Special Issue "Advances in Molecular Breeding of Vegetable 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: 31 October 2021.

Special Issue Editor

Prof. Dr. Yuyang Zhang
E-Mail Website
Guest Editor
Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Interests: the vegetable quality (nutrition, flavor) formation and its regulation; molecular biology and biotechnology applied in vegetable crops; vegetable germplasm enhancement and molecular breeding
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Vegetable crops provide the vast majority of vitamins, minerals, antioxidants and bioactivity substances that are necessary for humans—they are insufficient in grains or meat. With the demands for better and healthier diets, consumers require more vegetables and fruits. The increasing genome data and breeding technology facilitate the genetic improvement of vegetables on yield and tolerance to disease and abiotic stress. Nowadays, consumers demand more nutrition and taste from vegetables. Genes and genomes underlying the important horticultural traits—e.g., yield, quality, disease resistance, and stress tolerance—have been extensively investigated, which paves the way for the molecular breeding of vegetable crops.

Therefore, in this Special Issue of “Molecular Breeding of Vegetable Crops”, we aim to provide an updated review of recent advances in genes and genetics, and the molecular breeding of vegetables. Indeed, molecular breeding technology has been widely applied in vegetable improvement. We look forward to receiving your manuscripts (reviews and research articles) and are eager to share your knowledge within the research and industry communities.

Prof. Dr. Yuyang Zhang
Guest Editor

Manuscript Submission Information

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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 1400 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

  • genes
  • genetics
  • breeding
  • vegetable crop
  • improvement
  • yield
  • quality
  • disease resistance
  • stress tolerance

Published Papers (8 papers)

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Research

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Article
Identification of Major Loci and Candidate Genes for Anthocyanin Biosynthesis in Broccoli Using QTL-Seq
Horticulturae 2021, 7(8), 246; https://doi.org/10.3390/horticulturae7080246 - 13 Aug 2021
Viewed by 244
Abstract
Anthcyanins determine the colors of flowers, fruits, and purple vegetables and act as important health-promoting antioxidants. BT 126 represents a broccoli variety with a high content of anthocyanins (5.72 mg/g FW). Through QTL-seq bulk segregant analysis, the present study aimed to determine the [...] Read more.
Anthcyanins determine the colors of flowers, fruits, and purple vegetables and act as important health-promoting antioxidants. BT 126 represents a broccoli variety with a high content of anthocyanins (5.72 mg/g FW). Through QTL-seq bulk segregant analysis, the present study aimed to determine the quantitative trait loci (QTLs) involved in anthocyanin biosynthesis in the F2 population (n = 302), which was obtained by crossing BT 126 with a non-anthocyanin-containing SN 60. The whole-genome resequencing of purple (n = 30) and green (n = 30) bulk segregates detected ~1,117,709 single nucleotide polymorphisms (SNPs) in the B. oleracea genome. Two QTLs, tightly correlated with anthocyanin biosynthesis (p < 0.05), were detected on chromosomes 7 (BoPur7.1) and 9 (BoPur9.1). The subsequent high-resolution mapping of BoPur9.1 in the F2 population (n = 280) and F3 population (n = 580), with high-throughput genotyping of SNPs technology, narrowed the major anthocyanin biosynthesis QTL region to a physical distance of 73 kb, containing 14 genes. Among these genes, Bo9g174880, Bo9g174890, and Bo9g174900 showed high homology with AT5G07990 (gene encoding flavonoid 3′ hydroxylase), which was identified as a candidate gene for BoPur9.1. The expression of BoF3’H in BT 126 was significantly higher than that in SN60. Multiple biomarkers, related to these QTLs, represented potential targets of marker-assisted selection (MAS) foranthocyanin biosynthesis in broccoli. The present study provided genetic insights into the development of novel crop varieties with augmented health-promoting features and improved appearance. Full article
(This article belongs to the Special Issue Advances in Molecular Breeding of Vegetable Crops)
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Article
High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in Capsicum frutescens
Horticulturae 2021, 7(7), 187; https://doi.org/10.3390/horticulturae7070187 - 08 Jul 2021
Viewed by 480
Abstract
Capsicum frutescens, one of the domesticated species of pepper grown worldwide, is thought to be highly advantageous due to its strong resistance against plant pathogenesis, high productivity, and intense aroma. However, a shortage of molecular markers limits the efficiency and accuracy of [...] Read more.
Capsicum frutescens, one of the domesticated species of pepper grown worldwide, is thought to be highly advantageous due to its strong resistance against plant pathogenesis, high productivity, and intense aroma. However, a shortage of molecular markers limits the efficiency and accuracy of genetic breeding for pepper. With the newly developed next-generation sequencing technology, genome sequences of C. frutescens can be generated, which are now available for identifying SSR markers via data mining. In this study, a total of 278,425 SSRs were detected from the pepper genome using MISA software. It was observed that trinucleotides were the dominant repeat motif. This was followed by dinucleotides, tetranucleotides, pentanucleotides, and the hexanucleotides repeat types. (AT)n (TTG)n (AAAT)n (AAATA)n (TATAGA)n is known to be the most common repeat motifs corresponding to dinucleotide to hexanucleotide repeats, respectively. In addition, a total of 240 SSR primers evenly distributed over all 12 chromosomes were designed and screened against 8 C. frutescens cultivars. Of these, 33 SSR markers that have high polymorphism, have been scrutinized for 147 accessions from 25 countries. The dendrogram constructed clustered these accessions into seven major groups. The groups were found to be consistent with their origins. The results obtained in this study provided resources of SSR molecular markers and insight into genetic diversity of the C. frutescens. Full article
(This article belongs to the Special Issue Advances in Molecular Breeding of Vegetable Crops)
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Article
Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)
Horticulturae 2021, 7(6), 149; https://doi.org/10.3390/horticulturae7060149 - 10 Jun 2021
Viewed by 562
Abstract
Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, [...] Read more.
Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant. Full article
(This article belongs to the Special Issue Advances in Molecular Breeding of Vegetable Crops)
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Article
Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species
Horticulturae 2021, 7(6), 143; https://doi.org/10.3390/horticulturae7060143 - 08 Jun 2021
Viewed by 577
Abstract
Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif [...] Read more.
Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species. Full article
(This article belongs to the Special Issue Advances in Molecular Breeding of Vegetable Crops)
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Article
CaHSP18.1a, a Small Heat Shock Protein from Pepper (Capsicum annuum L.), Positively Responds to Heat, Drought, and Salt Tolerance
Horticulturae 2021, 7(5), 117; https://doi.org/10.3390/horticulturae7050117 - 18 May 2021
Viewed by 466
Abstract
Pepper is a thermophilic crop, shallow-rooted plant that is often severely affected by abiotic stresses such as heat, salt, and drought. The growth and development of pepper is seriously affected by adverse stresses, resulting in decreases in the yield and quality of pepper [...] Read more.
Pepper is a thermophilic crop, shallow-rooted plant that is often severely affected by abiotic stresses such as heat, salt, and drought. The growth and development of pepper is seriously affected by adverse stresses, resulting in decreases in the yield and quality of pepper crops. Small heat shock proteins (s HSPs) play a crucial role in protecting plant cells against various stresses. A previous study in our laboratory showed that the expression level of CaHSP18.1a was highly induced by heat stress, but the function and mechanism of CaHSP18.1a responding to abiotic stresses is not clear. In this study, we first analyzed the expression of CaHSP18.1a in the thermo-sensitive B6 line and thermo-tolerant R9 line and demonstrated that the transcription of CaHSP18.1a was strongly induced by heat stress, salt, and drought stress in both R9 and B6, and that the response is more intense and earlier in the R9 line. In the R9 line, the silencing of CaHSP18.1a decreased resistance to heat, drought, and salt stresses. The silencing of CaHSP18.1a resulted in significant increases in relative electrolyte leakage (REL) and malonaldehyde (MDA) contents, while total chlorophyll content decreased under heat, salt, and drought stresses. Overexpression analyses of CaHSP18.1a in transgenic Arabidopsis further confirmed that CaHSP18.1a functions positively in resistance to heat, drought, and salt stresses. The transgenic Arabidopsis had higherchlorophyll content and activities of superoxide dismutase, catalase, and ascorbate peroxidase than the wild type (WT). However, the relative conductivity and MDA content were decreased in transgenic Arabidopsis compared to the wild type (WT). We further showed that the CaHSP18.1a protein is localized to the cell membrane. These results indicate CaHSP18.1a may act as a positive regulator of responses to abiotic stresses. Full article
(This article belongs to the Special Issue Advances in Molecular Breeding of Vegetable Crops)
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Article
Comparative Transcriptome Analysis Reveals Different Low-Nitrogen-Responsive Genes in Pepper Cultivars
Horticulturae 2021, 7(5), 110; https://doi.org/10.3390/horticulturae7050110 - 13 May 2021
Viewed by 566
Abstract
The molecular mechanisms underlying the variation in N-use efficiency (NUE) in pepper (Capsicum annuum L.) genotypes are poorly understood. In this work, two genotypes (750-1, low-N tolerant; ZCFB, low-N sensitive) with contrasting low-N tolerance were selected from 100 pepper cultivars on the [...] Read more.
The molecular mechanisms underlying the variation in N-use efficiency (NUE) in pepper (Capsicum annuum L.) genotypes are poorly understood. In this work, two genotypes (750-1, low-N tolerant; ZCFB, low-N sensitive) with contrasting low-N tolerance were selected from 100 pepper cultivars on the basis of their relative leaf areas, shoot dry weights, root dry weights, and plant dry weights at the seedling stage. Subsequently, using RNA-Seq, the transcriptome of these two pepper genotypes under N starvation for 28 days was analyzed. We detected 2621/2470 and 3936/4218 different expressed genes (DEGs) in the leaves/roots of 750-1 and ZCFB, respectively. The changes in the expression of basic N metabolism genes were similar between 750-1 and ZCFB. However, different DEGs not directly involved in N metabolism were identified between the 750-1 and ZCFB cultivars. In 750-1, 110 unique DEGs were detected in the leaves, of which 103 were down-regulated, including genes associated with protein metabolism, photosynthesis, secondary metabolism, cell wall metabolism, stress response, and disease resistance. In ZCFB, 142 unique DEGs were detected in the roots, of which 117 were up-regulated, resulting in enhancement of processes such as protein degradation, secondary metabolites synthesis, lipid metabolism, endocytosis, the tricarboxylic acid cycle (TCA), transcriptional regulation, stress response, and disease resistance. Our results not only facilitate an understanding of the different regulatory process in low-N-tolerant and low-N-sensitive pepper cultivars, but also provide abundant candidate genes for improving the low-N tolerance of pepper cultivars. Full article
(This article belongs to the Special Issue Advances in Molecular Breeding of Vegetable Crops)
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Article
Generation of a High-Density Genetic Map of Pepper (Capsicum annuum L.) by SLAF-seq and QTL Analysis of Phytophthora capsici Resistance
Horticulturae 2021, 7(5), 92; https://doi.org/10.3390/horticulturae7050092 - 01 May 2021
Viewed by 618
Abstract
Pepper (Capsicum annuum L.) is an economically significant global crop and condiment. Its yield can be severely reduced by the oomycete plant pathogen, Phytophthora capsici (P. capsici). Here, a high-density genetic map was created with a mapping panel of F [...] Read more.
Pepper (Capsicum annuum L.) is an economically significant global crop and condiment. Its yield can be severely reduced by the oomycete plant pathogen, Phytophthora capsici (P. capsici). Here, a high-density genetic map was created with a mapping panel of F2 populations obtained from 150 individuals of parental lines PI201234 and 1287 and specific-locus amplified fragment sequencing (SLAF) that was then utilized to identify loci that are related to resistance to P. capsici. The sequencing depth of the genetic map was 108.74-fold for the male parent, 126.25-fold for the female parent, and 22.73-fold for the offspring. A high-resolution genetic map consisting of 5565 markers and 12 linkage groups was generated for pepper, covering 1535.69 cM and an average marker distance of 0.28 cM. One major quantitative trait locus (QTL) for the P. capsici resistance (CQPc5.1) was identified on Chr05 that explained the observed 11.758% phenotypic variance. A total of 23 candidate genes located within the QTL CQPc5.1 interval were identified, which included the candidate gene Capana05g000595 that encodes the RPP8-like protein as well as two candidate genes Capana05g000596 and Capana05g000597 that encodes a RPP13-like protein. Quantitative reverse-transcription PCR (qRT-PCR) revealed higher expression levels of Capana05g000595, Capana05g000596, and Capana05g000597 in P. capsici resistance accessions, suggesting their association with P. capsici resistance in pepper. Full article
(This article belongs to the Special Issue Advances in Molecular Breeding of Vegetable Crops)
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Review

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Review
CRISPR-Cas9 Gene Editing for Fruit and Vegetable Crops: Strategies and Prospects
Horticulturae 2021, 7(7), 193; https://doi.org/10.3390/horticulturae7070193 - 14 Jul 2021
Viewed by 536
Abstract
Fruit and vegetable crops are rich in dietary fibre, vitamins and minerals, which are vital to human health. However, many biotic stressors (such as pests and diseases) and abiotic stressors threaten crop growth, quality, and yield. Traditional breeding strategies for improving crop traits [...] Read more.
Fruit and vegetable crops are rich in dietary fibre, vitamins and minerals, which are vital to human health. However, many biotic stressors (such as pests and diseases) and abiotic stressors threaten crop growth, quality, and yield. Traditional breeding strategies for improving crop traits include a series of backcrosses and selection to introduce beneficial traits into fine germplasm, this process is slow and resource-intensive. The new breeding technique known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9) has the potential to improve many traits rapidly and accurately, such as yield, quality, disease resistance, abiotic stress tolerance, and nutritional aspects in crops. Because of its simple operation and high mutation efficiency, this system has been applied to obtain new germplasm resources via gene-directed mutation. With the availability of whole-genome sequencing data, and information about gene function for important traits, CRISPR-Cas9 editing to precisely mutate key genes can rapidly generate new germplasm resources for the improvement of important agronomic traits. In this review, we explore this technology and its application in fruit and vegetable crops. We address the challenges, existing variants and the associated regulatory framework, and consider future applications. Full article
(This article belongs to the Special Issue Advances in Molecular Breeding of Vegetable Crops)
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