INTRODUCTION TO PLANT BREEDING

AGRONOMY 815 / COURSE NOTES

P. STEPHEN BAENZIGER, 338 Keim Hall, 472-1538

DEPARTMENT OF AGRONOMY / UNIVERSITY OF NEBRASKA

CYTOGENETICS -- THE PHYSICAL BASIS FOR GENETICS

Fehr, Chapt. 3

LINKAGE:

Genes on the same chromosome are linked and tend to be carried in blocks. The effect of linkage is to influence the frequency of the various combinations of genes. It can be beneficial if positive alleles are linked together or negative if deleterious genes are linked to traits of interest. Usually it is assumed that breeders have built up useful linkage blocks, but that within a cross between two parents the genes of interest are in repulsion phase.

• How do we detect linkage?

Observe segregation ratios in F₂ (progeny test) or testcross generation. Compare with expected ratio based upon the assumption of independent assortment. Use Chi-square test to determine whether deviations are due to sampling error (chance).

The Chi-square test is used to test experimental results against expectations derived from a null hypothesis. The test generates a p value that is the probability of obtaining a specific deviation at least as great as that observed, assuming that the null hypothesis is correct.

• If linked, how closely linked are the genes?

Can calculate approximate distance in terms of crossover probabilities between the two loci (not actual physical distance although may be in close agreement).

Crossover units = (crossover progeny/total progeny) x 100. This is done using a test cross ratio usually so that all of the crossover progeny are readily counted (easiest method). It can also be done by measuring one recombinant class and assuming that the other recombinant class equally represented. In crops such as soybeans where crosses are difficult, F₂'s are used to estimate linkage. When two genes are involved, the doubled recessive class is used to estimate the number of recombinants:

e.g.,Table 3.3 in Poehlman.

Other genes on these chromosomes may also be linked. The greater the distance between linked genes, the more frequently crossovers will occur. From crossover percentages linkage maps can be drawn.

Note the largest map distance for linked traits that can be obtained is <.5 in that unlinked traits using the above crossover model have a value of .5.

General effect of linkage is to cause an overabundance of parental combinations and corresponding deficiency of recombinants.

• Important considerations with linkage:

1. Proportion of recombinations of two closely linked genes may be small therefore need larger F₂ population or more cycles of recombination if want to be able to select a recombinant genotype.

2. Percent recombination is fairly constant for any two linked genes. Exception is genes affecting recombination and chromosomal abnormalities.

3. Number of recombinations of linked genes obtained from a cross may be small. Can increase population size.

   Several generations if intercrossing following the F₁ would permit greater recovery of recombinants than with immediate selfing. Not always easy in self pollinated crop but can be aided by male sterile genes.

4. Linkage can be an aid to selection.

   e.g., Genes for resistance to stem rust and loose smut in barley are in the same linkage group with a low crossover value. Inoculation for stem rust screening is easier than for loose smut. However, if one only screens for stem rust resistance, rust resistant progeny most likely will also be resistant to loose smut.

5. 5. Often have some undesirable linkages also.
   e.g., Unadaptiveness linked to a desirable trait.

As we will see later, many possible uses for linkage have not been exploited due to the confining aspects of small breeding populations relative to the large populations used in commercial practice.

Effect of linkage upon the proportion of AB/ab genotypes expected in the F₂ from the double heterozygote.