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Germplasm Resource Identification and Genetic Improvement of Horticultural Crop

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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: closed (25 December 2023) | Viewed by 12916

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Special Issue Editors

Prof. Dr. Liwang Liu

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Guest Editor

College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Interests: genetics and breeding of vegetable crops; applied genomics; germplasm enhancement and utilization; biotechnology of vegetable crops
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Yangyong Zhang

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Guest Editor

Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
Interests: vegetable breeding; genetics and genomics; marker‑assisted selection; gene/QTL mapping; distant hybridization
Special Issues, Collections and Topics in MDPI journals

Dr. Juxun Wu

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Guest Editor

College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
Interests: fruit tree genetics and breeding; fruit development and ripening biology; functional genomics

Special Issue Information

Dear Colleagues,

Agriculture is fundamental to society, while seeds are the most important aspect of agriculture. Germplasm resources are the basis of genetic material for plant breeding and crop improvement. Germplasm resources can be better enhanced and genetic information can be completely understood by germplasm identification. Furthermore, in certain technologies, including heterosis utilization, genotyping, marker-assisted selection, high-throughput phenotyping, molecular design breeding and gene editing, genomic selection could provide a constant driving force for innovating and expanding germplasm resources. In addition, the development of new methods for upgrading and innovating germplasms, which is vital for accelerating the procedure of breeding innovation and developing modern agriculture should be encouraged and widely studied by more researchers.

In order to make better use of the germplasms of horticultural crops and promote the development and innovation of breeding technology, Horticulturae is launching a Special Issue on the topic of germplasm identification and genetic improvements of horticultural crops and is beginning to collect necessary high-quality articles.

This Special Issue is entitled “Germplasm Resource Identification and Genetic Improvement of Horticultural Crop”. The topics of submissions to this Special Issue include (but are not limited to):

Accurately identifying the germplasm resources of relevant horticultural crops, deeply understanding the characteristics of different varieties of the same species, and make better use of germplasm resources;
Utilization of heterosis methods (utilization of self-incompatibility, utilization of male sterile lines, etc.) to generate new excellent cultivars;
Application of molecular breeding technology, including gene editing, which can improve horticultural crops and improve adaptability;
Development of speed breeding and other new technologies for improving germplasms, which provides faster and more precise strategies for the breeder.

We sincerely welcome all colleagues in the horticultural industry to contribute manuscripts and share your research progress and general academic views on germplasm resource identification and the genetic improvement of horticultural crops. The Special Issue accepts research papers and reviews related to the subject. We are looking forward to your excellent contributions to Horticulturae.

Prof. Dr. Liwang Liu
Prof. Dr. Yangyong Zhang
Dr. Juxun Wu
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 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. 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

germplasm resources
precise identification of the germplasm resources
heterosis
speed breeding
gene editing
genomic selection
marker-assisted selection

Published Papers (9 papers)

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Research

11 pages, 1295 KiB

Open AccessEditor’s ChoiceArticle

Screening and Selection for Herbicide Tolerance among Diverse Tomato Germplasms

by Gourav Sharma, Swati Shrestha, Te-Ming Tseng and Sanju Shrestha

Horticulturae 2023, 9(12), 1354; https://doi.org/10.3390/horticulturae9121354 - 18 Dec 2023

Viewed by 1116

Abstract

Solanum lycopersicum, the domesticated species of tomato, is produced and consumed globally. It is one of the most economically important vegetable crops worldwide. In the commercial production of tomatoes, tomatoes are extremely sensitive to herbicide drifts from row crops in the vicinity. Injury to tomatoes from auxin herbicides and glyphosate can occur at rates as low as 0.01×. This results in a substantial yield reduction, and at high drift rates, plants may not show signs of recovery. With the new herbicide-resistant crop technologies on the market, which include 2,4-D and dicamba-resistant crops, there is an increase in the usage of these herbicides, causing more serious drift problems. There is a diverse germplasm of tomatoes that includes wild relatives which are tolerant to numerous biotic and abiotic stresses. Herbicide/chemical stress is an abiotic stress, and wild tomato accessions may have a natural tolerance to herbicides and other abiotic stresses. In the current study, diverse tomato genotypes consisting of 110 accessions representing numerous species, Solanum habrochaites, S. cheesmaniae, S. pimpinellifolium, S. chilense, S. lycopersicum, S. pimpinellifolium, S. galapagense, S. chimelewskii, S. corneliomulleri, S. neorickii, and S. lycopersicoides, were used for screening drift rate herbicide tolerance. The herbicides tested included simulated drift rates of 2,4-D, dicamba, glyphosate, quinclorac, aminopyralid, aminocyclopyrachlor, and picloram. The visual injury rating of each accession for each herbicide treatment was taken 7, 14, 21, and 28 days after treatment (DAT) on a scale of 0–100%. Numerous accessions were found to have minimal injury (less than 20%) for each of the herbicides tested; nine accessions were found for both 2,4-D and glyphosate, eleven for dicamba, five for quinclorac, eight for aminocyclopyrachlor and two for both aminopyralid and picloram at 28 DAT. The identification of genotypes with a higher herbicide tolerance will provide valuable genetic resources for the development of elite tomato varieties that can resist herbicide injury and produce competitive yields. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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17 pages, 865 KiB

Open AccessArticle

Genetic Variability and Diversity in Red Onion (Allium cepa L.) Genotypes: Elucidating Morpho-Horticultural and Quality Perspectives

by Arshad Amir, Amit Baran Sharangi, Solanki Bal, Tarun Kumar Upadhyay, Mohd Suhail Khan, Irfan Ahmad, Nadiyah M. Alabdallah, Mohd Saeed and Umesh Thapa

Horticulturae 2023, 9(9), 1005; https://doi.org/10.3390/horticulturae9091005 - 5 Sep 2023

Viewed by 1356

Abstract

Onion (Allium cepa L.) is a prominent spice and vegetable crop farmed commercially worldwide. Variability is viewed as a key signal for any red onion enhancement effort. The current study was, therefore, carried out to learn about genetic variability and diversity among selected genotypes of 20 red onions at the C Block Farm, Bidhan Chandra Krishi Viswavidyalaya, India, during the winter (rabi) season of 2021–2022, in Randomized Complete Block Design (RCBD) with three replications. The characters, viz., average weight of bulbs (kg), neck thickness (cm), total soluble solids (°Brix), total sugar (%), and reducing sugar (%) demonstrated high heritability (97.38–99.97%) coupled with high genetic gain. Such traits were the least influenced by environmental effects, and additive gene action played a pivotal role in the manifestation of such characters. Traits with high heritability values (51.37–67.94%) demonstrate that the observed variability was under genetic control and provide an enormous range of possibilities for accomplishing selection depending on their phenotypic performances. For traits with moderate heritability, viz., bolting (%) and doubling (%), selection would be less effective but can still be given great importance. Based on correlation analysis, the character’s neck thickness, equatorial diameter, and polar diameter unveiled highly positive genetic correlation with the average weight of bulbs (0.120, 0.112; 0.194, 0.210 and 0.120, 0.112 for phenotypic and genotypic correlation coefficient values, respectively), which indicates that the average weight of a bulb would be increased by an increase in such components. According to path coefficient analysis, the equatorial diameter exhibited the most positive direct effect on the average weight of bulbs (0.968), followed by polar diameter (0.687) and neck thickness (0.159). A wide range of variations for qualitative traits, including foliage colour, leaf width, foliage behaviour, the degree of leaf waxiness, the shape of the bulb, and bulb skin colour were observed. Based on Mahalanobish D² analysis, the genotypes were divided into four clusters. The highest number of genotypes was found in cluster I (eleven), followed by cluster IV (six genotypes) and cluster II (two genotypes). Cluster III had a single genotype and was monogenic. The study confirmed that a wide genetic variation prevailed in the onion genotypes taken under study, which could thereby be utilized in breeding programmes. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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20 pages, 1047 KiB

Open AccessArticle

Sweet Potato Varietal Selection Using Combined Methods of Multi-Trait Index, Genetic Gain and Stability from Multi-Environmental Evaluations

by Amparo Rosero, William Burgos-Paz, Hernando Araujo, Iván Javier Pastrana-Vargas, Remberto Martínez, Jose-Luis Pérez and Laura Espitia

Horticulturae 2023, 9(9), 974; https://doi.org/10.3390/horticulturae9090974 - 29 Aug 2023

Viewed by 1051

Abstract

Adaptation to several environmental conditions is a challenge for breeders for producing new varieties. Breeders select genotypes which show higher performance according to desired traits compared to the average of a large segregant population. In several crops, the selection index is mainly based on traits such as yield, quality, adequate plant architecture, etc. Therefore, multi-trait selection allows for the identification of genotypes that integrally exhibit a better profile and stability, in addition to the dissection of promising varieties based on their superiority in an evaluated population. In this paper, a multi-trait index included in an R tool named CropInd was used to estimate the agronomic performance of 19 sweet potato genotypes in multi-environmental evaluations (three cycles and eight locations). Here, the multi-trait index incorporated variables such as total and commercial fresh root yield, along with survival percentage, which were used in this study. Simultaneously, stability and genetic gain analysis were included to select superior sweet potato genotypes. Results showed that the CropInd script is a suitable and convenient tool for genotype selection based on multi-trait and multi-environmental data. Indexes for specific environment and general behavior (combining multi-environments) were the main output used for genotype selection. Multi-trait selection index, stability, and genetic gain analysis assisted the phenotypic selection performed by breeders. This study resulted in the selection of 0113-672COR as new variety for the Colombian Caribbean region due to its multi-trait performance and stability. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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15 pages, 601 KiB

Open AccessArticle

Evaluation of Genetic Variability within a Collection of Cumin Genotypes Using RAPD, ISSR, SRAP and SCoT Markers and Variability of In Vitro Callus Induced Therefrom

by Magdi A. A. Mousa, Kamal A. M. Abo-Elyousr and Omer H. M. Ibrahim

Horticulturae 2023, 9(7), 742; https://doi.org/10.3390/horticulturae9070742 - 24 Jun 2023

Cited by 1 | Viewed by 909

Abstract

The availability of adequate information about the documentation and characterization of germplasm is fundamental for any crop improvement program. The importance of cumin as a medicinal plant yet the lack of information about its genetic variability encouraged us to initiate the current study aiming at assessing the genetic variability among 17 cumin genotypes from different geographical regions using four molecular markers (RAPD, ISSR, SRAP and SCoT). Further, the potential of six accessions to induce callus was studied under in vitro conditions on MS and B5 basal media supplemented with various combinations between 2,4-D and kinetin. Our findings showed that combining 87 primers, including 42, 15, 7 and 23 primers of RAPD, ISSR, SCoT and SRAP, respectively, facilitated detecting the relationship among the assessed cumin accessions. A total number of 765 bands were analyzed, among which only 74 bands were polymorphic. The polymorphism was low (9.67%) and varied among and within markers. The SCoT markers exposed the highest average values of polymorphism information content (0.06), resolving power (0.91) and diversity index (0.08), while ISSR induced the highest expected heterozygosity (0.06) and marker index (0.08). The UPGMA dendrogram based on data from all the molecular markers separated the genotypes into three main clusters, with a partial geographic-based relationship among the genotypes. Out of the six accessions evaluated for callus induction in vitro, five were potent to induce callus, with a frequency ranging from 90.4 to 97.5% and no significant differences among the five accessions tested using ANOVA. Two medium combinations showed superior results: MS amended with 2,4-D (4.44 mg/L) + Kin (0.22 mg/L) and B5 with 2,4-D (8.88 mg/L) + Kin (0.22 mg/L). Statistically significant variations in the relative growth rate of the produced callus were detected among accessions, where EG-4 accessions induced the highest values, followed by EG-5. All medium combinations, including 2,4-D alone, exhibited significant superiority compared with those including both 2,4-D and Kin. Our findings exposed low variability among the studied cumin accessions, implying the real need for more effort to assess wider populations from different geographic regions together with the need for reliable diversification programs. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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17 pages, 3619 KiB

Open AccessArticle

Genome-Wide Identification of the RsSWEET Gene Family and Functional Analysis of RsSWEET17 in Root Growth and Development in Radish

by Xiaoli Zhang, Yang Cao, Ruixian Xin, Liang Xu, Yan Wang, Lun Wang, Yinbo Ma and Liwang Liu

Horticulturae 2023, 9(6), 698; https://doi.org/10.3390/horticulturae9060698 - 14 Jun 2023

Cited by 1 | Viewed by 1065

Abstract

SWEET (Sugars Will Eventually be Exported Transporter) genes play essential roles in various biological processes, including phloem loading, sugar efflux, plant development and stress response. In this study, a total of 33 RsSWEET gene members were identified in the radish genome. They could be divided into four subfamilies and are distributed on eight radish chromosomes. Cis-acting regulatory element analysis indicated that these RsSWEET genes were potentially involved in the radish growth and development and stress response process, including circadian control and light response and responses to numerous stresses, including low-temperature and drought stress. Transcriptome data analysis revealed that a number of RsSWEET genes exhibited specific expression patterns in different tissues and developmental stages of radish. Moreover, several RsSWEET genes (e.g., RsSWEET2a, RsSWEET3a, RsSWEET16b and RsSWEET17) showed differential expression profiles under various abiotic stresses, including cold, heat, salt, Cd and Pb stress. Remarkably, the RsSWEET17 was specifically expressed in the cambium of radish. RsSWEET17 was heterologously expressed in yeast strain EBY.VW4000, which suggested that it has the ability to transport sugar. Notably, RsSWEET17-overexpressing Arabidopsis plants exhibited excessive root length, greater fresh weight and higher soluble sugar content (SSC) accumulation compared with wild-type (WT) plants, indicating that RsSWEET17 might positively regulate radish taproot development by strategically manipulating sugar accumulation. Collectively, these results clarify the molecular mechanisms underlying RsSWEET-mediated sugar accumulation and root growth and development in radish. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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12 pages, 1452 KiB

Open AccessArticle

Molecular Characterization, Population Structure Analysis, and Association Mapping of Turkish Parsley Genotypes Using iPBS Markers

by Ömer Faruk Coşkun

Horticulturae 2023, 9(3), 336; https://doi.org/10.3390/horticulturae9030336 - 3 Mar 2023

Cited by 4 | Viewed by 1346

Abstract

Parsley (Petroselinum crispum Mill.) is a vegetable that has many benefits for human health, and its cultivation is increasing. In order to carry out breeding studies in parsley, genotypes should be characterized in terms of some characteristics. In this study, some phytochemical properties of 18 different parsley genotypes were revealed, and their genetic diversity was determined with the iPBS (Inter Primary Binding Site) marker system. In the study, the polymorphism rate was 31.9%, the mean PIC (Polymorphic Information Content) was 0.17, and the similarity coefficients were between 0.87 and 0.99. The number of subpopulations was determined as two, and 10 markers were detected at expression levels of 19–33% related to phytochemical properties. The results of this study show that there is a phytochemical and genetic variation in parsley. Parsley genotypes with certain phytochemical properties and genetic structures can be used more effectively in breeding programs. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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14 pages, 3541 KiB

Open AccessArticle

Genome-Wide Characterization and Expression Profiling of NBS-LRR-Encoding Gene Family in Radish (Raphanus sativus L.)

by Liang Xu, Wei Zhang, Mingjia Tang, Xiaoli Zhang, Juanjuan Wang, Yan Wang and Liwang Liu

Horticulturae 2022, 8(12), 1164; https://doi.org/10.3390/horticulturae8121164 - 8 Dec 2022

Viewed by 1370

Abstract

Radish (Raphanus sativus L.) is an important root vegetable crop that is easily infected by various pathogens that result in decreased yield and quality. Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes play vital roles in resisting pathogen infection in plants. However, the genome-wide characterization and functional roles of NBS-LRR genes remain largely unexplored in radish. Here, a total of 187 RsNBS-LRR genes were identified at the whole-genome level in radish, among which 80 RsNBS-LRR genes were unevenly distributed on nine radish chromosomes. Interestingly, 15 clusters containing 36 RsNBS-LRR genes occurred in eight chromosomes. RNA-Seq data showed that several RsNBS-LRR genes exhibited significant differential expression profiles in different radish tissues. Moreover, a range of cis-acting regulatory elements associated with ABA, MeJA, or SA were identified in the promoter region of some RsNBS-LRR genes. RT-qPCR analysis showed that the expression of a few RsNBS-LRR genes (e.g., RsNBS021 and RsNBS163) was significantly induced under Peronospora parasitica infection and/or ABA treatment, indicating that they might play critical roles in ABA-dependent defense resistance processes. These results could enhance our understanding of the evolutionary relationship of RsNBS-LRR genes and facilitate the genetic manipulation of disease resistance in radish breeding programs. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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13 pages, 3214 KiB

Open AccessArticle

Genome-Wide Identification of Sucrose Transporter Genes and Functional Analysis of RsSUC1b in Radish (Raphanus sativus L.)

by Xiaofeng Zhu, Xiaoli Zhang, Yang Cao, Ruixian Xin, Yinbo Ma, Lun Wang, Liang Xu, Yan Wang, Rui Liu and Liwang Liu

Horticulturae 2022, 8(11), 1058; https://doi.org/10.3390/horticulturae8111058 - 10 Nov 2022

Cited by 3 | Viewed by 1728

Abstract

In most higher plants, sucrose is the significant form of carbohydrate for long-distance transportation. Sucrose transporters/sucrose carriers (SUTs/SUCs) are involved in the loading and unloading of sucrose in phloem and play an important role in the growth and development of plants. In this study, 12 RsSUC genes were first identified from the radish genome, and their phylogenetic relationships, gene structure, and conserved motifs were further analyzed. RT-qPCR results indicated that RsSUC genes exhibited various expression patterns in different tissues and development stages of the radish. Overexpression of RsSUC1b in Arabidopsis significantly improved the uptake efficiency of exogenous sucrose, and promoted leaves and lateral root growth. In addition, the transgenic plants flowered significantly earlier than wild-type (WT) plants, and the soluble sugar contents (SSCs) including sucrose, glucose, and fructose in the mature leaves and pods were increased. It could be inferred that RsSUC1b is a plasma membrane sucrose transporter and plays a vital role in sucrose transportation and sugar accumulation during plant growth and development. These findings provided novel insights into the biological function of RsSUC genes and facilitate dissecting the molecular mechanism underlying sugar transport during radish development. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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14 pages, 4640 KiB

Open AccessArticle

Genome-Wide Identification, Evolution, and Expression Analysis of the TCP Gene Family in Rose (Rosa chinensis Jacq.)

by Yi Hou, Chunguo Fan, Jingrui Sun, Yufei Chang, Jun Lu, Jingjing Sun, Changquan Wang and Jinyi Liu

Horticulturae 2022, 8(10), 961; https://doi.org/10.3390/horticulturae8100961 - 18 Oct 2022

Cited by 2 | Viewed by 1795

Abstract

Roses have not only high ornamental and economic values but also cultural importance worldwide. As a plant-specific transcription factor gene family, the TCP (TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR LAND 2) genes have been indicated to be involved in various aspects of plant biological processes, such as leaf morphogenesis and senescence, lateral branching, flower development, stress response and hormone signaling. Currently, TCP genes have been identified and analyzed in many plants, yet there is no systematic analysis in Rosa chinensis. Here, we identified 16 RcTCP genes from R. chinensis genome, which were unevenly distributed in five out of all seven chromosomes. Phylogenetic and structural analyses showed that RcTCP family could be classified into two classes, I (namely PCF) and II, and class II genes can be further divided into CIN and CyC/TB1 subclasses. The different classes of TCP genes were showed to have undergone different evolutionary processes, and genes in the same branch shared similar motifs, gene structures and conserved structural domains. Promoter analysis showed that RcTCPs had many cis-acting elements that are mainly associated with plant growth and development, plant hormones and abiotic/biotic stress responses. Furthermore, the expression levels of RcTCPs under vegetative and reproductive growth and drought stress treatments were analyzed based on public RNA-seq dataset, and it was shown that RcTCPs exhibited serious tissue-specific expression, with most of them dominantly expressed in flowers, leaves and stems, with high levels of expression at different stages of flower and bud differentiation, particularly during petal formation and gametophyte development. The high inducement of seven RcTCP genes from PCF class in drought stress indicated their important roles in biological processes against drought stress. Our results provide valuable information for the evolution and functional characterization of TCP genes in R. chinensis. Full article

(This article belongs to the Special Issue Germplasm Resource Identification and Genetic Improvement of Horticultural Crop)

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