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Agronomy
Special Issues
DNA-Informed Breeding in Fruit and Nut Crops
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DNA-Informed Breeding in Fruit and Nut Crops

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Horticultural and Floricultural Crops".

Deadline for manuscript submissions: closed (10 December 2022) | Viewed by 8382

Special Issue Editors

Prof. Dr. Nahla Bassil

E-Mail Website
Guest Editor
USDA-ARS, National Clonal Germplasm Repository, 33447 Peoria Rd., Corvallis, OR 97333, USA
Interests: genetics; plant breeding; plant biology; DNA markers; germplasm conservation; fingerprinting
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Cameron Peace

E-Mail Website
Guest Editor
Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, WA, 99164, USA
Interests: tree fruit genetics; DNA-informed breeding; pedigree reconstruction

Special Issue Information

Dear Colleagues, 

Advances in molecular genetic techniques and generation of whole genome reference sequences in fruit and nut crops have laid the foundation for enabling DNA-informed breeding. A chasm was recognized between genomic research and practical application of DNA information in breeding programs. Some breeders have successfully conducted DNA-informed breeding in their programs. In this Special Issue, we invite review articles that describe opportunities, resources, advances, gaps, and needs in the use of DNA information in supporting breeding decisions in a particular fruit or nut crop, crop group, or crop region. A specific breeding activity can be emphasized (e.g., pre-breeding, elite selection advancement). Authors are encouraged to highlight innovations and idiosyncrasies in their breeding situation. We also invite experimental articles that focus on your recent research to address an identified need. Both article categories must answer the question: What has and could be done to support breeding decisions with DNA-based genetic information toward delivering new and improved cultivars.

Prof. Dr. Nahla Bassil
Prof. Dr. Cameron Peace
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. Agronomy 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

  • plant breeding
  • pre-breeding
  • cultivars
  • parental selection
  • seedling selection
  • DNA markers
  • DNA tests
  • genomic prediction
  • quantitative traits
  • marker–trait associations
  • diploid
  • polyploidy
  • cost efficiency
  • genetic gain

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Published Papers (3 papers)

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Research

18 pages, 3192 KiB  
Article
Genome-Wide Association Study for Abscission Failure of Fruit Pericarps (Stick-Tights) in Wild Macadamia Germplasm
by Jasmine Nunn, Joanne De Faveri, Katie O’Connor, Mobashwer Alam, Craig Hardner, Olufemi Akinsanmi and Bruce Topp
Agronomy 2022, 12(8), 1913; https://doi.org/10.3390/agronomy12081913 - 14 Aug 2022
Cited by 4 | Viewed by 1897
Abstract
Macadamia pericarps that fail to abscise (‘stick-tights’) are an important trait to select against in breeding as they can harbour pests and diseases. Traditional macadamia breeding cycles are lengthy and expensive due to long juvenilities and large tree sizes. Thus, genome-wide association studies [...] Read more.
Macadamia pericarps that fail to abscise (‘stick-tights’) are an important trait to select against in breeding as they can harbour pests and diseases. Traditional macadamia breeding cycles are lengthy and expensive due to long juvenilities and large tree sizes. Thus, genome-wide association studies (GWAS) are an important investigative tool to identify candidate trait-linked markers to enable potential reductions in evaluation and selection cycles via marker-assisted selection (MAS) in young seedlings. This study assessed 199 wild macadamia germplasm accessions for stick-tight prevalence across two years. As the number of stick-tights per tree is limited by the number of nuts per tree, we conducted association analyses to identify SNPs linked with the number of stick-tights per tree, and examined whether such SNPs were also associated with, and thus confounded with, the number of nuts per tree. We also assessed associations with the proportion of stick-tights per total number of nuts. Thirty-two SNPs were associated with at least one of the stick-tight traits in one year (p < 0.001). Of all such SNPs, only one was associated with the number of nuts per tree (p < 0.001), indicating that most associations were not confounded with yield. Full article
(This article belongs to the Special Issue DNA-Informed Breeding in Fruit and Nut Crops)
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13 pages, 936 KiB  
Article
Large-Effect QTLs for Titratable Acidity and Soluble Solids Content Validated in ‘Honeycrisp’-Derived Apple Germplasm
by Baylee A. Miller, Sarah A. Kostick and James J. Luby
Agronomy 2022, 12(7), 1703; https://doi.org/10.3390/agronomy12071703 - 19 Jul 2022
Cited by 5 | Viewed by 2921
Abstract
Fruit acidity and sweetness are important fruit quality traits in the apple and are therefore targets in apple breeding programs. Multiple quantitative trait loci (QTLs) associated with titratable acidity (TA) and soluble solids content (SSC) have been previously detected. In this study a [...] Read more.
Fruit acidity and sweetness are important fruit quality traits in the apple and are therefore targets in apple breeding programs. Multiple quantitative trait loci (QTLs) associated with titratable acidity (TA) and soluble solids content (SSC) have been previously detected. In this study a pedigree-based QTL analysis approach was used to validate QTLs associated with TA and SSC in a ‘Honeycrisp’-derived germplasm set. TA and SSC data collected from 2014 to 2018 and curated genome-wide single nucleotide polymorphism (SNP) data were leveraged to validate three TA QTLs on linkage groups (LGs) 1, 8, and 16 and three SSC QTLs on LGs 1, 13, and 16. TA and SSC QTL haplotypes were characterized in six University of Minnesota apple breeding families representing eight breeding parents including ‘Honeycrisp’ and ‘Minneiska’. Six high-TA haplotypes, four low-TA haplotypes, 14 high-SSC haplotypes, and eight low-SSC haplotypes were characterized. The results of this study will enable more informed selection in apple breeding programs. Full article
(This article belongs to the Special Issue DNA-Informed Breeding in Fruit and Nut Crops)
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14 pages, 975 KiB  
Article
Apple Fruit Size QTLs on Chromosomes 8 and 16 Characterized in ‘Honeycrisp’-Derived Germplasm
by Sarah A. Kostick and James J. Luby
Agronomy 2022, 12(6), 1279; https://doi.org/10.3390/agronomy12061279 - 26 May 2022
Cited by 8 | Viewed by 2815
Abstract
Multiple quantitative trait loci (QTLs) associated with fruit size have been reported in apple (Malus domestica Borkh.); however, few have been fully characterized and/or validated. A pedigree-based QTL analysis approach was used to examine the genetic basis of fruit weight in ‘Honeycrisp’-derived germplasm. [...] Read more.
Multiple quantitative trait loci (QTLs) associated with fruit size have been reported in apple (Malus domestica Borkh.); however, few have been fully characterized and/or validated. A pedigree-based QTL analysis approach was used to examine the genetic basis of fruit weight in ‘Honeycrisp’-derived germplasm. Fourteen breeding parents were represented by 814 offspring from 13 full-sib families with breeding parents ‘Honeycrisp’ and ‘Minneiska’ being highly represented. Historical fruit weight data and curated genome-wide single nucleotide polymorphism (SNP) data were leveraged to map QTLs to chromosomes (Chrs) 8 and 16, which together accounted for 15% of the phenotypic variation. The Chr 16 QTL colocalized with other important Chr 16 trait loci. ‘Honeycrisp’ inherited two low fruit weight haplotypes at the Chr 8 QTL from progenitors ‘Northern Spy’ and ‘Grimes Golden’. At the Chr 16 QTL, ‘Honeycrisp’ inherited a low fruit weight haplotype from ‘Frostbite’ and a high fruit weight haplotype from ‘Duchess of Oldenburg’. The small-fruited ‘Honeycrisp’ progenitor ‘Frostbite’ had three low fruit weight haplotypes across the two QTLs. Non-additive interactions were observed at and across QTLs. Results will enable more informed parent selection and/or development of trait-predictive DNA tests for use in apple breeding programs. Full article
(This article belongs to the Special Issue DNA-Informed Breeding in Fruit and Nut Crops)
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