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Horticulturae
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Genetic Mapping and QTL Analysis for Key Traits in Horticultural...
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Genetic Mapping and QTL Analysis for Key Traits in Horticultural Crops

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: 30 November 2026 | Viewed by 3682

Special Issue Editors

Dr. Xianming Zhou

E-Mail Website
Guest Editor
School of Tropical Agriculture and Forestry, Sanya Institute of Breeding and Multiplication, Hainan University, Haikou 571100, China
Interests: QTL mapping; yield traits; quality traits; map-based cloning
Dr. Heping Wan

E-Mail Website
Guest Editor
Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Wuhan 430056, China
Interests: plant; abiotic stress; GWAS; epigenetics
Prof. Dr. Luming Yang

E-Mail Website
Guest Editor
College of Horticulture, Henan Agricultural University, Zhengzhou 450046, China
Interests: gene/QTL mapping; marker-assisted breeding; GWAS

Special Issue Information

Dear Colleagues,

The improvement in horticultural crops is pivotal for ensuring global food security, nutritional quality, and sustainable agricultural practices. Unraveling the genetic architecture of key agronomic traits (such as yield, fruit quality, abiotic and biotic stress resistance, and phenology) is a fundamental step in accelerating precision breeding. Genetic mapping and quantitative trait locus (QTL) analysis serve as powerful tools to dissect the complex genetic basis of these traits, facilitating the identification of candidate genes and the development of molecular markers for marker-assisted selection (MAS).

Despite significant advances, many important horticultural traits are governed by multiple genes with minor effects and are highly influenced by environmental factors, making them challenging to study. The advent of high-throughput sequencing technologies has revolutionized the field, enabling the construction of high-density genetic maps and genome-wide association studies (GWASs) at an unprecedented resolution. This Special Issue aims to collate cutting-edge research that leverages these technologies to advance our understanding of the genetics underlying critical traits in fruit, vegetable, ornamental, and other horticultural crops.

We invite researchers to contribute original research articles and reviews that showcase innovations in genetic mapping and QTL analysis.

Potential topics include, but are not limited to, the following:

  • Construction of high-density genetic linkage maps for horticultural crops;
  • QTL mapping for key traits (e.g., quality, yield, stress tolerance, morphology);
  • Genome-Wide Association Studies (GWASs) for key traits in horticultural crops;
  • Development and application of functional molecular markers (KASP, SSR, SNP);
  • Fine mapping and map-based cloning of genes governing key traits;
  • Integration of QTL mapping with omics data (transcriptomics, metabolomics);
  • Application of genetic maps in marker-assisted and genomic selection breeding programs.

Dr. Xianming Zhou
Dr. Heping Wan
Prof. Dr. Luming Yang
Guest Editors

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. Horticulturae 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 2200 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

  • QTL mapping
  • genetic linkage map
  • marker-assisted selection (MAS)
  • genome-wide association study (GWAS)
  • horticultural crops
  • complex traits
  • molecular breeding
  • candidate gene

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Published Papers (3 papers)

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Research

19 pages, 5695 KB  
Article
Genetic Architecture of Fruit Color and Morphology Revealed by Image-Based Phenotyping and Genome-Wide Association Analysis in Octoploid Strawberry
by Seolah Kim, Yoon Jeong Jang, Koeun Han, Eun Su Lee, Hong-Il Ahn, Youngjae Oh and Do-Sun Kim
Horticulturae 2026, 12(5), 547; https://doi.org/10.3390/horticulturae12050547 - 29 Apr 2026
Viewed by 1398
Abstract
Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid for which the genetic basis of fruit appearance traits has not been comprehensively elucidated. This study investigated the genetic architecture of fruit color and morphological traits using integrated digital phenotyping and genome-wide association [...] Read more.
Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid for which the genetic basis of fruit appearance traits has not been comprehensively elucidated. This study investigated the genetic architecture of fruit color and morphological traits using integrated digital phenotyping and genome-wide association analysis of a core collection of diverse strawberry germplasm maintained for Korean breeding programs. A 108-accession core collection was assembled, genotyped, and phenotyped for 12 fruit quality traits. Population structure analysis identified K = 10 genetic clusters, and a Mantel test confirmed significant genotype–phenotype correspondence (r = 0.38, p < 0.001). Genome-wide association studies (GWAS) using BLINK and MLMM identified 15 significant marker–trait associations across six traits. Pleiotropic loci on chromosomes 15 (4C) and 22 (6B) were consistently associated with fruit lightness (L*) and red channel intensity (R) in both models, and the 6B locus explained approximately 18% of the phenotypic variance for each trait. Gene Ontology enrichment implicated transcriptional regulation, SUMOylation, and plastid-to-chromoplast transition, suggesting that the identified loci influenced fruit coloration through cellular regulatory mechanisms rather than direct pigment biosynthesis. These findings provide a genomic foundation for dual-trait marker-assisted selection targeting light and vividly red fruits for strawberry breeding. Full article
(This article belongs to the Special Issue Genetic Mapping and QTL Analysis for Key Traits in Horticultural Crops)
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16 pages, 5150 KB  
Article
A Single-Nucleotide Mutation in the α-Tubulin Gene Underlies Dwarfism in Watermelon (Citrullus lanatus)
by Peisen Tang, Huanhuan Niu, Shixiang Duan, Yaomiao Guo, Qishuai Kang, Xiaojiu Liu, Yachen Liu, Shibo Peng, Weige Yuan, Mengyuan Yan, Huayu Zhu, Dongming Liu, Wenkai Yan, Jianbin Hu, Luming Yang, Junling Dou and Junyi Tan
Horticulturae 2026, 12(5), 539; https://doi.org/10.3390/horticulturae12050539 - 29 Apr 2026
Viewed by 847
Abstract
Plant architecture is a critical agronomic trait in watermelon (Citrullus lanatus), with vine length directly influencing planting density, light interception, and field management efficiency. Short-vine forms have become important agronomic targets in breeding due to their advantages of high-density planting, efficient [...] Read more.
Plant architecture is a critical agronomic trait in watermelon (Citrullus lanatus), with vine length directly influencing planting density, light interception, and field management efficiency. Short-vine forms have become important agronomic targets in breeding due to their advantages of high-density planting, efficient light utilization, and simplified field management. In this study, a dwarf mutant, designated PKH207, was identified from an ethyl methanesulfonate (EMS)-mutagenized population of the watermelon inbred line G42. The mutant exhibited significantly reduced plant height and shortened internodes due to decreased cell expansion in stem tissues. Genetic analysis indicated that the dwarf phenotype in PKH207 is controlled by a single recessive gene, which was named Cldw2 (Citrullus lanatus dwarf mutant 2). Using a population of 558 F2 plants, bulked segregant analysis sequencing (BSA-seq) and linkage mapping delimited the causal locus to a 540.6 kb region on chromosome 10. Within this interval, a single-nucleotide polymorphism (SNP) mutation was identified in the gene ClG42_10g0100600, encoding an α-tubulin, and this gene was determined to be the candidate gene for the dwarf phenotype. Transcriptome analysis revealed that this mutation significantly disrupts key biological processes, including cell wall biosynthesis, microtubule cytoskeleton organization, and auxin signaling pathways, contributing to the dwarfism phenotype. This study identifies a novel dwarfing allele in cucurbits and provides a direct molecular target for breeding compact watermelon cultivars suited to high-density production. Full article
(This article belongs to the Special Issue Genetic Mapping and QTL Analysis for Key Traits in Horticultural Crops)
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13 pages, 5153 KB  
Article
Fine Mapping of McFFFN4.1 and Identification of a Candidate Gene and KASP Marker for the First Female Flower Node in Bitter Gourd
by Xiaoxi Liu, Ming He, Yangyi Zheng, Jianning Luo, Junxing Li, Hao Gong, Haibin Wu, Gangjun Zhao, Liting Deng, Xueting Wang, Chengcheng Feng and Xiaoming Zheng
Horticulturae 2026, 12(5), 520; https://doi.org/10.3390/horticulturae12050520 - 23 Apr 2026
Viewed by 1096
Abstract
The first female flower node (FFFN) is a crucial trait affecting earliness and yield in bitter gourd (Momordica charantia L.). To identify the genetic locus and candidate gene controlling FFFN, we performed phenotypic and genetic analyses using two parental lines, ‘M144’ (average [...] Read more.
The first female flower node (FFFN) is a crucial trait affecting earliness and yield in bitter gourd (Momordica charantia L.). To identify the genetic locus and candidate gene controlling FFFN, we performed phenotypic and genetic analyses using two parental lines, ‘M144’ (average FFFN: 6.3 ± 2.0) and ‘K55’ (average FFFN: 22.0 ± 4.5), along with their F1 hybrid and an F2 population consisting of 317 individuals. The results show that the low FFFN trait was incompletely dominant over the high FFFN trait. Using BSA-seq, we mapped a FFFN locus to an interval of 18.8–22.5 Mb on chromosome 4. Fine mapping with KASP markers narrowed the McFFFN4.1 to a 73.05 kb interval between markers 25QP334 and 26QP20, which contained seven predicted genes. Transcriptome analysis revealed that only Moc04g29650, which is annotated as cytochrome b-c1 complex subunit Rieske, was differentially expressed between the parents within this mapping interval. Sequence comparison identified a single SNP (C > A) in the promoter region of Moc04g29650, which was located within a putative YAB1/FIL-binding motif. Given the known role of FILAMENTOUS FLOWER (FIL) in regulating floral transition in Arabidopsis thaliana, Moc04g29650 is proposed as the most likely candidate gene for McFFFN4.1. The KASP marker 26QP20, located near Moc04g29650, showed the strongest association with FFFN in the F2 population, with a maximum LOD score of 5.45, and thus represents a valuable tool for marker-assisted selection (MAS) breeding in bitter gourd. This study lays a foundation for cloning McFFFN4.1 and genetically improving early maturity in bitter gourd. Full article
(This article belongs to the Special Issue Genetic Mapping and QTL Analysis for Key Traits in Horticultural Crops)
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