THEORY AND APPLICATION Department of Agronomy PHENOTYPIC SELECTION THEORY AND APPLICATION Kendall R. Lamkey USDA-ARS Department of Agronomy Iowa State University Ames, IA 50011 1/9/97

OUTLINE Mendelian vs. Quantitative Traits Genotypic Value Average Effect Breeding Value Heritability Genetic Gain Empirical Results 1/9/97

REFERENCES Falconer, D. S. 1981. Introduction to quantitative genetics. 2nd ed. Longman, New York. Lush, J. L. 1994. The genetics of populations. Iowa Agriculture and Home Economics Experiment Station, College of Agriculture, Iowa State University, Ames. 1/9/97

QUANTITATIVE GENETICS Continuous Variation Mendelism Fisher, R. A. 1918. The correlation between relatives on the supposition of Mendelian Inheritance. Trans. Roy. Soc. Edinburgh 52:399-433. Haldane, J. B. S. 1932. The causes of evolution. Longmans, Green, London Wright, S. 1921. Systems of Mating. Genetics 6:111-178 1/9/97

QUANTITATIVE GENETICS Temperature Precipitation Etc. Genes Environment Genotype Phenotype 1/9/97

QUANTITATIVE GENETICS SELECTION Selection Must Be on Phenotype or Some Function of Phenotype Breeders Only Rarely Know Genotypes for More Than a Few of the Loci an Individual Possesses Individuals Chosen As Parents Transmit Only a Sample of Half of the Genes It Has 1/9/97

QUANTITATIVE GENETICS SELECTION Show Us How to Choose Individuals With the Best Merit (Breeding Value) Predict the Outcome of Selection to Compare Different Breeding Schemes 1/9/97

QUANTITATIVE GENETICS P = G + E PHENOTYPIC VALUE (P) = Value observed when the character is measured on an individual GENOTYPIC VALUE (G) = Value attributable to the particular assemblage of genes possessed by an individual ENVIRONMENTAL DEVIATION (E) = Value attributable to all nongenetic circumstances that influence phenotype 1/9/97

QUANTITATIVE GENETICS Assumptions Random Mating Equilibrium No Linkage No Epistasis Diploid Inheritance f(A) = p f(a) = q p + q = 1 p2AA + 2pqAa + q2aa Random Mating Population 1/9/97

GENOTYPIC VALUE aa Aa AA -a -4 d 2 a 4 aa Aa AA 6 12 14 Yield d 2 a 4 aa Aa AA 6 12 14 Yield MP = (14 + 6)/2 = 10 a = 14 - 10 = 4 d = 12 - 10 = 2 d/a = 2/4 = 0.5 1/9/97

GENOTYPIC VALUE Genotype Frequency Value Freq x Value AA p2 a p2a Aa 2pq d 2pqd aa q2 -a -q2a Mean = a(p-q) + 2pqd 1/9/97

GENOTYPIC VALUE With selection we are concerned with the transmission of value from parent to offspring. This cannot be determined based on genotypic value alone. Parents pass on their genes and not their genotypes to the next generation. Genotypes are created anew in each generation. 1/9/97

GENOTYPIC VALUE Individuals transmit genes (alleles) to their progeny. One result of this is that some aspects of the value of a particular genotype are unpredictable. Selection theory can work only with the predictable aspects of the union of two gametes. Therefore, we need to introduce the average effect of a gene. 1/9/97

P = ai + aj + dij + E ai = Average (or additive) effect of allele i AVERAGE EFFECT P = ai + aj + dij + E ai = Average (or additive) effect of allele i dij = Dominance deviation 1/9/97

AVERAGE EFFECT Average effect of a gene - the mean deviation from the population mean, of individuals that received the gene from one parent, the gene received from the other parent having come at random from the population. Average effect of a gene - let a number of gametes carrying A unite at random with gametes from the population; then the mean of the genotypes so produced deviates from the population mean by an amount that is the average effect of the A gene. 1/9/97

AVERAGE EFFECT Mean = a(p-q) + 2pqd Mean = pa + qd p2AA + 2pqAa + q2aa pA + qa A pA + qa pAA + qaa Mean = pa + qd 1/9/97

AVERAGE EFFECT aA= q[a + d(q - p)] aa= -p[a + d(q - p)] a = aA - aa Average effect of a gene substitution - The mean change in value produced by changing (a) genes at random into (A) genes. 1/9/97

AVERAGE EFFECT Dependent on genotypic value. Dependent on gene frequencies. Property of the population as well as the genes concerned. Average effect of a gene cannot be measured. So, we introduce the concept of breeding value. 1/9/97

BREEDING VALUE Breeding value is the value of an individual judged by the mean value of its progeny. The Breeding Value of an individual is equal to the sum of the average effects of the genes it carries. The summation is over pairs of alleles at a locus and over all loci. Genotype Breeding Value AA 2aA Aa aA + aa aa 2aa 1/9/97

BREEDING VALUE 2qa +a d (q - p)a a -2pa -a 1 2 aa Aa AA q2 2pq p2 (q - p)a a -2pa -a 1 2 aa Aa AA q2 2pq p2 1/9/97

Cp Cs Z c P PHENOTYPIC SELECTION 1/9/97

PHENOTYPIC SELECTION R = bopS R = Response S = Selection Differential 1/9/97

PHENOTYPIC SELECTION Base Population C1 C2 . Cn Develop Progenies Intermate Selections Evaluate Progenies 1/9/97

OBJECTIVES OF SELECTION PHENOTYPIC SELECTION OBJECTIVES OF SELECTION Increase the Frequency of Favorable Alleles, Which Is to Increase the Mean of the Population in the Favorable Direction Maintain Genetic Variability for Continued Selection by Intermating Superior Progenies for Each Cycle of Selection. Therefore, Enhancing the Probability of Obtaining Superior Genotypes (Lines or Hybrids) From the Population. 1/9/97

PHENOTYPIC SELECTION Original Population Improved Population Best Hybrid From Original Population Best Hybrid From Improved Population 1/9/97

PHENOTYPIC SELECTION Plant Breeders Determine Merit Based on Phenotypes. The Goal of Plant Breeding Is to Separate the Environment From the Breeding Value. From a Quantitative Genetic Point of View This Is Equivalent to Maximizing the Heritability. From a Statistics/Regression Point of View This Is Equivalent to Maximizing the Correlation Between Phenotype and Breeding Value. 1/9/97

V(P) = V(ai) + V(aj) + V(dij) + V(E) HERITABILITY V(P) = V(G) + V(E) V(P) = V(ai) + V(aj) + V(dij) + V(E) V(P) = V(A) + V(D) + V(E) 1/9/97

HERITABILITY V(P) = Variance among phenotypes Phenotypic variance V(A) = Variance among breeding values Additive variance V(D) = Variance among dominance deviations Dominance Variance 1/9/97

HERITABILITY h2 = V(A)/V(P) Heritability = The extent to which phenotypes are determined by genes transmitted from the parents. h2 = V(A)/V(P) The goal of an artificial selection program is to maximize heritability 1/9/97

GENETIC GAIN 1/9/97

GENETIC GAIN p Z 1/9/97

GENETIC GAIN where, i = Standardized selection differential c = parental control y = years per cycle r = number of replications per environment e = number of environments 1/9/97

INCREASING GENETIC GAIN Increase Selection Intensity Increase Genetic Variance Decrease Years per Cycle Decrease Phenotypic Variance 1/9/97

INCREASING GENETIC GAIN Increase Selection Intensity Proportion Selected I 30 of 100 1.149 20 of 100 1.386 10 of 100 1.730 5 of 100 2.018 1 of 100 2.508 1/9/97

INCREASING GENETIC GAIN Increase Genetic Variance 1/9/97

INCREASING GENETIC GAIN Decrease Years per Cycle 1/9/97

INCREASING GENETIC GAIN Decrease Phenotypic Variance 1/9/97

APPLICATION EMPIRICAL RESULTS PHENOTYPIC SELECTION APPLICATION EMPIRICAL RESULTS 1/9/97

RECIPROCAL RECURRENT SELECTION BSSSC0 BSCB1C0 HS Families BSSS(R)C1 BSCB1(R)C1 BSSS(R)C9 BSCB1(R)C9 BSSS(R)C12 BSCB1(R)C12 BSSS(R)C1 X BSCB1(R)C1 FS Families BSSS(R)C12 X BSCB1(R)C12 S1 1/9/97

RECIPROCAL RECURRENT SELECTION BSSS - Iowa Stiff Stalk Synthetic - 16 Inbred Line Synthetic - Synthesized in Early 1930s BSCB1 - Iowa Corn Borer Synthetic #1 - 12 Inbred Line Synthetic - Synthesized in 1940s 1/9/97

IOWA STIFF STALK SYNTHETIC Os WD Ind Ill CI CI Ill Oh Ind TR A3G- CI Le I159 I224 420 456 461-3 12E 617 540 HY 3167B AH83 9116 F1B1 313 187-2 23 Single Crosses Double Crosses Double-Double Crosses Bulk Equal Quantities Seed BSSSC0 1/9/97

IOWA STIFF STALK SYNTHETIC 1/9/97

IOWA STIFF STALK SYNTHETIC 1/9/97

IOWA STIFF STALK SYNTHETIC BSSS(R)C0 X BSCB1(R)C0 BSSS(R)C5 X BSCB1(R)C5 BSSS(R)C11 X BSCB1(R)C11 1/9/97 Grain Yield Mg ha-1

IOWA STIFF STALK SYNTHETIC BSSS(R) BSCB1(R) C4 C4 C0 C0 C7 C9 C7 C9 C11 C11 1/9/97

IOWA STIFF STALK SYNTHETIC Heterozygosity Population Observed Expected Progenitors 0.01 0.59 C0 0.44 0.49 C12 0.31 0.34 1/9/97

IOWA CORN BORER SYNTHETIC #1 Heterozygosity Population Observed Expected Progenitors 0.05 0.61 C0 0.52 0.58 C12 0.30 0.32 1/9/97

NEI’S GENETIC DISTANCE BSSS(R) BSCB1(R) P C12 0.33 0.26 0.07 0.66 1/9/97

Gene diversity GENE DIVERSITY BSSS(R) and BSCB1(R) 0.7 Total 0.6 0.5 P 0.5 Gene diversity C0 Mean 0.4 within 0.3 C12 0.2 BSSS(R) and BSCB1(R) 1/9/97

BS11 SELECTION METHODS STUDY Last Cycle Method Evaluated Full-sib (FS) 5 Half-sib with Inbred Test. (HI) 4 Modified Ear-to-row (MER) 5 Mass selection (MASS) 10 Reciprocal Full-sib (FR) 5 S1 Progeny (S1) 5 S2 Progeny (S2) 4 1/9/97

BS11 SELECTION METHODS STUDY Cycle # Progeny Selection Method Tester Time Evaluated * Intermated Intensity FS BS11 2 100 20 20 MER BS11 2 100 20 20 HI B79 3 100 20 20 S2 BS11 3 100 20 20 S1 BS11 2 100 20 20 FR BS10 2 175 20 11 MASS BS11 1 10000 100 1 *Evaluations based on 2 Reps at 3 Locations 1/9/97

BS11 SELECTION METHODS STUDY Grain Yield - Populations Per Se 5.8 Response R2 = 0.83 Per Cycle % S2 MER 5.6 S2 0.21** 4.5 MER 0.17** 3.6 FR 0.12** 2.6 S1 0.09** 1.9 HI 0.08** 1.6 FS 0.07** 1.4 MASS 0.03** 0.6 5.4 FR Mg ha-1 5.2 S1 HI FS 5.0 4.8 MASS 4.6 1 2 3 4 5 Cycle 1/9/97

BS11 SELECTION METHODS STUDY Stalk Lodging - Populations Per Se 24.0 MASS 22.0 FR 20.0 18.0 Response S2 -2.4** MER -2.2** FS -2.2** HI -2.1** S1 -2.0** FR 0.0 MASS 0.3** Per Cycle % 16.0 14.0 HI 12.0 S1 10.0 S2 FS R2 = 0.85 MER 8.0 1 2 3 4 5 Cycle 1/9/97

ACKNOWLEDGEMENTS Dr. Joanne Labate Roger Weyhrich Jode Edwards Peter Guzman Chris Mack Kebede Mulatu John Golden Jim Sears Dr. Arnel R. Hallauer Dr. Michael Lee Dr. Howie Smith Dr. Paul Scott 1/9/97

U.S. CORN YIELD - 1866 to 1996 R2 = 0.96 Single Crosses b = 2.06 Double Crosses b = 1.10 Open pollinated b = -0.08 1/9/97