Slide 6.2

Slide 6.3 Dominance and recessiveness - both alleles may encode proteins; example - eye colour -the gene that encodes the protein that "does the job" is dominant. -most alleles are codominant (both proteins contribute to function) -in agricultural breeding, many useful alleles are dominant, caused by quantitative gain-of-function alleles (eg. disease resistance) Because evolution favored having two alleles per gene, evolution created sexes (male and female), each parent giving one copy to the progeny (parent = P; progeny = F1) Allele A Functional protein No protein or little protein Allele B Sex brings these two sets of alleles together. Problem: To maintain 2 copies/gene in the progeny, each parent must only contribute one copy of the two it has = meiosis Fig Fig 5.1 Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. WH Freeman and Co. Publishers, NY, 1996

B. Meiosis and Meiotic Recombination meiosis = the process of producing gametes that involves reducing the allele number from two to one per gene to facilitate inheritance via sex (demo showing duplication/reduction) Meiosis Mitosis Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. Figure 5.2 WH Freeman and Co. Publishers, NY, 1996 Slide 6.4

Meiosis permits the independent assortment of genes because of the existence of multiple chromosomes to allow the progeny to try out new combinations of alleles. This is useful because many genes are involved in producing a trait such as seed yield. Independent assortment - for each chromosome pair, each gamete can contribute the maternal or the paternal chromosome. If two genes in a genome do not assort independently after meiosis (from a sample of many meiosis), then the two genes are likely on the same chromosome. In such a case, the two genes are said to be linked In addition to mixing and matching entire chromosomes, evolution selected for segments within chromosomes to be mixed and matched = meiotic recombination demo Why is a genome divided into multiple chromosomes instead of one large chromosome? (demo of advantage of >2 chromos vs 1 chromosome) Fig 19.1 Fig 19.3 Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. Chapter 19 WH Freeman and Co. Publishers, NY, 1996 Slide 6.5 Chiasmata

For meiotic recombination to occur, the two chromosome pairs must be aligned perfectly = chromosome pairing. This pairing is mediated by precise recognition proteins that recognize homologous DNA sequences and align them. Fig 3.27Fig 3.28 Synaptonemal Complex Proteins “zip” the pairs together The result of meiotic recombination is that blocks of genes (chromosomal segments) are inherited intact from each parent, NOT entire chromosomes. In the discipline of Genetics, it has been observed that the physical distance between alleles of two linked genes ("map units" or CentiMorgans, cM) is directly proportional to the number of meiotic recombination events that occur in the gametes. Fig 5.9 Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. Chapters 3 and 5 WH Freeman and Co. Publishers, NY, 1996 Slide 6.6 Fig 5.7

Therefore, the percentage of "recombinants" that are recovered equals the relative, physical map distance between the two genes. This method (called "linkage mapping") is used to determine the order and physical distances of genes on each chromosome. Once a gene has been assigned a relative location on the chromosome (relative to other genes), the gene is said to be "mapped". Once a gene is mapped, it accelerates breeding and accelerates being able to isolate ("clone") that gene. Fig 5.15C Slide 6.7 A tomato linkage map Map distances between linked benes (m.u. = map unit) Fig 5.10 Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al Chapter 5 WH Freeman and Co. Publishers, NY, 1996

Meiotic recombination allows new allelic block combinations to be generated (demo with lethal flags) Independent assortment and meiotic recombination are only useful if different alleles exist. Extremely different alleles can be found if the parents were previously geographically isolated from each other and hence developed independent sets of mutations. Meiotic recombination allows blocks of alleles to be exchanged between parental chromosomes -- this is the basis of breeding. C. Breeding Sex between these two parents ("breeding") can bring the two sets of alleles together. Sometimes, the F1 progeny resulting from the cross between two geographically-diverse parents results in hybrid vigor, which can increase yields (corn, rice, etc.) by >15%. The mechanistic basis of hybrid vigor is not understood and is very controversial. Any hypotheses? -each parent has different recessive, harmful mutations -by crossing them, the progeny inherit a dominant, functional allele for each locus (gene) Slide 6.8 Small plant A x small plant B = large plant Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. Figure 5.21 WH Freeman and Co. Publishers, NY, 1996

Slide 6.9 Meiotic recombination allows small chromosomal segments containing useful genes (eg. disease resistance) to be bred into locally adapted lines Goal: Problem Local x wild progeny = F1 50% = wild Local variety Wild variety disease resistance allele Solution Allow meiosis to recombine Disease R gene onto “local” chromosome 2 background Backcross recombined chromosome 2 to Local lines for 5-6 generations (BC1-BC6) to regenerate a nearly-pure Local variety genetic background. source: M.Raizada

Independent assortment and meiotic recombination are only useful if different alleles ("genetic diversity") exist; otherwise new combinations of alleles cannot be mixed up for breeding. These alleles can come from diverse geographic populations (such as from seedbanks) or they can be generated artificially using chemicals or high energy radiation ("mutagens"). This is called mutation breeding, which has been practiced since ~World War II: Fig Table 15.5 Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. Chapter 15 WH Freeman and Co. Publishers, NY, 1996 Slide 6.10

D. Evolution of genomes and the speciation of crops Mistakes during meiosis contribute to large changes in genome evolution and speciation, and have been critical to the evolution of crop species. meiotic recombination involves breaking and pasting of chromosome segments such that all genes are conserved. However, due to mistakes in chromosome alignment or DNA repair, a block of a chromosome can randomly break and reattach to itself or to other chromosomes resulting: (demonstrations of) These mistakes allow for genes to becoming duplicated (and initially redundant), but then they mutate to create related, but novel genes (through gradual spontaneous mutations). This is a way for gene numbers to rapidly increase and create more complexity = gene families. Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. Figure 17.1A WH Freeman and Co. Publishers, NY, 1996 Slide 6.11 What are each of these? tandem duplication deletion inversion translocation loss or gain of an entire chromosome

Change - Merging Entire Genomes at Fertilization Mistakes in reproduction that permit the chromosomes from the pollen and eggs from different species to unite can result in the production of new species: 1 set of chromosomes = haploid 2 sets of chromosomes = diploid 4 sets of chromosomes = tetraploid 6 sets of chromosomes = hexaploid bread wheat = hexapoloid - recent fusion of 3 species pasta wheat = tetraploid - recent fusion of 2 species modern corn = tetraploid - ancient fusion of 2 species -because ancient, genes have diverged, so appeared to be a diploid Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. Figure WH Freeman and Co. Publishers, NY, 1996 Figure 6.12

It appears as if most crop species have undergone multiple genome fusions during the last 100 million years. This appears to be a common way to rapidly recombine large numbers of different alleles together, perhaps during periods of rapid or extreme environmental change. Slide 6.13 Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al. Figure WH Freeman and Co. Publishers, NY, 1996

***The result is that genomes are "a mess", an ancient record of the mistakes in recombination, the fusion of genomes, the gain and loss of blocks of chromosomes, and many, many rearrangements***** eg. Corn vs rice, highly related, though overall synteny, has 15,000 local chromosomal rearrangements The rearrangements, duplications in the 5 chromosomes of Arabidopsis thaliana (related to canola) TAGI (2000) Nature 408, Nature Publishing Group, U.K. Slide 6.14

E. Lecture 6 - Summary of Concepts Therefore, how did different crop plants and evolution of higher plants evolve? --New alleles for natural selection and breeding selection from: -Point mutations -Jumping Genes -Segmental gene duplications -inheritance or loss of entire chromosomes or entire genomes -All of these recombine, mix and match, due to meiosis (independent assortment of chromosomes) and meiotic recombination (exchange of blocks within each chromosome) meiotic recombination with sex drives the mixing of blocks of chromosomal DNAto generate new combinations of alleles -- this is the basis of evolution and breeding alleles are inherited as chromosomal blocks the genome is not ordered, but messy, the result of mistakes in DNA recombination, resulting in new genes Questionnaire please Slide 6.15