Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array

Hardner, Craig; Hayes, Ben J.; Kumar, Satish; Vanderzande, Stijn; Cai, Lichun; Piaskowski, Julia; Quero-Garcia, José; Campoy, José Antonio; Barreneche, Teresa; Giovannini, D.; Liverani, A.; Charlot, Gérard; Villamil-Castro, Miguel; Oraguzie, Nnadozie; Peace, Cameron

doi:10.1038/s41438-018-0081-7

Cited by 31 publications

(29 citation statements)

References 66 publications

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“…The performance of breeding material in tested as well as untested but similar environments can be predicted accurately using genomic prediction models taking into account genotype by environment interactions 34 . We found a moderate but noticeable effect of the genotype by environment interaction on both phenology traits evaluated in 2018, which contrasts with the limited effect of genotype by environment interaction on a trait similar to harvest date reported in sweet cherry 34 . The replication of the apple REFPOP across six environments will enable the inclusion of these interactions into genomic prediction models.…”

Section: Discussionmentioning

confidence: 99%

The apple REFPOP—a reference population for genomics-assisted breeding in apple

et al. 2020

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Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker–trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.

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Section: Discussionmentioning

confidence: 99%

The apple REFPOP—a reference population for genomics-assisted breeding in apple

et al. 2020

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“…Large global performance and genotypic data sets were assembled for sweet cherry (762 accessions, 19 locations) 173 , peach (1193 accessions, five locations) 174 , apple (3659 accessions, 19 locations), and strawberry (3368 accessions, eight locations) 175 . Using data for fruit maturity timing in sweet cherry from one location in the U.S. and three locations in Europe, high prediction accuracy (0.85) and genome-by-environment correlations (0.90) were observed 176 . Preliminary analyses in peach using multi-year data from trials at Fresno Calif., College Station, Tex., Clarksville Ark., and Seneca, S.C. demonstrated an increase in prediction accuracy from 0.54, using only local data, to 0.77 when data were combined across locations, and to 0.86 with the inclusion of genotypic categorization by a large-effect QTL (C. Hardner, pers.…”

Section: Genomics and Socio-economics Knowledge Informs All Stages Ofmentioning

confidence: 99%

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

et al. 2020

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The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a “chasm” existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project (“Ros” signifying a Rosaceae genomics, genetics, and breeding community initiative, and “BREED”, indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.

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“…Recently, as advocated by Gupta et al (2001), progress has also been made in the development and use of SNPs in woody plants, including some crop and tree species as apple (Bianco et al , 2016), walnut (Marrano et al , 2019), sweet cherry (Hardner et al , 2019), pear (X. Li et al , 2019), and coffee (Merot-L’anthoene et al , 2019).…”

Section: Introductionmentioning

confidence: 99%

Mining downy mildew susceptibility genes: a diversity study in grapevine

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et al. 2020

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AcknowledgmentsCP acknowledges funding from a FEM PhD fellowship at University of Udine, including a support from SciENZA Biotechnologies bv. Conflict of Interest StatementThe authors declare no conflict of interest. AbstractSeveral pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted on Arabidopsis, the putative hortologues of genes associated with downy mildew susceptibility in this species, have been discovered also in the grapevine genome. In this work, we deep-resequenced four putative susceptibility genes in 190 highly genetically diverse grapevine genotypes to discover new sources of broad-spectrum recessively inherited resistance. The scouted genes are VvDMR6-1, VvDMR6-2, VvDLO1, VvDLO2 and predicted to be involved in susceptibility to downy mildew. From all identified mutations, 56% were Single Nucleotide Polymorphisms (SNPs) in heterozygosity, while the remaining 44% were homozygous. Regarding the identified mutations with putative impact on gene function, we observed ~4% genotypes mutated in VvDMR6-1 and ~8% mutated in VvDMR6-2, only a handful of genotypes that were mutated in both genes. ~2% and ~7% genotypes showed mutations in VvDLO1 and VvDLO2 respectively, and again a few genotypes resulted mutated in both genes. In particular, 80% of impacting mutations were heterozygous while 20% were homozygous.The current results will inform grapevine genetics and corroborate genomic-assisted breeding programs for resistance to biotic stresses.A survey on the genetic diversity of downy mildew susceptibility genes in grapevine varieties and wild species reveals a potential valuable for genomic-assisted breeding as well as tailored gene editing to induce disease resistance.

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Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array

Cited by 31 publications

References 66 publications

The apple REFPOP—a reference population for genomics-assisted breeding in apple

The apple REFPOP—a reference population for genomics-assisted breeding in apple

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

Mining downy mildew susceptibility genes: a diversity study in grapevine

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