Basic concepts and definitions in multienvironment

Transcription

1 Basc concepts and defntons n multenvronment data: G, E, and GxE Marcos Malosett, Danela Bustos-Korts, Fred van Eeuwk, Pter Bma, Han Mulder Contents The basc concepts: ntroducton and defntons Phenotype, genotype, and envronment Reacton norms Termnology: plastcty, envronmental senstvty, adaptablty Concepts of stablty n plant breedng 2 1

2 Learnng outcomes To understand and apply the basc concepts of GxE and the dfferent termnology n dfferent dscplnes To understand and apply the dfferent concepts of stablty n plant breedng 3 Some basc defntons... Phenotype... Genotype... Envronment... and GxE! 4 2

3 What s the phenotype? P t = t f G, E dt 0 5 The phenotype, the outcome of... Genotype : P t = t f G, E dt 0 DNA consttuton of the organsm o Alleles present and ther ntra and nter-loc combnatons o... but much more than that! Envronment : External stmul provded by the surroundng where the organsm develops / lves: o Temperature / lght / humdty / nutrents / management / etc Development : Tme span when the lfe cycle of the organsm occurs o Condtons both the genotype and the envronment 6 3

4 Phenotype a hgh-dmensonal problem... Genotypes Envronments Genotypes Envronments G-E landscape: complex outcome of multple genotypc and envronmental factors nteractng wth each other... Genotypc dmenson: populaton or sample of a populaton. Envronmental dmenson: Target Populaton of Envronments (TPE), set of condtons that the genotypes or the populaton under study are lkely to experence. 7 Indvdual genotype response: A slce from ths landscape... Genotypes Envronments The red lne s the path that represents the phenotype of a partcular genotype across the envronmental gradent... That path related wth the reacton norm of that partcular genotype. 8 4

5 Reacton norms Reacton norm: Genotype-specfc functonal relatonshp between phenotypc response and envronmental gradent(s). Whch factor(s) drve the envronmental gradent? Here gradent expressed n terms of envronmental means. 9 GxE and reacton norms Genotypes can react dfferently to the same envronmental gradent. Reacton norms change from genotype to genotype... Wth dfferent reacton norms G x E! Whch factor(s) drve the envronmental gradent? Important component n GxE research... Why genotypes respond dfferently? And to what? 10 5

6 GxE occurs when reacton norms are not parallel! Non-parallel reacton norms reveals GxE GxE: dfferental reacton of genotypes to envronmental changes Varaton n adaptaton / plastcty / envronmental senstvty / stablty / Examples of pars of reacton norms Addtvty No GxE Convergence Dvergence Cross-over nteracton 12 6

7 G x E consdered as nteracton Dfferent genotypes respond dfferently to a change n the envronment y GE 22 G 2 E 2 Int. E1 E2 Model: y = nt + G + E + GE y 11 = nt y 12 = nt + E 2 y 21 = nt + G 2 y 22 = nt + G 2 + E 2 + GE 22 GE = 0 no GxE-nteracton 13 G x E and (phenotypc) Plastcty A genotype changes ts phenotype when the envronment changes Plastcty does not necessarly mply GxE-nteracton! y Plastc y Non-plastc E1 E2 E1 E2 14 7

8 G x E and envronmental senstvty Refers to the slope of the reacton norm Measures degree of plastcty y Senstve Non-senstve E1 E2 15 General versus specfc adaptaton Adapted genotype a genotype whose reacton norm s above certan standard or reference genotype. General or wde adaptaton: superor across the entre TPE Specfc or narrow adaptaton: superor but only over a range of the TPE 16 8

9 G x E, adaptaton, plastcty and envronmental senstvty - Non-parallel reacton norms - Genetc varaton n adaptaton - Genetc varaton n plastcty - Genetc varaton n envronmental senstvty G x E P Wth many genotypes, rankng dffers between envronments. Correlaton of the ranks between envronments 1 E1 E2 Varance among genotypes may dffer between envronments 17 GxE and heterogenety of varaton addtvty GxE Addtvty: constant varance across envronments. If GxE: varablty changes from envronment to envronment typcally low varance n poor envronments, hgh n good envronments. No effect on rankng of genotypes, therefore no consequences for selecton 18 9

10 G x E and rerankng Treat the trat n each envronment as a genetcally dstnct trat Genetc correlaton between trat n dfferent envronments s a measure of G x E (Falconer, 1952) r g < 1 G x E Model: y k = + G + k r g = corr(g,g ) Trat 2 Trat 2 y Trat 1 y Trat 1 E1 E2 No GxE: r g = 1 E1 GxE: r g < 1 E2 19 Typcal research questons regardng GxE n plant breedng Related wth the genotypes: Adaptaton: are partcular genotypes adapted to certan envronmental range? Adaptablty / senstvty: are partcular genotypes able to be adapted to mprovements n the envronment? Stablty: s the performance of partcular genotypes consstent? Related wth the envronments: Groupng of trals nto mega-envronments: fndng structure n the TPE. Gven a structure of the TPE optmze the choce of trals to represent the TPE

11 Summary G x E = Dfferent genotypes respond dfferently to a change n the envronment G x E may result n heterogenety of varance and rerankng Reacton norm s an mportant concept Non-parallel reactons norms = G x E = genetc varaton n envronmental senstvty/plastcty/adaptablty 21 Concepts of stablty 22 11

12 Dfferent concepts of stablty Stablty s a measure of varablty n performance across envronments Constant performance s better than no performance (food securty) Predctable response to mprovement of envronment s desrable, E.g. fertlzer Dfferent defntons needed 23 Stablty and predctablty Desrable: Low senstvty to unpredctable changes n E E.g. Temporal fluctuaton n E, such as the weather Hgh senstvty to predctable changes n E E.g. Good response to fertlzer 24 12

13 Key dfferences n stablty concepts Slope of the reacton norm Varablty around reacton norm 25 Defntons of stablty Statc and dynamc stablty (Becker and Leon, 1988) Type 1 to 4 (Ln et al., 1986; Ln and Bnns, 1988) Macro-envronmental, mcro-envronmental senstvty and unformty (Falconer and Mackay, 1996; Mulder et al. 2013) 26 13

14 Statc stablty = Bologcal concept of stablty Measures the overall varablty of a genotype (or a lne ) over envronments General model: μ μ G E GE Statc (n)stablty: var( μ.) across envronments 27 Dynamc stablty Agronomc concept of stablty Does not nclude the predctable varablty n performance across envronments General model: μ μ G E GE Dynamc (n)stablty: σ 2 G E Does not penalze genotypes for varaton due to 2 a predctable response to the envronment ( ) σ E 28 14

15 Dynamc versus statc stablty n fgures Not statc Not dynamc stable b=1.5 Statc Dynamc stable b= Fnlay-Wlknson regresson & stablty measures FW-regresson = Lnear reacton-norm model For the average performance of lne n envronment () μ μ G E (1 β ) δ = overall mean G = overall value of genotype E = overall value of envronment = (lnear) senstvty of genotype to envronment > 0: above average senstve < 0: below average senstve E s the average performance n envronment = measure of qualty of envronment 30 15

16 Fnlay-Wlknson Regresson μ μ G E (1 β ) δ μ μ G E β E δ GE β E δ FW-regresson tres to capture GxE-nteracton as a lnear functon of the envronment Idea: - Some genotypes are generally more responsve to envronmental change ( >0) - Other genotypes are generally less responsve to envronmental change ( <0) 31 Type 1 stablty = statc stablty FW-regresson: μ μ G E (1 β ) δ Lttle change of phenotype over envronments Lttle plastcty Slope of reacton norm of ~0-1 Dynamc stable, b=1 Statc stable, b=

17 Type 2 stablty = dynamc stablty FW-regresson: Expected response to envronment Slope of reacton norm ~1 0 and var( ) s small GE 0 μ μ G E (1 β ) δ Dynamc stable, b=1 Statc stable, b=0 33 Type 3 stablty FW-regresson: μ μ G E (1 β ) δ Predctable change of phenotype over envronments Lnearly predctable GxE-nteracton can take any value, but var( ) s small Stable genotype has low resdual varance or hgh R 2 Dynamc stablty measure Eberhart and Russell (1966) 34 17

18 Stablty type 4 FW-regresson: μ μ G E (1 β ) δ Consders locaton vs yearly varaton Good response to locaton varaton Lttle response to temporal varaton ( weather ) Responsve to predctable changes, robust aganst unpredctable changes Dynamc stablty Refnement of type 3 stablty Ln and Bnns (1988) 35 Macro- and mcro-envronmental senstvty Macro-envronment: known envronmental factor or the envronmental mean (=Fnlay-Wlknson) Dfferences n slope of reacton norm Type 2 stablty Mcro-envronment: unknown envronmental factor Dfferences n resdual varance Type 3/4 stablty Envronmental canalzaton 36 18

19 Unformty = less varablty Usually wthn an envronment But can be hdden varaton n reacton norm P = A + E; Unformty = lttle varaton n E Type 3/4 stablty In evoluton called envronmental canalzaton Lectures Wednesday 37 Summary Dfference n slope of reacton norm Dfference n resdual varance Type 1 and type 2 stablty Macro-envronmental senstvty Plastcty Adaptaton Type 3 and type 4 stablty Mcro-envronmental senstvty Unformty Canalzaton 38 19