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Genes
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Molecular Breeding Approaches in Tropical Horticulture Species
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Molecular Breeding Approaches in Tropical Horticulture Species

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

Deadline for manuscript submissions: closed (25 August 2021) | Viewed by 14423

Special Issue Editors

Dr. Rebecca Ford

E-Mail Website
Guest Editor
Environmental Futures Research Institute, Griffith University, 170 Kessels Rd, Nathan, QLD 4111, Australia
Interests: chickpea; lentil; papaya; genomics; molecular assisted breeding; fruit quality; disease resistance; population genetics; biosensors
Dr. Chat Kanchana-udomkan

E-Mail Website
Guest Editor
Environmental Futures Research Institute, Griffith University, 170 Kessels Rd, Nathan, QLD 4111, Austrilia
Interests: papaya; gene identification; breeding strategies; markers assisted selection; QTL analysis; genomics; transcriptome analysis; fruit quality traits; productivity traits; disease resistance

Special Issue Information

Dear colleagues,

The quality traits of horticultural products are key to their economic worth, tightly conditioned by consumer-driven demand and subsequent marketing and branding. Hence, it should be possible to robustly select the most desirable quality traits using strategic breeding practices, and the underlying genetic factors that condition them should be reproducibly inherited and expressed.

However, despite their domestication, the genomes of horticultural plant species are often complex, with a high degree of heterozygosity and polyploidy. Often multigenetic and quantitative in nature, the expression of desirable traits may be open to large influences from the growing environment. Therefore, the identification, characterization, and application of the genomic sequences and their governing elements, that condition desirable trait expression under a range of environmental factors, offers huge potential to fast track and stabilise new varieties and higher quality products.

The goal of this Special Issue is to bring together the very latest information about gene and sequence targets under investigation and application in ‘omics-guided advanced breeding practices in a wide range of tropical horticultural crop species. This will include contributions from researchers at the forefront of genetic investigations and novel approach development. The Special Issue will comprise original research articles, highly informative, comprehensive, and up-to-date reviews, and method development papers.

We are seeking contributions to this Special Issue specifically in the areas of gene discovery and characterisation methods and their application towards strategic and applied tropical horticultural species improvement and selective breeding.

Dr. Rebecca Ford
Dr. Chat Kanchana-udomkan
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. Genes 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 2600 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

  • genomics
  • transcriptomics
  • genome-wide association study (GWAS)
  • genomic selection
  • high-throughput genotyping
  • quantitative trait loci (QTL)
  • molecular markers
  • single-nucleotide polymorphism (SNP)
  • RNA sequencing
  • quantitative real time PCR (qPCR)

Published Papers (3 papers)

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Research

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20 pages, 1868 KiB  
Article
Genetic and Transcription Profile Analysis of Tissue-Specific Anthocyanin Pigmentation in Carrot Root Phloem
by Florencia Bannoud, Sofia Carvajal, Shelby Ellison, Douglas Senalik, Sebastian Gomez Talquenca, Massimo Iorizzo, Philipp W. Simon and Pablo F. Cavagnaro
Genes 2021, 12(10), 1464; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101464 - 22 Sep 2021
Cited by 14 | Viewed by 2948
Abstract
In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be [...] Read more.
In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNA-seq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP. Full article
(This article belongs to the Special Issue Molecular Breeding Approaches in Tropical Horticulture Species)
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Review

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41 pages, 4438 KiB  
Review
Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content
by Malarvizhi Mathiazhagan, Bhavya Chidambara, Laxman R. Hunashikatti and Kundapura V. Ravishankar
Genes 2021, 12(12), 1881; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12121881 - 25 Nov 2021
Cited by 20 | Viewed by 4772
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently [...] Read more.
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here. Full article
(This article belongs to the Special Issue Molecular Breeding Approaches in Tropical Horticulture Species)
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15 pages, 1042 KiB  
Review
Papaya (Carica papaya L.) Flavour Profiling
by Ziwei Zhou, Rebecca Ford, Ido Bar and Chutchamas Kanchana-udomkan
Genes 2021, 12(9), 1416; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12091416 - 15 Sep 2021
Cited by 11 | Viewed by 5617
Abstract
A major challenge to the papaya industry is inconsistency in fruit quality and, in particular, flavour, which is a complex trait that comprises taste perception in the mouth (sweetness, acidity, or bitterness) and aroma produced by several volatile compounds. Current commercial varieties vary [...] Read more.
A major challenge to the papaya industry is inconsistency in fruit quality and, in particular, flavour, which is a complex trait that comprises taste perception in the mouth (sweetness, acidity, or bitterness) and aroma produced by several volatile compounds. Current commercial varieties vary greatly in their taste, likely due to historical prioritised selection for fruit appearance as well as large environmental effects. Therefore, it is important to better understand the genetic and biochemical mechanisms and biosynthesis pathways underpinning preferable flavour in order to select and breed for better tasting new commercial papaya varieties. As an initial step, objectively measurable standards of the compound profiles that provide papaya’s taste and aroma, together with ‘mouth feel’, are required. This review presents an overview of the approaches to characterise the flavour profiles of papaya through sugar component determination, volatile compound detection, sensory panel testing, as well as genomics-based studies to identify the papaya flavour. Full article
(This article belongs to the Special Issue Molecular Breeding Approaches in Tropical Horticulture Species)
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