PBG 650 Advanced Plant Breeding

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

2. 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

3. Probability of fixing favorable alleles during inbreeding Standardized effect of a locus • 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 Relative fitness A1A1 A1A2 A2A2 (no dominance) • Recombinant inbred from an F2 • without selection • with selection (Because p=1/2)

4. Mean with selfing • Inbreeding decreases the mean if there is dominance • At fixation (with no selection): Genotypic Value A1A1 A1A2 A2A2 p2+pqF 2pq(1-F) q2+pqF Frequency does not depend on dominance RI = recombinant inbred lines

5. Mean of recombinant inbreds from a single-cross Mean of recombinant inbreds derived from F2 of a single-cross Means of the parents (for a single locus) • 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

6. 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

7. Selfed families from a single-cross F2 ¼A1A1 ½A1A2 ¼A2A2 F3 ¼A1A1 ⅛A1A1 ¼A2A2 ¼A1A2 ⅛A2A2 Bernardo, Chapt. 9

8. Variance among and within selfed families F3 ¼A1A1 ⅛A1A1 ¼A2A2 ¼A1A2 ⅛A2A2

9. Genetic variance with selfing

10. 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

11. Testcrosses • The choice of tester will determine if an allele is favorable or not Bernardo, Section 4.5

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

13. 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

14. Testcross means • 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

15. 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 Bernardo, Chapt. 12

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

17. 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

18. 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

19. 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]

20. 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

21. 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

22. 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

23. What is a synthetic? • Lonnquist, 1961: • 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

24. 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