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Genetics and Genomics of Edible Rosaceae
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Genetics and Genomics of Edible Rosaceae

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

Deadline for manuscript submissions: closed (20 August 2022) | Viewed by 11551

Special Issue Editors

Dr. Sook Jung

E-Mail Website
Guest Editor
Department of Horticulture, Washington State University, Pullman, WA, USA
Interests: rosaceae genomics; genome evolution; comparative genomics
Prof. Dr. Ksenija Gasic

E-Mail Website
Guest Editor
College of Agriculture, Forestry and Life Sciences, Plant and Environmental Sciences Department, Clemson University, Clemson, SC 29634 USA
Interests: fruit quality; peach; breeding; genetics

Special Issue Information

Dear Colleagues,

We are pleased to invite you to submit a paper on Genetics and Genomics of Edible Rosaceae. Rosaceae includes numerous edible fruit and nut crops. In recent years, we have witnessed an explosive amount of data and resources produced from genomics research on Rosaceae. For example, whole genome sequences are available for most Rosaceae crops—providing an opportunity to explore collinearity and synteny within this family—multiple SNP arrays are available for major crops, and QTLs for many important traits are rapidly accumulating for major crops. This opens new avenues of research questions and methodologies that have not been previously possible. This Special Issue is to provide insights into the status of genetics and genomics research on these biologically and economically important crops.

In this Special Issue, original research articles and reviews are both welcome. Research areas may include (but are not limited to) the following:

  • Structural, functional and comparative genomics;
  • Evolutionary and quantitative genetics;
  • Molecular, cellular and developmental genetics;
  • Germplasm diversity;
  • Breeding and applied genetics;
  • Bioinformatics and database resources.

We look forward to receiving your contributions.

Dr. Sook Jung
Prof. Dr. Ksenija Gasic
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

  • Prunus
  • Malus
  • Fragaria
  • Pyrus
  • Rubus
  • fruit quality
  • productivity
  • germplasm diversity
  • disease resistance
  • DNA-based breeding

Published Papers (5 papers)

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Research

14 pages, 2331 KiB  
Article
Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica
by Mattia Tabarelli, Mickael Malnoy and Katrin Janik
Genes 2022, 13(10), 1696; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13101696 - 22 Sep 2022
Cited by 1 | Viewed by 1518
Abstract
The 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in Malus × domestica (M. × domestica) were identified in 2014 on the first genome assembly, which was released in 2010. In 2017, a higher quality genome [...] Read more.
The 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in Malus × domestica (M. × domestica) were identified in 2014 on the first genome assembly, which was released in 2010. In 2017, a higher quality genome assembly for apple was released and is now considered to be the reference genome. Moreover, as in several other species, the identified TCP genes were named based on the relative position of the genes on the chromosomes. The present work consists of an update of the TCP gene family based on the latest genome assembly of M. × domestica. Compared to the previous classification, the number of TCP genes decreased from 52 to 40 as a result of the addition of three sequences and the deduction of 15. An analysis of the intragenic identity led to the identification of 15 pairs of orthologs, shedding light on the forces that shaped the evolution of this gene family. Furthermore, a revised nomenclature system is proposed that is based both on the intragenic identity and the homology with Arabidopsis thaliana (A. thaliana) TCPs in an effort to set a common standard for the TCP classification that will facilitate any future interspecific analysis. Full article
(This article belongs to the Special Issue Genetics and Genomics of Edible Rosaceae)
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13 pages, 2704 KiB  
Article
The Rm1 and Rm2 Resistance Genes to Green Peach Aphid (Myzus persicae) Encode the Same TNL Proteins in Peach (Prunus persica L.)
by Henri Duval, Laure Heurtevin, Naïma Dlalah, Caroline Callot and Jacques Lagnel
Genes 2022, 13(8), 1489; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13081489 - 20 Aug 2022
Cited by 1 | Viewed by 1845
Abstract
The green peach aphid (GPA), Myzus persicae, is an important pest of the peach crop. Three major dominant resistance genes have already been detected, Rm1 in the Weeping Flower Peach (WFP) clone, Rm2 in the Rubira clone, and Rm3 in the Fen [...] Read more.
The green peach aphid (GPA), Myzus persicae, is an important pest of the peach crop. Three major dominant resistance genes have already been detected, Rm1 in the Weeping Flower Peach (WFP) clone, Rm2 in the Rubira clone, and Rm3 in the Fen Shouxing clone. In this study, after NGS resequencing of WFP and Rubira, we found that their genomic sequences in the Rm1 and Rm2 region were similar but very different from that of the susceptible reference peach Lovell. We constructed a BAC library for the GPA-resistant WFP and screened four BAC clones to sequence the target region. The new sequence was 61.7 Kb longer than Lovell and was annotated with four different TIR_NBS_LRR genes. Among them, the TNL1 gene was very overexpressed in WFP leaves 24 h after GPA infestation. This gene was also present and expressed in the Rubira clone and had the same sequence as the candidate Rm3 gene, supporting the hypothesis that the three genes share the same origin. In addition, we identified a second TNL, TNL2, located at 35.4 Kb from TNL1 and slightly overexpressed after GPA infestation. Kasp and size molecular markers were designed for use in marker-assisted selection and were validated in a peach segregating population. Full article
(This article belongs to the Special Issue Genetics and Genomics of Edible Rosaceae)
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10 pages, 1448 KiB  
Article
Development of an HRMA-Based Marker Assisted Selection (MAS) Approach for Cost-Effective Genotyping of S and M Loci Controlling Self-Compatibility in Apricot (Prunus armeniaca L.)
by Bianca Maria Orlando Marchesano, Remo Chiozzotto, Irina Baccichet, Daniele Bassi and Marco Cirilli
Genes 2022, 13(3), 548; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030548 - 20 Mar 2022
Cited by 3 | Viewed by 1845
Abstract
The apricot species is characterized by a gametophytic self-incompatibility (GSI) system. While GSI is one of the most efficient mechanisms to prevent self-fertilization and increase genetic variability, it represents a limiting factor for fruit production in the orchards. Compatibility among apricot cultivars was [...] Read more.
The apricot species is characterized by a gametophytic self-incompatibility (GSI) system. While GSI is one of the most efficient mechanisms to prevent self-fertilization and increase genetic variability, it represents a limiting factor for fruit production in the orchards. Compatibility among apricot cultivars was usually assessed by either field pollination experiments or by histochemical evaluation of in vitro pollen tube growth. In apricots, self-compatibility is controlled by two unlinked loci, S and M, and associated to transposable element insertion within the coding sequence of SFB and ParM-7 genes, respectively. Self-compatibility has become a primary breeding goal in apricot breeding programmes, stimulating the development of a rapid and cost-effective marker assisted selection (MAS) approach to accelerate screening of self-compatible genotypes. In this work, we demonstrated the feasibility of a novel High Resolution Melting Analysis (HRMA) approach for the massive screening of self-compatible and self-incompatible genotypes for both S and M loci. The different genotypes were unambiguously recognized by HRMA, showing clearly distinguishable melting profiles. The assay was developed and tested in a panel of accessions and breeding selections with known self-compatibility reaction, demonstrating the potential usefulness of this approach to optimize and accelerate apricot breeding programmes. Full article
(This article belongs to the Special Issue Genetics and Genomics of Edible Rosaceae)
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21 pages, 1556 KiB  
Article
Analysis of a Multi-Environment Trial for Black Raspberry (Rubus occidentalis L.) Quality Traits
by Matthew R. Willman, Jill M. Bushakra, Nahla Bassil, Chad E. Finn, Michael Dossett, Penelope Perkins-Veazie, Christine M. Bradish, Gina E. Fernandez, Courtney A. Weber, Joseph C. Scheerens, Lisa Dunlap and Jonathan Fresnedo-Ramírez
Genes 2022, 13(3), 418; https://doi.org/10.3390/genes13030418 - 25 Feb 2022
Cited by 1 | Viewed by 2221
Abstract
U.S. black raspberry (BR) production is currently limited by narrowly adapted, elite germplasm. An improved understanding of genetic control and the stability of pomological traits will inform the development of improved BR germplasm and cultivars. To this end, the analysis of a multiple-environment [...] Read more.
U.S. black raspberry (BR) production is currently limited by narrowly adapted, elite germplasm. An improved understanding of genetic control and the stability of pomological traits will inform the development of improved BR germplasm and cultivars. To this end, the analysis of a multiple-environment trial of a BR mapping population derived from a cross that combines wild ancestors introgressed with commercial cultivars on both sides of its pedigree has provided insights into genetic variation, genotype-by-environment interactions, quantitative trait loci (QTL), and QTL-by-environment interactions (QEI) of fruit quality traits among diverse field environments. The genetic components and stability of four fruit size traits and six fruit biochemistry traits were characterized in this mapping population following their evaluation over three years at four distinct locations representative of current U.S. BR production. This revealed relatively stable genetic control of the four fruit size traits across the tested production environments and less stable genetic control of the fruit biochemistry traits. Of the fifteen total QTL, eleven exhibited significant QEI. Closely overlapping QTL revealed the linkage of several fruit size traits: fruit mass, drupelet count, and seed fraction. These and related findings are expected to guide further genetic characterization of BR fruit quality, management of breeding germplasm, and development of improved BR cultivars for U.S. production. Full article
(This article belongs to the Special Issue Genetics and Genomics of Edible Rosaceae)
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15 pages, 1259 KiB  
Article
Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of Potentilla anserina
by Xiaolong Gan, Shiming Li, Yuan Zong, Dong Cao, Yun Li, Ruijuan Liu, Shu Cheng, Baolong Liu and Huaigang Zhang
Genes 2021, 12(12), 1993; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12121993 - 15 Dec 2021
Cited by 6 | Viewed by 3392
Abstract
Potentilla anserina is a perennial stoloniferous plant with edible tuberous roots in Rosaceae, served as important food and medicine sources for Tibetans in the Qinghai-Tibetan Plateau (QTP), China, over thousands of years. However, a lack of genome information hindered the genetic study. Here, [...] Read more.
Potentilla anserina is a perennial stoloniferous plant with edible tuberous roots in Rosaceae, served as important food and medicine sources for Tibetans in the Qinghai-Tibetan Plateau (QTP), China, over thousands of years. However, a lack of genome information hindered the genetic study. Here, we presented a chromosome-level genome assembly using single-molecule long-read sequencing, and the Hi-C technique. The assembled genome was 454.28 Mb, containing 14 chromosomes, with contig N50 of 2.14 Mb. A total of 46,495 protein-coding genes, 169.74 Mb repeat regions, and 31.76 Kb non-coding RNA were predicted. P. anserina diverged from Potentilla micrantha ∼28.52 million years ago (Mya). Furthermore, P. anserina underwent a recent tetraploidization ∼6.4 Mya. The species-specific genes were enriched in Starch and sucrose metabolism and Galactose metabolism pathways. We identified the sub-genome structures of P. anserina, with A sub-genome was larger than B sub-genome and closer to P. micrantha phylogenetically. Despite lacking significant genome-wide expression dominance, the A sub-genome had higher homoeologous gene expression in shoot apical meristem, flower and tuberous root. The resistance genes was contracted in P. anserina genome. Key genes involved in starch biosynthesis were expanded and highly expressed in tuberous roots, which probably drives the tuber formation. The genomics and transcriptomics data generated in this study advance our understanding of the genomic landscape of P. anserina, and will accelerate genetic studies and breeding programs. Full article
(This article belongs to the Special Issue Genetics and Genomics of Edible Rosaceae)
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