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Detection of Breeding-Relevant Fruit Cracking and Fruit Firmness Quantitative Trait Loci in Sweet Cherry via Pedigree-Based and Genome-Wide Association Approaches

Breeding for decreased fruit cracking incidence and increased fruit firmness in sweet cherry creates an attractive alternative to variable results from cultural management practices. DNA-informed breeding increases its efficiency, yet upstream research is needed to identify the genomic regions assoc...

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Autores principales: Crump, William Wesley, Peace, Cameron, Zhang, Zhiwu, McCord, Per
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8924583/
https://www.ncbi.nlm.nih.gov/pubmed/35310633
http://dx.doi.org/10.3389/fpls.2022.823250
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author Crump, William Wesley
Peace, Cameron
Zhang, Zhiwu
McCord, Per
author_facet Crump, William Wesley
Peace, Cameron
Zhang, Zhiwu
McCord, Per
author_sort Crump, William Wesley
collection PubMed
description Breeding for decreased fruit cracking incidence and increased fruit firmness in sweet cherry creates an attractive alternative to variable results from cultural management practices. DNA-informed breeding increases its efficiency, yet upstream research is needed to identify the genomic regions associated with the trait variation of a breeding-relevant magnitude, as well as to identify the parental sources of favorable alleles. The objectives of this research were to identify the quantitative trait loci (QTLs) associated with fruit cracking incidence and firmness, estimate the effects of single nucleotide polymorphism (SNP) haplotypes at the detected QTLs, and identify the ancestral source(s) of functional haplotypes. Fruit cracking incidence and firmness were evaluated for multiple years on 259 unselected seedlings representing 22 important breeding parents. Phenotypic data, in conjunction with genome-wide genotypic data from the RosBREED cherry 6K SNP array, were used in the QTL analysis performed via Pedigree-Based Analysis using the FlexQTL™ software, supplemented by a Genome-Wide Association Study using the BLINK software. Haplotype analysis was conducted on the QTLs to identify the functional SNP haplotypes and estimate their phenotypic effects, and the haplotypes were tracked through the pedigree. Four QTLs (two per trait) were consistent across the years and/or both analysis methods and validated the previously reported QTLs. qCrack-LG1.1m (the label given to a consistent QTL for cracking incidence on chromosome 1) explained 2–15.1% of the phenotypic variance, while qCrack-LG5.1m, qFirm-LG1.2m, and qFirm-LG3.2m explained 7.6–13.8, 8.8–21.8, and 1.7–10.1% of the phenotypic variance, respectively. At each QTL, at least two SNP haplotypes had significant effects and were considered putative functional SNP haplotypes. Putative low-cracking SNP haplotypes were tracked to an unnamed parent of ‘Emperor Francis’ and ‘Schmidt’ and unnamed parents of ‘Napoleon’ and ‘Hedelfingen,’ among others, and putative high-firmness haplotypes were tracked to an unnamed parent of ‘Emperor Francis’ and ‘Schmidt,’ an unnamed grandparent of ‘Black Republican,’ ‘Rube,’ and an unknown parent of ‘Napoleon.’ These four stable QTLs can now be targeted for DNA test development, with the goal of translating information discovered here into usable tools to aid in breeding decisions.
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spelling pubmed-89245832022-03-17 Detection of Breeding-Relevant Fruit Cracking and Fruit Firmness Quantitative Trait Loci in Sweet Cherry via Pedigree-Based and Genome-Wide Association Approaches Crump, William Wesley Peace, Cameron Zhang, Zhiwu McCord, Per Front Plant Sci Plant Science Breeding for decreased fruit cracking incidence and increased fruit firmness in sweet cherry creates an attractive alternative to variable results from cultural management practices. DNA-informed breeding increases its efficiency, yet upstream research is needed to identify the genomic regions associated with the trait variation of a breeding-relevant magnitude, as well as to identify the parental sources of favorable alleles. The objectives of this research were to identify the quantitative trait loci (QTLs) associated with fruit cracking incidence and firmness, estimate the effects of single nucleotide polymorphism (SNP) haplotypes at the detected QTLs, and identify the ancestral source(s) of functional haplotypes. Fruit cracking incidence and firmness were evaluated for multiple years on 259 unselected seedlings representing 22 important breeding parents. Phenotypic data, in conjunction with genome-wide genotypic data from the RosBREED cherry 6K SNP array, were used in the QTL analysis performed via Pedigree-Based Analysis using the FlexQTL™ software, supplemented by a Genome-Wide Association Study using the BLINK software. Haplotype analysis was conducted on the QTLs to identify the functional SNP haplotypes and estimate their phenotypic effects, and the haplotypes were tracked through the pedigree. Four QTLs (two per trait) were consistent across the years and/or both analysis methods and validated the previously reported QTLs. qCrack-LG1.1m (the label given to a consistent QTL for cracking incidence on chromosome 1) explained 2–15.1% of the phenotypic variance, while qCrack-LG5.1m, qFirm-LG1.2m, and qFirm-LG3.2m explained 7.6–13.8, 8.8–21.8, and 1.7–10.1% of the phenotypic variance, respectively. At each QTL, at least two SNP haplotypes had significant effects and were considered putative functional SNP haplotypes. Putative low-cracking SNP haplotypes were tracked to an unnamed parent of ‘Emperor Francis’ and ‘Schmidt’ and unnamed parents of ‘Napoleon’ and ‘Hedelfingen,’ among others, and putative high-firmness haplotypes were tracked to an unnamed parent of ‘Emperor Francis’ and ‘Schmidt,’ an unnamed grandparent of ‘Black Republican,’ ‘Rube,’ and an unknown parent of ‘Napoleon.’ These four stable QTLs can now be targeted for DNA test development, with the goal of translating information discovered here into usable tools to aid in breeding decisions. Frontiers Media S.A. 2022-03-02 /pmc/articles/PMC8924583/ /pubmed/35310633 http://dx.doi.org/10.3389/fpls.2022.823250 Text en Copyright © 2022 Crump, Peace, Zhang and McCord. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Crump, William Wesley
Peace, Cameron
Zhang, Zhiwu
McCord, Per
Detection of Breeding-Relevant Fruit Cracking and Fruit Firmness Quantitative Trait Loci in Sweet Cherry via Pedigree-Based and Genome-Wide Association Approaches
title Detection of Breeding-Relevant Fruit Cracking and Fruit Firmness Quantitative Trait Loci in Sweet Cherry via Pedigree-Based and Genome-Wide Association Approaches
title_full Detection of Breeding-Relevant Fruit Cracking and Fruit Firmness Quantitative Trait Loci in Sweet Cherry via Pedigree-Based and Genome-Wide Association Approaches
title_fullStr Detection of Breeding-Relevant Fruit Cracking and Fruit Firmness Quantitative Trait Loci in Sweet Cherry via Pedigree-Based and Genome-Wide Association Approaches
title_full_unstemmed Detection of Breeding-Relevant Fruit Cracking and Fruit Firmness Quantitative Trait Loci in Sweet Cherry via Pedigree-Based and Genome-Wide Association Approaches
title_short Detection of Breeding-Relevant Fruit Cracking and Fruit Firmness Quantitative Trait Loci in Sweet Cherry via Pedigree-Based and Genome-Wide Association Approaches
title_sort detection of breeding-relevant fruit cracking and fruit firmness quantitative trait loci in sweet cherry via pedigree-based and genome-wide association approaches
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8924583/
https://www.ncbi.nlm.nih.gov/pubmed/35310633
http://dx.doi.org/10.3389/fpls.2022.823250
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