Barreneche, Teresa

Cai, Lichun

Campoy, José Antonio

Giovannini, Daniela

Hardner, Craig

Hayes, Ben

Kazantzis, Konstantinos

Kumar, Satish

Liverani, Alessandro

Oraguzie, Nnadozie

Peace, Cameron

Piaskowski, Julia

Quero García, José

Sotiropoulos, Thomas

Vanderzande, Stijn

Wünsch, Ana

citaREA Repositorio Electrónico Agroalimentario

88th InternationalRosaceae Genomics ConferenceJUNE 21-24 /2016ANGERS - FRANCERGC 85JUNE 21-24/2016   ANGERS - FRANCEUsing SNP arrays to leverage historic data sets for improved prediction accuracy and estimation of GxE of fruit maturity in sweetcherry S6O5Craig Hardner1, Stijn Vanderzande2, Lichun Cai3, Julia Piaskowski2, Nnadozie Oraguzie4, Jose Quero-Garcia5, José Antonio Campoy5, Teresa Barreneche5, Ana Wünsch6, Daniela Giovannini7, Alessandro Liverani7, Thomas Sotiropoulos8,  Konstantinos Kazantzis8, Satish Kumar9, Ben Hayes2, Cameron Peace21 university of Queensland, Queensland alliance for agriculture and food innovation, st lucia 4072 QlD, australia, 306 Carmody Road, St Lucia 4076, Australia2 Department of horticulture, washington state university, Pullman, WA 99164, USA3 michigan state univ, Dept hort, E Lansing, MI 48824 USA4 washington state univ, irrigated agr res & extens ctr, 24106 n bunn rd, Prosser, WA 99350, USA5 inra, umr biol fruit & pathol 1332, F-33140 Villenave Dornon, France6 ctr invest & tecnol agroalimentaria aragon cita, Zaragoza, Spain7 cra frf unita ric frutticoltura forli, I-47121 Forli, Italy8 agr & agri food canada, pacific agri food res ctr, Summerland, BC V0H 1Z0, Canada9 new Zealand inst plant & food res ltd, Havelock North 4157, New ZealandImproved prediction accuracy of the genetic potential of advanced selections and cultivars for commercially relevant traits in commercially relevant conditions will lead to increased response to breeding. While a large number of loci might influence quantitative traits, QTLs with major trait effect have been identified, and can be used for selection if the effect of alleles on commercial performance can be accurately predicted. However, selection response will be compromised if the effect of major trait loci are confounded with polygenetic effects from the background genome - if not accounted for, and external factors such as management practices or environment conditions also influence the trait. Here, we propose a novel approach to improve prediction accuracy of genetic potential under commercial conditions by using SNP arrays to characterise variation at major effect QTLs and estimate realised additive and dominance relationships among individuals that have also been evaluated for traits of interest. This approach enables data from otherwise disconnected historical data sets to be combined into a single analysis, thereby increasing prediction accuracy, without the need for replication of individuals. In addition, the different locations from which the performance data have been collected represent samples of the variability of external factors. As such, this analysis can be also used to investigate the influence of these factors on the stability of both major-effect QTLs and polygenetic effects. As part of the RosBREED project, we demonstrate this approach and results using 800 sweet cherry individuals that have were genotyped using the 6K SNP sweet cherry array and evaluated in the USA (Prosser, Washington),Canada (Summerland British Columbia), France (Boudreaux), and Italy (Forli).

Using SNP arrays to leverage historic data  sets for improved prediction accuracy and  estimation of GxE of fruit maturity in sweet cherry (abstract)

http://citarea.cita-aragon.es/citarea/bitstream/10532/3315/1/2016_143.pdf

Using SNP arrays to leverage historic data sets for improved prediction accuracy and estimation of GxE of fruit maturity in sweet cherry (abstract)

Abstract

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citaREA Repositorio Electrónico Agroalimentario