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

William Wesley Crump; Cameron Peace; Zhiwu Zhang; Per McCord

doi:10.3389/fpls.2022.823250

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

Front Plant Sci. 2022 Mar 2:13:823250. doi: 10.3389/fpls.2022.823250. eCollection 2022.

Authors

William Wesley Crump¹, Cameron Peace², Zhiwu Zhang³, Per McCord¹

Affiliations

¹ Department of Horticulture, Washington State University, Prosser, WA, United States.
² Department of Horticulture, Washington State University, Pullman, WA, United States.
³ Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States.

Abstract

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.

Keywords: BLINK; FlexQTL; Prunus avium L.; breeding; cracking; firmness; genome-wide association study; pedigree-based analysis.