Choice of Parental Germplasm and Population Formation

1. Choice of Parental Germplasm and Population Formation The breeding method ultimately implemented is irrelevant if the necessary genetic variation and overall level of adaptation and yield have not been built into the population upon which you impose selection. • Knowledge of the evolution of the genus, plus a classification of the cultivated species and its relatives.  • A comprehensive history of cultivar development in the species.  • Knowledge of the biotic and abiotic stresses found in your target environments and their relative levels of importance to crop production.  • Knowledge of the germplasm resources available. Of particular importance is their adaptation to your target environments.

2. Classification of the cultivated species and its relatives Variation patterns in cultivated plants can be very different from those of wild species. Taxonomists have traditionally spent little time on cultivated species, and those who did may have reached remarkably different conclusions, even when working with the same materials For example, broccoli, brussel sprouts, cabbage and cauliflower are grossly different morphologically but they are in the same species in a biological sense--i.e., they can be crossed and the hybrids are fertile. Frustrated with this sort of vacillation and indecision among taxonomists who cannot agree on species limits, breeders have adopted Harlan and deWet’s more informal and intuitive classifications as to what constitutes useful groupings based on practical experience.

3. Harlan and deWet’s Gene Pool System Informal genetic perspective Primary gene pool: Biological species Secondary gene pool : Allele transfer a struggle Tertiary gene pool: Outer limit of potential genetic reach. Every other plant and animal?

4. A Comprehensive History of Cultivar Development in the Species The in-depth compilations published in the United States Department of Agriculture Yearbooks of 1936 and 1937 provide a valuable starting point for many species. Species monographs published by The American Society of Agronomy and similar organizations. Pedigrees and methodologies utilized in cultivar development in a diverse range of species can be found in Registration articles in the journal Crop Science.

5. Biotic and Abiotic Stresses in Your Target Area Resistance, or tolerance to all economically important biotic and abiotic stresses must be incorporated into breeding populations constructed for cultivar development. Although a thorough knowledge of all the stresses that are found in your target areas is vital, one needs to be aware of economic thresholds and the frequency of occurrence of each stress when priorities are being decided. Life cycles - sexual or asexual - Races or Biotypes - virulence changes (e.g. powdery mildew in wheat) - host resistance quantitative or qualitative - - average life of qualitative allele – pyramids available - effective alleles (Cereal Disease Lab)

6. Am I in trouble? Attacks Rust race Cereal Disease Lab USDA / U. Minn. Track virulence patterns of rust fungi Isoline series? Each isoline contains a major gene in a common genetic background

7. Recessive

8. Knowledge of Available Germplasm Resources An overwhelming majority of all germplasm incorporated into cultivar development breeding populations comes from cultivated species adapted to your target environment Note: ‘Exotic germplasm’ refers to not just wild or progenitor species, but to cultivated types adapted to different target environments.

11. Step 1: Adapted/Exotic Cross. An adapted, high yielding cultivar with excellent baking quality, but poor fungal resistance, is crossed to an exotic cultivar with excellent fungal resistance but poor baking quality characteristics. The fungal resistance is controlled qualitatively, so the breeder is only seeking a single resistance allele . The inbred progeny from this cross will contain some excellent fungal resistance, but none will contain the required baking quality, which is quantitatively controlled Step 2: Adapted/Exotic/2/Adapted Backcross.Next the breeder backcrosses the F1 to an adapted parent. A step in the right direction, but still one is unlikely to recover inbred progeny with acceptable baking quality. Step 3: Adapted/Exotic/2/Adapted/3/Adapted Backcross. Thus an extended backcrossing program (prebreeding or parent building) is required.

12. In general, when unadapted, exotic parents must be utilized to provide the necessary genetic variation the order of preference will be:  1. Improved cultivars and breeding lines  2. Landraces or older cultivars  3. Closely related species  4. More distantly related species and genera

13. A List of Parents for Cultivar Development. • The Reliables/Anchors • They serve as ‘anchors’ to provide the breeding population with overall adaptation and high yield potential. • Elite Germplasm. • These genotypes are important because they may contain new combinations of alleles that are superior to the Reliables described above.

15. Allele Sources for Specific Traits. • Consists of cultivars, breeding lines or germplasms that may or may not be adapted to your target environments. Typically contain pathogen resistance or novel physiological or morphological characteristics. (http://www.ars-grin.gov/)

16. Remnant Single- and Two-Way Hybrids. • Remnant F1 hybrid seeds are found in most programs and can serve as building blocks over many crossing seasons for three- and four-way hybrid populations.

17. The Search for Alternative Methods of Parental Selection The approach whereby 'good by good' parental hybridizations are made has shown time and again to have the highest probability of producing superior progenies. Breeders desire to increase the frequencies of parental combinations that produce superior advanced generation lines. The general objective of the studies is to measure the genetic distance between all potential parents. By combining two parents with high mean trait values and the maximum genetic distance, one should be able to construct a breeding population that maximizes the probability of containing high transgressive segregates because the population mean would be high and the trait would exhibit a broad genetic variance.

18. Coefficient of Parentage • A methodology that has received much attention is in-depth pedigree analysis that measures the probability that two parents have the same allele at any given locus (coefficient of parentage).

19. 2. Multivariate Analysis Grain  C3 yield C2  C1    Heading date The distance between the three cultivars on the plot is one measure of their genetic distinctiveness, or genetic distance, based on the traits grain yield and heading date.

20. Principal Component Analysis (PCA)Creates a new set of dimensions (usually two or three) based on the best combination of the original set of multiple dimensions. This permits the plotting of the cultivars in two- or three-dimensional space to obtain estimates of genetic distances between cultivars that are based on multiple variables

21. Bhatt (1973) conducted one of the original studies comparing the use of multivariate analysis for selecting parents compared to the conventional methods described above Eleven parental combinations were made and he developed 27 random F4:5 progenies in each of the resulting 11 populations • Conventional basis, whereby parents were chosen on their ability to complement weaknesses in each other.  • Random basis, whereby parents were chosen at random. This practice would be rare, for obvious reasons. • Multivariate analysis, whereby parents were chosen on the basis of their genetic distance estimates. • Ecogeographical diversity, whereby parents were chosen because they were adapted to different ecogeographic zones. Such geographical diversity is a reasonable index of genetic diversity.

22. Population number, basis on which parents were selected, estimated parental divergence (rank), genetic variability among lines in cross (rank), and number of high transgressive segregates for yield. Rank No. of Basis forParentalMean Variation transgressive Population parent selection divergence1 yield among lines segregates 1 Conventional 8 8 10 1 2 Conventional 10 11 8 0 3 Random 6 4 7 3 4 Random 11 7 11 0 5 M. Anal. – Distant 2 1 2 10 6 M. Anal. – Distant 1 6 1 9 7 M. Anal. – Close 5 10 6 4 8 M. Anal. – Close 7 9 9 2 9 M. Anal. – Close 9 3 5 0 10 Ecogeographical 4 5 4 7 11 Ecogeographical 3 2 3 5 1 all parental divergence estimates based on multivariate analysis

23. Molecular Markers • The development of marker technologies such as isozymes, RFLPs, RAPDs, AFLPs, SSRs, etc., has provided the ability to measure, not just infer, differences at the DNA level. Heterotic groups are germplasm groupings, determined on the basis of heterosis levels expressed in F1 progeny from crosses between different parents. The two most important heterotic groups in corn are Reid Yellow Dent and Lancaster Sure Crop. One of the biggest selling hybrids ever was the F1 from the cross between the inbreds B73 (a Reid type) and MO17 (a Lancaster type).

24. Lee et al. (1989) examined the RFLP fingerprints of seven inbreds and evaluated their F1 hybrids for yield in multienvironment tests. Three of the inbreds were from the: BSSS sub-set of the Reid group, Three inbreds were from the: C103 sub-set of the Lancaster group, One inbred (B79) was of unknown heterotic group. The more bands (alleles at RFLP loci) they had in common, the closer their DNA structure.

25. Summary by heterotic group of hybrid yields, genetic distance between their inbred parents, and number of heterozygous RFLP loci in F1 hybrids (after Lee et al., 1989). Hybrid F1 hybrid Parental F1 hybrid combination yield genetic distance heterozygous loci   Mg ha-1 BSSS x BSSS 7.0 0.55 33 C103 x C103 6.9 0.64 44 BSSS x C103 8.6 0.79 68 BSSS x B79 7.4 0.72 56 C103 x B79 8.2 0.77 65 LSD (0.05) 0.8 Thus the RFLP data on inbreds and predictions for their crosses were consistent with expectations based on known pedigrees. These data suggest that B79 may be more closely related to BSSS germplasm than C103 germplasm.

26. Burkhamer et al. (1998) utilized STS-PCR primer sets and AFLP primer combinations to estimate genetic distances between 10 spring wheats. They used this relationship data to predict genetic variance for nine traits among 50 random F3:5 lines in 12 crosses involving the parents. The coverage of the genome was extensive in this study as 505 polymorphic bands were observed with the STS primers and an additional 145 polymorphic fragments were observed with the AFLPs.

27. Simple correlation between genetic variance and genetic distance based on STS-PCR primer sets and AFLP primer combinations in 12 wheat populations for nine traits. Genetic distance based on Trait STS AFLP Tillers m-2 0.31 0.15 Plant height 0.33 0.22 Stem solidness 0.34 0.13 Grain yield 0.41 0.13 Test weight 0.44 0.34 Heading date 0.54 0.44 Maturity 0.56 0.20 Grain filling 0.54 0.55 Grain protein 0.50 0.36

28. The authors point out that one possible reason for this was that they had no indication if any of the polymorphic markers were linked to loci controlling any of the traits and that linkage relationships are likely more important than absolute marker number. The results seem to indicate that, for markers to be useful as predictors, the effects of QTL 'alleles' linked to specific marker alleles must be ascertained (Stuber et al., 1999). Population Formation by Hybridization Required reading: Chapter 12, Fehr, pp. 136-155.

29. Types of Crosses • Single cross • Three way cross • Four way cross • Complex cross

30. Single cross • Easy to make good x good • Choose parents to complement one another • Choose parents from different “heterotic groups” • Some crops have many breeding targets • Two parents unlikely to have all traits

31. Three Way Cross • True or modified backcross • Widely used in wheat • Third parent is critical (50%)

34. Four Way Cross • Cross two single cross F1’s • Not as successful as 3 way crosses in wheat • One modification: Use two F1’s which have one parent in common - same genetic composition as 3 way, but increased recombination

35. Complex Crosses • > 4 parents • See Fehr chapter 12 for methods of combining parents • Will discuss polycrosses with Dr. Phillips

36. Assessing Parental Value • Can make crosses using parents to evaluate their “combining ability” • Typically we would cross parents in all possible combinations - referred to as a diallel • Requires considerable time; most breeders will not do this