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Horticulturae
Special Issues
Genome Alignment and Regulatory Genomics in Horticultural Crops
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Genome Alignment and Regulatory Genomics 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: 20 January 2027 | Viewed by 3495

Editors

Dr. Peng Jia

E-Mail Website
Guest Editor
Department of Non-Wood Forest, College of Forestry, Hebei Agricultural University, Baoding, China
Interests: abiotic stress; axillary bud; dwarf, epigenetic regulation; flower induction; plant hormones; rootstocks
Dr. Han Jiang

E-Mail Website
Guest Editor
Department of Fruit Science, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
Interests: fruit quality; nitrate; oxalate; sugar metabolism and signaling; wax synthesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The advent of advanced genomic technologies has revolutionized our understanding of horticultural crops, particularly in the domains of genome alignment and regulatory genomics. Genome alignment enables precise comparison of genetic sequences across diverse horticultural species, facilitating the identification of conserved elements and evolutionary relationships crucial for crop improvement. Regulatory genomics, on the other hand, delves into the intricate networks of gene regulation that govern key agricultural traits such as yield, quality, and stress resilience. This Special Issue, titled "Genome Alignment and Regulatory Genomics in Horticultural Crops" aims to gather cutting-edge research that explores the application of genome alignment techniques to uncover genetic diversity and the functional annotation of regulatory elements in horticultural species. We welcome contributions that elucidate how these genomic insights can be translated into practical breeding strategies, enhancing crop productivity and sustainability. Manuscripts focusing on novel computational tools, comparative genomics studies, and functional genomics approaches are particularly encouraged. Join us in advancing the frontiers of horticultural genomics for a more sustainable future.

Dr. Peng Jia
Dr. Han Jiang
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

  • comparative genomics
  • epigenetic regulation
  • functional genomics
  • gene family
  • gene regulatory network
  • genome alignment algorithms
  • genome-wide association analysis
  • quantitative trait locus
  • single-nucleotide polymorphism
  • transposon

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Published Papers (3 papers)

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Research

19 pages, 2463 KB  
Article
The Effects of the Apple MdLTPG17 in Mediating Drought Stress Tolerance and Regulating Fruit Gloss Formation
by Huai-Na Gao, Yu-Feng Zhang, Shu Chen, Si-Ji Fang, Rui-Han Qi, Cheng-Lin Liang, Shun-Feng Ge, Yan-Hui Lv, Shang Wu, Ya-Li Zhang, Han Jiang and Yuan-Yuan Li
Horticulturae 2026, 12(4), 463; https://doi.org/10.3390/horticulturae12040463 - 8 Apr 2026
Viewed by 1025
Abstract
Apple (Malus domestica Borkh.) is the most widely cultivated deciduous fruit tree with the largest industrial scale and the highest economic value in China. Fruit surface glossiness and plant stress tolerance are two core traits that determine the economic benefits and sustainable [...] Read more.
Apple (Malus domestica Borkh.) is the most widely cultivated deciduous fruit tree with the largest industrial scale and the highest economic value in China. Fruit surface glossiness and plant stress tolerance are two core traits that determine the economic benefits and sustainable development of the apple industry. The plant epidermal cuticle is not only the core material basis for determining fruit glossiness but also the first barrier for plants to resist abiotic and biotic stresses. Glycosylphosphatidylinositol-anchored lipid transfer proteins (LTPGs) are the core functional factors mediating trans-cell wall lipid transport in plants. At present, the functions and action mechanisms of LTPG family members that simultaneously regulate fruit appearance quality and stress tolerance in apple remain largely unclear. In this study, we took the MdLTPG17 gene as the research object, clarified its biological function of stress resistance under drought stress, and dissected the molecular mechanism by which it mediates fruit glossiness formation via regulating fruit cuticle thickening. The results of this study provide important genetic resources and a theoretical basis for molecular breeding of stress resistance and targeted improvement of fruit appearance quality in apple. Full article
(This article belongs to the Special Issue Genome Alignment and Regulatory Genomics in Horticultural Crops)
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19 pages, 4299 KB  
Article
Exogenous Abscisic Acid Alleviated the PEG-Induced Drought Stress of Malus sieversii by Regulating the Metabolic Pathway of Starch and Sucrose
by Lijun Liu, Hongxi Ma, Deen Zhang, Xiaoyun Zhang and Xiaoyan Lu
Horticulturae 2026, 12(4), 399; https://doi.org/10.3390/horticulturae12040399 - 24 Mar 2026
Cited by 1 | Viewed by 938
Abstract
Drought is a major limiting factor for apple growth and development. Abscisic acid (ABA) is a key hormone in plant abiotic stress responses, playing a vital role in mediating adaptation to drought. Malus sieversii, the wild ancestor of cultivated apple, exhibits superior [...] Read more.
Drought is a major limiting factor for apple growth and development. Abscisic acid (ABA) is a key hormone in plant abiotic stress responses, playing a vital role in mediating adaptation to drought. Malus sieversii, the wild ancestor of cultivated apple, exhibits superior drought tolerance. However, the specific ABA-dependent regulatory module underlying its exceptional drought tolerance remains to be elucidated. In this study, we investigated the role of ABA in the drought response of M. sieversii seedlings using a combination of exogenous ABA and the ABA biosynthesis inhibitor fluridone. Plants were subjected to four treatments: CK, PEG (20% PEG-6000), PEG+ABA (100 μM ABA) and PEG+FLU (100 μM fluridone). The results showed that ABA application significantly reduced the wilting rate by 45.53% and electrolyte leakage by 20.50% compared to the PEG treatment. Furthermore, it alleviated the decline in fresh weight and relative water content while reducing the accumulation of starch, sucrose, glucose, and fructose after seven days of stress. Conversely, FLU application intensified the adverse effects of drought. RNA-Seq analysis of the PEG+ABA vs. PEG comparison identified 5642 differentially expressed genes (DEGs), with significant enrichment in the starch and sucrose metabolism pathway, photosynthesis, carbon fixation, and MAPK signaling pathways. Exogenous ABA up-regulated BGLU23 while down-regulating BAM1. In contrast, no significant changes in their expression were observed under FLU treatment, suggesting their likely regulation in an ABA-dependent manner. In summary, ABA enhances osmotic-stress tolerance in M. sieversii through multiple pathways, among which starch and sucrose metabolism may represent a core and highly responsive regulatory pathway. Functional validation of key candidate genes BAM1 and BGLU23 remains an important direction for future investigation. These findings provide a theoretical basis for breeding drought-resistant apple rootstocks and for understanding ABA-mediated osmotic-stress tolerance mechanisms. Full article
(This article belongs to the Special Issue Genome Alignment and Regulatory Genomics in Horticultural Crops)
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19 pages, 4265 KB  
Article
Establishing a Virus-Free Rapid Propagation System for Strawberry ‘Miaoxiang 7’ Through Anther Culture
by Runyu Tian, Shanxin Chen, Jingru Guo, Ke Liu, Zhaoyang Li, Lixiang Meng, Xiaoyue Zhang, Shanshan Gao, Huitian Wei, Jingjing Luo and Futian Peng
Horticulturae 2026, 12(2), 227; https://doi.org/10.3390/horticulturae12020227 - 12 Feb 2026
Cited by 1 | Viewed by 1118
Abstract
Shoot tip culture is currently the most widely used method for strawberry virus elimination, yet its efficiency has approached the theoretical limit of 80–85%. While anther culture offers a higher virus-free rate, it faces the technical bottleneck of low callus differentiation rates. To [...] Read more.
Shoot tip culture is currently the most widely used method for strawberry virus elimination, yet its efficiency has approached the theoretical limit of 80–85%. While anther culture offers a higher virus-free rate, it faces the technical bottleneck of low callus differentiation rates. To address this issue, this study used ‘Miaoxiang 7’ strawberry anthers as explants and systematically optimized key culture parameters. Different combinations of cytokinins and auxins were tested across various culture stages—including callus induction, adventitious bud differentiation from callus, proliferation, and rooting—to determine the most efficient plant growth regulator (PGR) formulations. This approach enhanced both the callus induction rate and differentiation efficiency. The regenerated plants obtained in this study achieved a virus-free rate of 98.39%. Flow cytometric ploidy analysis revealed that octoploids constituted the highest proportion, reaching 73.64%, among the regenerated plants. SSR molecular marker analysis indicated a genetic similarity coefficient of 0.9778–1.0000 between the regenerated plants and the maternal parent. Virus-free treatment holds potential for enhancing physiological growth indicators and fruit quality, demonstrating advantages in certain key metrics such as leaf area and soluble solids content. This technological system provides a viable approach for obtaining virus-free plants through anther culture, overcoming the technical limitation of low callus differentiation rates in anther culture. It offers reliable technical support for the sustainable development of the strawberry industry. Full article
(This article belongs to the Special Issue Genome Alignment and Regulatory Genomics in Horticultural Crops)
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