Character integration, breeding goals compatibility and selection indexes using genome wide breeding values: a study case.

Transcription

1 Character integration, breeding goals compatibility and selection indexes using genome wide breeding values: a study case. Alix ALLARD, François LAURENS, Evelyne COSTES June22 nd th RosaceaeGenomicConference 1

2 Apple tree biological characteristics Malus x domestica Borkh Perennial plant Long juvenile phase Breeding in apple 3 main traits Several economical actors Disease sensitivity Self-sterile flowers Complexe genome Photo A. Allard Breedingstrategiesdepend on agronomical, economical and business factors Laurens et al, 2012 Narrow genetic background Will to broadengenetic background with ancient varieties or wild species Photo D. Gomez, CTIFL orchard 2

3 Biennial or irregular bearing Habit Two original traits Control Yield per tree (kg) NPK Regulation Chemical (or manual) thinning Regulatory framework Decrease in chemical product use Year Tiller et al., 1959 Climate change Temperature rising Bud phenology Photo A. Allard Adaptative risk during chill and heat requirement satisfaction Heritable traits Bearinghabit genetic determinism: Guitton et al, 2012; Durand et al, 2013; Durand et al, 2016 (submitted) Budphenologygenetic determinism: Celton et al., 2011;Dyk et al., 2010; Cornelissen and Rees, 2014; Allard et al, 2016 Breedingnew varietiesisa solution to adaptto the new regulatoryframeworkand the changing climate 3

4 Objective and approach Integrate two new traits to fruit quality traits in a multi-trait genetic value estimation approach. Geneticvalue estimation Trait by trait Ideotype definition Study of correlation space between traits Selection Ideotype Index Biologicalmodel Linear combinationof gatheringbreedingobjectives individualvalues, weighted for several by the traits. importance Dependenton of characters. the agronomical, climatic and economicalcontext. Hazel, 1943; Gallais, 1990 Donald, 1968; Dickmann, 1985; Dickmann et al., 1994; Costes, 2009 Trait integration Multi-trait genetic value estimation Selection Index 4

5 Material & Methods 5

6 Trait integrationby selectionindex: linearcombinationsof geneticvalues Weight Sugar Content 1 Bearing habit Major traits Fruit Size 1 Yield 1 BBI -1 Autocov 1 Additionnaltraits Bud phenology Weight Acidity 1 Firmness 1 BBcd -1 Delta 1 Additive Combination (Index= weight*trait 1 + weight*trait 2 + ) 6

7 Plant material Family Female Parents Male Plantation year Nb individuals Rep Orchard management SG Starkrimson ( Delicious mutant ) Granny Smith Slightly pruned Slightly thinned Irrigated and treated XB X-3263 Belrène Not pruned Not thinned Irrigated and treated Planted in Montpellier, south of France 7

8 Bearing habit phenotyping Occurrence of flowering events (1) vs. vegetative events (0) along axes. Morphological marker specific to apple tree: bourse Photo S. Martinez Quantification of yield difference between years(biennial Bearing Index, BBI) Hoblyn et al., 1936, Wilcox et al., 1944 Quantification of interdependency of yield between consecutive years (Autocov) PhD B. Guitton, 2011 Guitton et al., 2012 Durand et al., 2013 Year 6 Year 5 Year 4 Year 3 Year 2 Year 1 Autocov BBI 8

9 Environmentaland genotypiceffects Biennial Bearing ~+ +(+ +ξ, ) +ε,,, Intercept Slope BBI Autocov t year g r repetitions Bud phenology BBcd ~++ +( )+ Mixed model Variance structure on Year BLUPs for Genotype and Gentoype*Year 9

10 Fruit Qualityand yieldphenotyping Trait Unit methods years Yield (Y) Nb fruit, weight Count and weight Fruit Size (FS) weight Sugar Content (SC) % Brix Acidity (Ac) g malic acid / L Robot Pimprenelle 2013 Firmness(Firm) Kg/cm² 10

11 Geneticvalue estimation -FlexQTL TM Bink et al., 2008, 2012, and 2014 Geneticparametersestimation (geneticvariance, marker effects, allele frequency, genotype estimation, ) QTL mapping (for more information seeallard et al., 2016) Genetic value estimation Gebv i =,+-,+-) For each trait and eachindividual!"#$% (% &('!"#$% ) () () () * () +,( () ( Genetic Map 20K SNP array (Bianco et al, 2014) Consensus map(21 families) (van de Weg, Di Pierro, unpublished) n./0 : loci number.12: iteration number.32: QTLnumber & λ ( : indicator of QTL * +,( () : estimated genotype at locus q ( () : additive effect at locus q 11

12 Results 12

13 Correlationspacebetweentraits PCA with genetic values XB SG Families different on fruits size, yield and bud phenology Following results: by family 13

14 Correlationspacebetweentraits PCA -genetic values -SG PCA -genetic values -XB Bearing habit Bearing habit Fruit size Bearing habit Fruit size Bearing habit Synergism BBI/Autocov(Bearing habit) Fruit Size / BearingHabit 14

15 Correlationspacebetweentraits PCA -genetic values -SG PCA -genetic values -XB Yield Yield Bearing habit Bearing habit Fruit size Bearing habit Fruit size Bearing habit Antagonism Yield / Fruit Size Yield / BearingHabit Neutral Yield / Fruit Size Yield / BearingHabit (Parent X-3263 auto-thinning) Synergisms and antagonisms expected 15

16 QTL mappingand colocalizations LG2 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 Y_nbfrt-2lnBF=4.5 Ac-2lnBF=8.4 Y_nbfrt-2lnBF=7.5 Firm-2lnBF=5 Delta-2lnBF=3.5 Firm-2lnBF=3.4 BBcd-2lnBF=6.1 Y_nbfrt-2lnBF=10 Y_nbfrt-2lnBF=4.7 BBcd-2lnBF=3 Delta_GDH-2lnBF=4 BBcd-2lnBF=4.8 BBcd-2lnBF=5.1 Y_nbfrt-2lnBF=5.1 FS-2lnBF=11.1 BBcd-2lnBF=4 Ac-2lnBF=3.8 SC-2lnBF=2.6 Firm-2lnBF=9.9 BBIresnorm-2lnBF=5.9 FS-2lnBF=3.1 Y_nbfrt-2lnBF=

17 Multi-trait genetic potential Sugar Content Fruit Size Yield Bearing Habit Major traits Additionnal Groupe 2traits Acidity Fimness Bud Phenologie SG XB SG SG XB XB Higher potential for SG SG013, SG087 XB291, XB308 SG013, SG023 XB301, XB306 What are their genetic value, by trait? Whatare their genotypesat main loci? 17

18 Yield BBI LG8 0 5 Fruit Size FS-2lnBF=11.1 Y_nbfrt-2lnBF=5.1 BBcd-2lnBF=5.1 Indiv. Fruit Size Yield SG013 FF UU SG087 FF UU Autocov XB FF XB UU Sugar Content BBcd-2ln F: favorable allele U: Unfavorable allele Breeding Objective 18

19 Conclusion & Perspectives 19

20 Selection of best individuals based on their multi-trait geneticvalue Similar to index based phenotypic selection In case of antagonistic correlation, QTLs can be used to identify: - Loci responsible for genetic correlation - Possibility of recombination between colocalizing QTL But Alsoto monitorthe selection by - Identification of the loci of importance - Attribution of genetic weights depending on traits and colocalizations

21 Multi-trait Analysis - For studying traits with low heritability, with correlated traits (Schutlthess et al, 2015) - For better estimation of genetic parameters(malosetti et al, 2008; Calus et al, 2011) Selection Index + molecular markers - For maximization of selection response(dekkers et al, 2007; Lande and Thompson, 1990) Objective in apple and this study case To estimate and predict a multi-trait potential based on moleculars markers only - Avoid complex and time consuming phenotyping steps - Breeding for quantitative traits To apply in a context of multi-trait genomewide selection (First studies on apple: Kumar et al., 2012, Muranty et al., 2015)

22 Thanksfor your attention AFEF Team, INRA Montpellier, France