PBG 650 Advanced Plant Breeding Module 12: Selection Inbred Lines and Hybrids

Selection for a high mean Success is a function of the population mean  the deviation of the best segregants from  ability to identify the best segregants Advanced Cycle Breeding = “inbred recycling” cross best by best (often related) pedigree and backcross selection emphasis on high mean at the expense of G2 need methods for predicting  Bernardo Chapt. 4

Probability of fixing favorable alleles during inbreeding Standardized effect of a locus Relative fitness (no dominance) A1A1 A1A2 A2A2 Recombinant inbred from an F2 without selection with selection (Because p=1/2) For most quantitative traits, probability of fixing the favorable allele is closer to ½ than to one. Bernardo calls s the selection coefficient – related to “fitness” concepts Three approaches to increase chances of fixing favorable alleles selection before inbreeding selection during inbreeding one or more backcrosses to the better parent before inbreeding

Mean with selfing Genotypic Value A1A1 A1A2 A2A2 Frequency p2+pqF q2+pqF Inbreeding decreases the mean if there is dominance At fixation (with no selection): does not depend on dominance RI = recombinant inbred lines

Mean of recombinant inbreds from a single-cross Means of the parents (for a single locus) Mean of recombinant inbreds derived from F2 of a single-cross The mean of recombinant inbreds derived from an F2 or backcross population can be predicted as a simple function of allele frequencies (the contribution of the parents) A = 6 t/ha B = 4 t/ha RI[(AxB)(A)BC1] = ¾*6 + ¼*4 = 5.5 t/ha

Selfed families from a single-cross F2=S0 plant F3=S1 plant F4=S2 plant F5=S3 plant F3=S1 family F4=S2 family F5=S3 family represents S0 plant represents S1 plant represents S2 plant

Selfed families from a single-cross ¼A1A1 ½A1A2 ¼A2A2 F3 ¼A1A1 ⅛A1A1 ¼A2A2 ¼A1A2 ⅛A2A2 Bernardo, Chapt. 9

Variance among and within selfed families ¼A1A1 ⅛A1A1 ¼A2A2 ¼A1A2 ⅛A2A2

Genetic variance with selfing

Inbreeding as a Selection Tool for OPVs More genetic variation among lines Increased uniformity within lines Visual selection can be done for some traits Permits repeated evaluation of fixed genotypes in diverse environments, for many traits Sets of inbred lines can be used to identify marker-phenotype associations for important traits Best lines can be intermated to produce synthetic varieties with defined characteristics

Genotypic value of testcross Testcrosses The choice of tester will determine if an allele is favorable or not Testcross genotypic values with complete dominance Genotypic value of testcross Parent of cross A2A2 tester A1A1 tester A1A1 d a = d A1A2 ½(d - a) A2A2 - a Bernardo, Section 4.5

Effect of alleles in testcrosses Tester is an inbred line or population in HWE Genotypic Value A1A1 A1A2 A2A2 Frequency ppT pqT + pTq qqT

Testcross mean of recombinant inbreds Testcross means of parental inbreds Testcross mean of recombinant inbreds derived from F2 of a single-cross The testcross mean of recombinant inbreds derived from an F2 or backcross population can be predicted as a simple function of allele frequencies (the contribution of the parents) T=AxC and BxC TA = 8 t/ha TB = 6 t/ha For RI derived from the F2 of AxB TRI(AxB) = ½*8 + ½*6 = 7 t/ha

Testcross means p2+pqF T+qT 2pq(1-F) T+½(q - p)T q2+pqF T - pT Genotype Frequency Testcross Mean A1A1 p2+pqF T+qT A1A2 2pq(1-F) T+½(q - p)T A2A2 q2+pqF T - pT Testcross mean of the heterozygote is half-way between the two homozygotes Cross “good” by “good” But, the correlation between the performance of inbred lines per se and their performance in testcrosses is very poor for yield and some other agronomic traits

Heterosis or Hybrid Vigor Quantitative genetics: superiority over mean of parents Applied definition superiority over both parents economic comparisons need to be made to nonhybrid cultivars Various types population cross single-, three-way, and double-crosses topcrosses modified single-cross definition of a modified single-cross advantages and disadvantages of double-crosses Bernardo, Chapt. 12

Amount of heterosis due to a single locus = d A1A1 x A2A2 A1A2 F1 F2 ¼A1A1 ½A1A2 ¼A2A2 Amount of heterosis due to a single locus = d 50% is lost with random-mating

Theories for Heterosis Dominance theory: many loci with d  a Should be possible to obtain inbred  single-cross Expect skewed distribution in F2 (may not be the case if many loci control the trait) Overdominance theory: d > a Pseudo-overdominance - decays over time +1 -2 -1 +2 +1 tight, repulsion phase linkages partial to complete dominance A1 B2 A2 B1 A1 B2 X A1 B2 A2 B1 A2 B1 +2

Heterosis – some observations Experimental evidence suggests that heterosis is largely due to partial or complete dominance Yields of inbred lines per se are poor predictors of hybrid performance due to dominance hybrids from vigorous lines may be too tall, etc. due to heritability <1 Heterosis generally increases with level of genetic divergence between populations, however…. There is a limit beyond which heterosis tends to decrease A high level of divergence does not guarantee that there will be a high level of heterosis Extremely divergent populations or lines may not be adapted to the same environments

Heterosis – more observations Epistasis can also contribute to heterosis does not require d>0 Selection can influence heterosis Iowa Stiff Stalk Synthetic (BSSS) Iowa Corn Borer Synthetic (BSCB1) High density SNP array shows increasing divergence over time in response to reciprocal recurrent selection Gerke, J.P. et al., 2013 arXiv:1307.7313 [q-bio.PE]

Heterotic groups Parents of single-crosses generally come from different heterotic groups Two complementary heterotic groups are often referred to as a “heterotic pattern” Temperate maize ‘Reid Yellow Dent’ x ‘Lancaster Sure Crop’ Iowa Stiff Stalk x Non Stiff Stalk Tropical maize Tuxpeño x Caribbean Flint

Identifying heterotic patterns Diallel crosses among populations Crosses to testers representing known heterotic groups Use molecular markers to establish genetic relationships, and make diallel crosses among dissimilar groups initial studies were disappointing markers must be linked to important QTL

Exploiting heterosis Recycle inbreds within heterotic groups Evaluate testcrosses between heterotic groups elite inbreds often used as testers BLUP can predict performance of new single-crosses using data from single-crosses that have already been tested fairly good correlations between observed and predicted values

What is a synthetic? Lonnquist, 1961: Poehlman and Sleper: Open-pollinated populations derived from the intercrossing of selfed plants or lines Subsequently maintained by routine mass selection procedures from isolated plantings Poehlman and Sleper: Advanced generation of a seed mixture of strains, clones, inbreds, or hybrids Propagated for a limited number of generations by open- pollination Must be periodically reconstituted from parents Parents selected based on combining ability or progeny tests

Predicting hybrid performance Three-way crosses Double-crosses Wright’s Formula Synthetics = avg yield of all F1 hybrids n = number of parents = avg yield of parents