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Genetic Mapping of Agronomic Traits in Crops
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Genetic Mapping of Agronomic Traits in Crops

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 November 2026 | Viewed by 1909

Special Issue Editor

Dr. Fengxia Liu

E-Mail Website
Guest Editor
Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
Interests: cloning and mechanism of genes related to important agronomic traits and abiotic stress resistance in wild rice

Special Issue Information

Dear Colleagues,

The global challenge of feeding a growing population under climate change necessitates accelerated crop improvement. Revealing the genetic basis of key agronomic traits including yield, disease resistance, abiotic stress tolerance, and nutrient efficiency—is critical for sustainable crop improvement. This Special Issue invites original research and reviews leveraging genetic mapping approaches (e.g., QTL analysis, GWAS, multi-omics integration, and CRISPR-based validation) to dissect the molecular architecture of the traits in crops. Contributions addressing gene-environment interactions, epigenomic regulation, or translational applications (e.g., marker-assisted breeding) are also particularly encouraged. By advancing our understanding of crop genetics, this collection aims to accelerate the development of climate-resilient and high-yielding varieties, ensuring global food security.

Dr. Fengxia Liu
Guest Editor

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 250 words) can be sent to the Editorial Office for assessment.

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. Plants 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 2700 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

  • genetic mapping
  • QTL
  • GWAS
  • abiotic stress
  • yield traits
  • multi-omics
  • CRISPR
  • functional analysis

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Published Papers (2 papers)

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Research

20 pages, 1367 KB  
Article
QTL Mapping for RVA Profile Characteristics in a Recombinant Inbred Line Population Derived from High-Harvest-Index Yuexiangzhan Rice
by Yunyi Zhan, Zhanhua Lu, Wei Liu, Shiguang Wang, Tengkui Chen, Yongchun He, Weifeng Yang, Liting Zhang and Xiuying He
Plants 2026, 15(6), 880; https://doi.org/10.3390/plants15060880 - 12 Mar 2026
Viewed by 411
Abstract
Rapid Visco Analyzer (RVA) profile characteristics are important indicators of rice (Oryza sativa L.) eating quality. In this study, based on the high-density genetic linkage map constructed under the genetic background of Yuexianghzan (YXZ) and Shengbasimiao (SBSM), combined with the RVA profile [...] Read more.
Rapid Visco Analyzer (RVA) profile characteristics are important indicators of rice (Oryza sativa L.) eating quality. In this study, based on the high-density genetic linkage map constructed under the genetic background of Yuexianghzan (YXZ) and Shengbasimiao (SBSM), combined with the RVA profile characteristic data of recombinant inbred lines (RILs) grown in two environments, QTL scanning was performed using the ridge regression analysis method. A total of 59 QTLs associated with RVA profile characteristics were detected across 11 chromosomes in the two environments, with individual QTLs explaining 0.12% to 85.16% of the phenotypic variation. Moreover, 11 QTLs were repeatedly detected in two environments with large effects. The QTL located in the 1.44–1.85 Mb interval on chromosome 6 simultaneously controlled eight RVA profile characteristics and contained the cloned waxy (Wx) gene. Additionally, the intervals 20.58–20.70 Mb on chromosome 5 and 24.96–25.42 Mb on chromosome 8 were repeatedly mapped and influenced multiple RVA characteristics. Based on gene annotation information, a total of nine candidate genes (LOC_Os05g34730, LOC_Os05g34830, LOC_Os05g34854, LOC_Os06g03910, LOC_Os06g04200, LOC_Os06g42720, LOC_Os08g39830, LOC_Os08g39850, and LOC_Os08g39860) that directly or indirectly influence the starch synthesis pathway were identified. The results of this study lay a foundation for further map-based cloning of genes related to rice RVA profile characteristics and molecular design breeding. Full article
(This article belongs to the Special Issue Genetic Mapping of Agronomic Traits in Crops)
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14 pages, 3243 KB  
Article
Fine-Mapping of a Red-Skinned Taproot Gene in Radish (Raphanus sativus L.)
by Zhao Liu, Zhenzhen Li, Gaizhen Li and Linyi Qiao
Plants 2025, 14(19), 3065; https://doi.org/10.3390/plants14193065 - 3 Oct 2025
Viewed by 1172
Abstract
The skin color of radish taproots is an important commodity character that directly affects the choice behavior of consumers. Here, we identified a skin color gene carried by a red-skinned inbred line, SXAU-R2. Genetic population was constructed by the crossing of SXAU-R2 and [...] Read more.
The skin color of radish taproots is an important commodity character that directly affects the choice behavior of consumers. Here, we identified a skin color gene carried by a red-skinned inbred line, SXAU-R2. Genetic population was constructed by the crossing of SXAU-R2 and a white-skinned inbred line, SXAU-W2, and the taproots of F1 plants exhibited intermediate color. In the F2 population, the separation ratio of taproot skin color indicated that the phenotype was controlled by one major locus, named RST1 (Red-Skinned Taproot 1). Combined with bulked segregant analysis and RNA sequencing (BSA-seq), 2640 single nucleotide polymorphisms (SNPs) were detected between the annotated genes of the red skin bulk and white skin bulk. Molecular markers were developed in the SNP-enriched 27~32 Mbp region of chromosome 7, and then RST1 was mapped in the genetic interval between flanking markers SSR-14 and SSR-22. Using F2:3 lines derived from a key F2 heterozygote, RST1 was narrowed down into a 530 Kbp interval. There were 46 expressed annotated genes in the fine-mapping region, and a gene encoding MYB was selected as the candidate of RST1. Finally, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and RT-qPCR, we identified the potential interacting genes RsbHLH and RsWD, as well as the latent target genes RsDFR and RsANS of RST1 in the anthocyanin synthesis pathway. These results provide an understanding of the genetic mechanisms regulating anthocyanin synthesis and offer an efficient molecular marker for the radish breeding of skin color. Full article
(This article belongs to the Special Issue Genetic Mapping of Agronomic Traits in Crops)
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