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Marker-Trait Association Analysis in Horticultural Crops
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Marker-Trait Association Analysis in Horticultural Crops

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

Deadline for manuscript submissions: closed (31 October 2020) | Viewed by 10775

Special Issue Editor

Dr. Mario Di Guardo

E-Mail Website
Guest Editor
Department of Agriculture, Food and Environment (Di3A), University of Catania, Via Valdisavoia 5, 95123 Catania, Italy

Special Issue Information

Dear Colleagues,

The world demand for horticultural crop is in continuous increase. Thus, to meet consumers’ expectations, novel cultivars showing enhanced agricultural traits (e.g., fruit quality, yield, resistance to biotic and abiotic stress) must be developed. To this extent, a deep understanding of the genetic basis regulating phenotypes of interest represents an important prerequisite both to understand the trait physiology and for breeding. The rapid advent of high-throughput genotyping platforms enabled the simultaneous interrogation of hundreds of thousands of single nucleotide polymorphisms (SNP) employing a dedicated array or through whole-genome resequencing (WGS) approaches. This unprecedented source of genotypic variability can be linked to phenotypes of interest through marker-trait association analysis such as: genome-wide association study (GWAS), genome selection (GS), pedigree-based analysis (PBA), and bi-parental approaches. The identification of molecular markers in strong linkage with a quantitative trait locus (QTL) provides useful insights to understand the genetic determinism of traits of agronomical relevance. Furthermore, molecular markers can represent a valuable tool for breeders for a genetic-guided seedling or parental selection. Indeed, the use of molecular markers in strong linkage with an agronomical trait allows a fast and relatively inexpensive screening of seedlings with consequent reduction in the time and space needed to develop novel cultivars showing superior phenotypic characteristics.

Dr. Mario Di Guardo
Guest Editor

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Keywords

  • genome-wide association analysis
  • QTL analysis
  • pedigree-based analysis
  • genome selection
  • quantitative-trait locus
  • single nucleotide polymorphism
  • marker-assisted selection
  • plant breeding
  • fruit quality
  • biotic/abiotic stress

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Published Papers (3 papers)

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Research

12 pages, 2145 KiB  
Article
Functional Diversification of the Dihydroflavonol 4-Reductase from Camellia nitidissima Chi. in the Control of Polyphenol Biosynthesis
by Lina Jiang, Zhengqi Fan, Ran Tong, Xingwen Zhou, Jiyuan Li and Hengfu Yin
Genes 2020, 11(11), 1341; https://doi.org/10.3390/genes11111341 - 12 Nov 2020
Cited by 14 | Viewed by 2769
Abstract
Plant secondary metabolism is complex in its diverse chemical composition and dynamic regulation of biosynthesis. How the functional diversification of enzymes contributes to the diversity is largely unknown. In the flavonoids pathway, dihydroflavonol 4-reductase (DFR) is a key enzyme mediating dihydroflavanol into anthocyanins [...] Read more.
Plant secondary metabolism is complex in its diverse chemical composition and dynamic regulation of biosynthesis. How the functional diversification of enzymes contributes to the diversity is largely unknown. In the flavonoids pathway, dihydroflavonol 4-reductase (DFR) is a key enzyme mediating dihydroflavanol into anthocyanins biosynthesis. Here, the DFR homolog was identified from Camellia nitidissima Chi. (CnDFR) which is a unique species of the genus Camellia with golden yellow petals. Sequence analysis showed that CnDFR possessed not only conserved catalytic domains, but also some amino acids peculiar to Camellia species. Gene expression analysis revealed that CnDFR was expressed in all tissues and the expression of CnDFR was positively correlated with polyphenols but negatively with yellow coloration. The subcellular localization of CnDFR by the tobacco infiltration assay showed a likely dual localization in the nucleus and cell membrane. Furthermore, overexpression transgenic lines were generated in tobacco to understand the molecular function of CnDFR. The analyses of metabolites suggested that ectopic expression of CnDFR enhanced the biosynthesis of polyphenols, while no accumulation of anthocyanins was detected. These results indicate a functional diversification of the reductase activities in Camellia plants and provide molecular insights into the regulation of floral color. Full article
(This article belongs to the Special Issue Marker-Trait Association Analysis in Horticultural Crops)
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16 pages, 2675 KiB  
Article
Transcriptional Analysis of Carotenoids Accumulation and Metabolism in a Pink-Fleshed Lemon Mutant
by Giuseppe Lana, Jaime Zacarias-Garcia, Gaetano Distefano, Alessandra Gentile, María J. Rodrigo and Lorenzo Zacarias
Genes 2020, 11(11), 1294; https://doi.org/10.3390/genes11111294 - 30 Oct 2020
Cited by 9 | Viewed by 3931
Abstract
Pink lemon is a spontaneous bud mutation of lemon (Citrus limon, L. Burm. f) characterized by the production of pink-fleshed fruits due to an unusual accumulation of lycopene. To elucidate the genetic determinism of the altered pigmentation, comparative carotenoid profiling and [...] Read more.
Pink lemon is a spontaneous bud mutation of lemon (Citrus limon, L. Burm. f) characterized by the production of pink-fleshed fruits due to an unusual accumulation of lycopene. To elucidate the genetic determinism of the altered pigmentation, comparative carotenoid profiling and transcriptional analysis of both the genes involved in carotenoid precursors and metabolism, and the proteins related to carotenoid-sequestering structures were performed in pink-fleshed lemon and its wild-type. The carotenoid profile of pink lemon pulp is characterized by an increased accumulation of linear carotenoids, such as lycopene, phytoene and phytofluene, from the early stages of development, reaching their maximum in mature green fruits. The distinctive phenotype of pink lemon is associated with an up-regulation and down-regulation of the genes upstream and downstream the lycopene cyclase, respectively. In particular, 9-cis epoxycarotenoid dioxygenase genes were overexpressed in pink lemon compared with the wild-type, suggesting an altered regulation of abscisic acid biosynthesis. Similarly, during early development of the fruits, genes of the carotenoid-associated proteins heat shock protein 21, fibrillin 1 and 2 and orange gene were overexpressed in the pulp of the pink-fleshed lemon compared to the wild-type, indicating its increased capacity for sequestration, stabilization or accumulation of carotenes. Altogether, the results highlighted significant differences at the transcriptomic level between the pink-fleshed lemon and its wild-type, in terms of carotenoid metabolism and the capacity of stabilization in storage structures between the two accessions. Such changes may be either responsible for the altered carotenoid accumulation or in contrast, a metabolic consequence. Full article
(This article belongs to the Special Issue Marker-Trait Association Analysis in Horticultural Crops)
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15 pages, 8650 KiB  
Article
Identification of QTLs Controlling α-Glucosidase Inhibitory Activity in Pepper (Capsicum annuum L.) Leaf and Fruit Using Genotyping-by-Sequencing Analysis
by Doie Park, Geleta Dugassa Barka, Eun-Young Yang, Myeong-Cheoul Cho, Jae Bok Yoon and Jundae Lee
Genes 2020, 11(10), 1116; https://doi.org/10.3390/genes11101116 - 23 Sep 2020
Cited by 10 | Viewed by 3245
Abstract
Diabetes mellitus, a group of metabolic disorders characterized by hyperglycemia, is one of the most serious and common diseases around the world and is associated with major complications such as diabetic neuropathy, retinopathy, and cardiovascular diseases. A widely used treatment for non-insulin-dependent diabetes [...] Read more.
Diabetes mellitus, a group of metabolic disorders characterized by hyperglycemia, is one of the most serious and common diseases around the world and is associated with major complications such as diabetic neuropathy, retinopathy, and cardiovascular diseases. A widely used treatment for non-insulin-dependent diabetes is α-glucosidase inhibitors (AGIs) such as acarbose, which hinders hydrolytic cleavage of disaccharides and retard glucose absorption. The ability to inhibit α-glucosidase activity has been reported in leaf and fruit of pepper (Capsicum annuum L.). In this study, we aimed to identify quantitative trait loci (QTLs) controlling α-glucosidase inhibitory activity (AGI activity) in pepper leaf and fruit using enzyme assay and genotyping-by-sequencing (GBS) analysis. The AGI activity at three stages of leaf and one stage of fruit development was analyzed by 96 F2 individuals. GBS analysis identified 17,427 SNPs that were subjected to pepper genetic linkage map construction. The map, consisting of 763 SNPs, contained 12 linkage groups with a total genetic distance of 2379 cM. QTL analysis revealed seven QTLs (qAGI1.1, qAGI11.1, qAGI5.1, qAGI9.1, qAGI12.1, qAGI5.2, and qAGI12.2) controlling AGI activity in pepper leaf and fruit. The QTLs for AGI activity varied by plant age and organ. This QTL information is expected to provide a significant contribution to developing pepper varieties with high AGI activity. Full article
(This article belongs to the Special Issue Marker-Trait Association Analysis in Horticultural Crops)
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