance, stress resilience, and disease resistance.
  2. Genetic analysis and QTL mapping, such as combining ability analysis, QTL mapping, GWAS, and multi-omics integration.
  3. Breeding methodologies for trait improvement, including marker-assisted selection (MAS), genomic selection (GS), genomic–enviromic selection (GES), and gene editing applications.

By combining the fields of phenomics, genetics, and breeding, this Special Issue aims to advance the understanding and manipulation of complex traits for sustainable crop improvement.

Dr. Zifeng Guo
Dr. Hongwei Zhang
Guest Editors

Dr. Yinglun Li
Guest Editor Assistant

Manuscript Submission Information

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. Agronomy 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

  • phenomics
  • quantitative trait locus (QTL)
  • genomic selection (GS)
  • genomic-enviromic selection (GES)
  • molecular design breeding

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

15 pages, 1266 KB  
Article
Genetic Dissection of Yield-Related Traits in a Set of Maize Recombinant Inbred Lines Under Multiple Environments
by Donglin Li, Weiwei Zeng, Zhongmin Han, Jiawei Shang, Tai An, Yuan Li, Yuan Xu, Fengyu Wang, Xiaochun Jin, Jinsheng Fan, Jianqian Qi, Rui Wang, Liang Li, Kaijian Fan, Dequan Sun and Yuncai Lu
Agronomy 2025, 15(9), 2109; https://doi.org/10.3390/agronomy15092109 - 1 Sep 2025
Viewed by 215
Abstract
Agronomic advancements have led to significant increases in maize yield per hectare in Northeast China, primarily through improved density tolerance. However, the genetic mechanism underlying grain yield responses to density stress remains poorly understood. Here, a population of 193 recombinant inbred lines (RILs) [...] Read more.
Agronomic advancements have led to significant increases in maize yield per hectare in Northeast China, primarily through improved density tolerance. However, the genetic mechanism underlying grain yield responses to density stress remains poorly understood. Here, a population of 193 recombinant inbred lines (RILs) derived from the cross between ZM058 and PH1219 was employed to identify quantitative trait loci (QTLs) under two planting densities across three locations over two years. Six yield-related traits were investigated: ear tip-barrenness length (BEL), cob diameter (CD), ear diameter (ED), ear length (EL), kernel number per row (KNR), and kernel row number (KRN). These traits exhibited distinct and divergent responses to density stress, with the values of CD, ED, EL, KNR and KRN decreasing as planting density increased, except for BEL. A total of 81 QTLs were identified for these traits: 39 were unique to low planting density, 22 to high planting density, and 20 were shared across both conditions. Additionally, nine QTL clusters implicated in the development of multiple traits were detected. The results indicate that planting density significantly affects yield traits, primarily through the interaction of numerous minor QTLs with multiple effects. This insight enhances our understanding of the genetic basis of yield-related traits and provides valuable guidance for breeding high-density-tolerant varieties. Full article
(This article belongs to the Special Issue From Phenotype to Gene: A Holistic Approach to Improving Crop Agronomic Traits)
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16 pages, 2163 KB  
Article
Arbuscular Mycorrhizal Fungi Mitigate Lead Toxicity in Maize by Restructuring Rhizosphere Microbiome and Enhancing Antioxidant Defense Mechanisms
by Xiaoxiang Zhang, Bin Zhao, Yan Zheng, Min Li, Huaisheng Zhang, Pingxi Wang, Shilin Chen, Xining Jin and Xiangyuan Wu
Agronomy 2025, 15(6), 1310; https://doi.org/10.3390/agronomy15061310 - 27 May 2025
Cited by 2 | Viewed by 619
Abstract
The remediation of lead (Pb)-contaminated soils through eco-friendly strategies is critical for sustainable agriculture. This study investigated the role of arbuscular mycorrhizal fungi (AMF) in enhancing maize tolerance to Pb stress and modulating rhizosphere microbial communities. A pot experiment was conducted with maize [...] Read more.
The remediation of lead (Pb)-contaminated soils through eco-friendly strategies is critical for sustainable agriculture. This study investigated the role of arbuscular mycorrhizal fungi (AMF) in enhancing maize tolerance to Pb stress and modulating rhizosphere microbial communities. A pot experiment was conducted with maize (Baiyu833) under four Pb concentrations (0, 900, 1800, 2700 mg·kg−1) and three AMF treatments: non-inoculation (Non), Funneliformis mosseae (Fm), or Rhizophagus intraradices (Ri). The results demonstrated that AMF inoculation significantly increased plant biomass, boosted antioxidant enzyme activities (SOD, POD), and reduced malondialdehyde (MDA) levels, mitigating Pb-induced oxidative stress. AMF restricted Pb translocation to aerial parts, with root Pb accumulation reaching 2110.76 mg·kg−1 (Fm) and 2090.56 mg·kg−1 (Ri) under Pb2700, enhancing phytostabilization. High-throughput sequencing revealed that AMF inoculation enriched α-diversity indices and restructured bacterial communities, favoring beneficial taxa like Promicromonospora, which are linked to heavy metal resistance and plant growth promotion. Principal coordinate analysis highlighted distinct clustering of microbial communities driven by AMF, emphasizing their role in alleviating Pb toxicity. These findings underscore that AMF enhance maize resilience to Pb by regulating antioxidant defense, immobilizing Pb in roots, and recruiting stress-tolerant rhizosphere microbiomes. This study provides insights into AMF-assisted phytoremediation as a sustainable strategy for Pb-contaminated soils. Full article
(This article belongs to the Special Issue From Phenotype to Gene: A Holistic Approach to Improving Crop Agronomic Traits)
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