Genetic Improvement for Horticultural Plants

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (10 July 2021) | Viewed by 11199

Special Issue Editors


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Guest Editor
DISAFA Plant Genetics, University of Torino, 10095 Grugliasco, Italy
Interests: genomics; bioinformatics; quantitative trait locus (QTL); next-generation sequencing (NGS); genome-wide association selection (GWAS) and mapping; genotyping-by-sequencing (GBS); molecular assisted selection (MAS)
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
1. Department of Biotechnology, Institute for Conservation and Improvement of Valencian Agrodiversity (COMAV), School of Agricultural Engineering and Environment (ETSIAMN), Vera Campus, Polytechnic University of Valencia (UPV), Camino de Vera s/n, Building 8E, 46022 Valencia, Spain
2. Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
Interests: plant breeding; introgression breeding; crop wild relatives (CWRs); solanaceae vegetable crops; genomics; genetics; molecular markers; genetic mapping
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo (LO), Italy
Interests: Introgression breeding; molecular markers; Quantitative trait locus (QTL); eggplant; gene expression; crop improvement

Special Issue Information

Dear Colleagues,

The world population is projected to reach about 9 billion people in 2050, which in turn means that market demand for food will continue to grow. These issues are even more heightened by global warming, which is changing the Earth’s climate with already visible negative effects on the growth and reproductive success of crops, as well as the onset and spread of new pests and diseases.

The identification and selection of better-performing and resilient genotypes related to biotic and abiotic stresses, as well as to agronomic-related traits, can be exploited by means of different approaches, including a more traditional gene/QTL (including metabolic and expression quantitative trait loci (mQTL/eQTL)) mapping from inter- and intraspecific bi-parental crosses or quantitative trait nucleotides (QTNs) mapping by applying genome-wide association (GWA) studies, which takes advantage of multiple rounds of historical recombination in multiple accessions of direct relevance to crop improvement.

In recent years, the advent of next-generation sequencing (NGS) technologies has made available genetic and genomic tools and high-quality whole-genome sequences for several crops. Furthermore, several methodologies have been developed to identify single nucleotide polymorphism (SNP), including RAD-Seq/GBS, single primer enrichment technology (SPET), amplicon-based NGS, as well as the re-sequencing of several genotypes. This, combined with high-throughput phenotyping, has supported both traditional bi-parental QTL mapping, as well as GWA studies in crops.

This Special Issue welcomes original, reviews and explorative articles that cover current knowledge and methods that foster the genetic improvement of horticultural plants, with a special emphasis on mapping and association studies. New approaches that facilitate the dissection of important domestication and agronomic traits in horticulture crops are also welcome.

Prof. Dr. Lorenzo Barchi
Dr. Pietro Gramazio
Dr. Laura Toppino
Guest Editors

Manuscript Submission Information

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Keywords

  • Genetic mapping 
  • GWAS 
  • QTLs and QTNs 
  • Next-generation sequencing 
  • Horticulturals 
  • Omics

Published Papers (3 papers)

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Research

15 pages, 1391 KiB  
Article
QTL Analysis of Stem Elongation and Flowering Time in Lettuce Using Genotyping-by-Sequencing
by O New Lee, Keita Fukushima, Han Yong Park and Saneyuki Kawabata
Genes 2021, 12(6), 947; https://doi.org/10.3390/genes12060947 - 21 Jun 2021
Cited by 5 | Viewed by 2796
Abstract
Lettuce plants tend to undergo floral initiation by elongation of flower stalks (bolting) under high-temperature and long-day conditions, which is a serious problem for summer lettuce production. Our objective was to generate a high-density genetic map using SNPs obtained from genotyping-by-sequencing (GBS) analysis [...] Read more.
Lettuce plants tend to undergo floral initiation by elongation of flower stalks (bolting) under high-temperature and long-day conditions, which is a serious problem for summer lettuce production. Our objective was to generate a high-density genetic map using SNPs obtained from genotyping-by-sequencing (GBS) analysis of F5 recombinant inbred lines (RILs) and to map QTLs involved in stem growth and flowering time in lettuce. A set of 127 intra-specific RIL mapping populations derived from a cross between two varieties, green and red leaf lettuce, were used to identify QTLs related to the number of days from sowing to bolting (DTB), to flowering of the first flower (DTF), to seed-setting of the first flower (DTS), and the total number of leaves (LN), plant height (PH), and total number of branches of main inflorescence (BN) for two consecutive years. Of the 15 QTLs detected, one that controls DTB, DTF, DTS, LN, and PH detected on LG 7, and another QTL that controls DTF, DTS, and PH detected on LG 1. Analysis of the genomic sequence corresponding to the QTL detected on LG 7 led to the identification of 22 putative candidate genes. A consistent QTL related to bolting and flowering time, and corresponding candidate genes has been reported. This study will be valuable in revealing the genetic basis of stem growth and flowering time in lettuce. Full article
(This article belongs to the Special Issue Genetic Improvement for Horticultural Plants)
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18 pages, 3991 KiB  
Article
Discovery of a Major QTL Controlling Trichome IV Density in Tomato Using K-Seq Genotyping
by Estefanía Mata-Nicolás, Javier Montero-Pau, Esther Gimeno-Paez, Ana García-Pérez, Peio Ziarsolo, José Blanca, Esther van der Knaap, María José Díez and Joaquín Cañizares
Genes 2021, 12(2), 243; https://doi.org/10.3390/genes12020243 - 8 Feb 2021
Cited by 12 | Viewed by 3405
Abstract
Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Therefore, for sustainable management of this crop, [...] Read more.
Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Therefore, for sustainable management of this crop, breeding programs could incorporate some natural defense mechanisms, such as those afforded by trichomes, present in certain Solanum species. We have identified a S. pimpinellifolium accession with very high density of this type of trichomes. This accession was crossed with a S. lycopersicum var. cerasiforme and a S. lycopersicum var. lycopersicum accessions, and the two resulting F2 populations have been characterized and genotyped using a new genotyping methodology, K-seq. We have been able to build an ultra-dense genetic map with 147,326 SNP markers with an average distance between markers of 0.2 cm that has allowed us to perform a detailed mapping. We have used two different families and two different approaches, QTL mapping and QTL-seq, to identify several QTLs implicated in the control of trichome type IV developed in this accession on the chromosomes 5, 6, 9 and 11. The QTL located on chromosome 9 is a major QTL that has not been previously reported in S. pimpinellifolium. This QTL could be easily introgressed in cultivated tomato due to the close genetic relationship between both species. Full article
(This article belongs to the Special Issue Genetic Improvement for Horticultural Plants)
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15 pages, 1677 KiB  
Article
Detection of Quantitative Trait Loci (QTL) Associated with the Fruit Morphology of Tomato
by Pragya Adhikari, James McNellie and Dilip R. Panthee
Genes 2020, 11(10), 1117; https://doi.org/10.3390/genes11101117 - 24 Sep 2020
Cited by 12 | Viewed by 4013
Abstract
Tomato (Solanum lycopersicum L.) is the second most-consumed vegetable in the world. The market value and culinary purpose of tomato are often determined by fruit size and shape, which makes the genetic improvement of these traits a priority for tomato breeders. The [...] Read more.
Tomato (Solanum lycopersicum L.) is the second most-consumed vegetable in the world. The market value and culinary purpose of tomato are often determined by fruit size and shape, which makes the genetic improvement of these traits a priority for tomato breeders. The main objective of the study was to detect quantitative trait loci (QTL) associated with the tomato fruit shape and size. The use of elite breeding materials in the genetic mapping studies will facilitate the detection of genetic loci of direct relevance to breeders. We performed QTL analysis in an intra-specific population of tomato developed from a cross between two elite breeding lines NC 30P × NC-22L-1(2008) consisting of 110 recombinant inbred lines (RIL). The precision software Tomato Analyzer (TA) was used to measure fruit morphology attributes associated with fruit shape and size traits. The RIL population was genotyped with the SolCAP 7720 SNP array. We identified novel QTL controlling elongated fruit shape on chromosome 10, explaining up to 24% of the phenotypic variance. This information will be useful in improving tomato fruit morphology traits. Full article
(This article belongs to the Special Issue Genetic Improvement for Horticultural Plants)
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