Lecture 1 Plant Genetics Overview. How plants are different from animals?

1. Lecture 1 Plant Genetics Overview. How plants are different from animals? Variation in quantity of DNA Polyploidy Mitochondrial Genome Chloroplast Genome Crossing Strategies and Plant Breeding Cytoplasmic Male Sterility

2. Plants From space, the land is green!! They represent our food source and the basis for a vast array of products we depend on. 400,000 species of plants Phylum - Eukaryota Kingdom- Plantae (Viridiplantae) Chlorophyta Streptophyta (green algae) Higher plants Algae other than green algae (e.g. liverworts, mosses, (brown, red, yellow-green) ferns, gymnosperms and flowering plants)

3. Flowering Plants- Angiosperms Evolved about 130 million years ago at the same time as birds and mammals. 234,000 species (800,000 insects, 4,600 mammals)

4. Variation in quantity of DNA Species Common Ploidy Genome size name level in bp Saccharomyces cerevisiae Yeast 1.3 x 106 Homo sapiens Human 2 3 x 109 Arabidopsis thalina Thale cress 2 1.4 x 108 Oryza sativa Rice 2 4.2 x 108 Beta vulgaris Sugar Beet 2 7.6 x 108 Vicia sativa Common vetch 2 1.6 x 109 Solanum tuberosum Potato 4 1.8 x 109 Hordeum vulgare Barley 2 4.9 x 109 Vicia faba Broad bean 2 1.2 x 1010 Triticum aestivum BreadWheat 6 1.6 x 1010 There are probably 30-38,000 functional genes in plants. Big genomes have more repetitive DNA.

5. Variation in quantity of DNA Classes of DNA Single or Low-Copy sequences -genes including introns (probably 30-38,000) Repetitive DNA Multiple copy genes - e.g. ribosomal genes Telomeres- (CCCTAAA - repeated many times) Mobile elements transposons and retrotransposons (which comprise up to 50% of genome) Tandemly repeated DNA- short sequences in tandem, being present in blocks of multiple copies e.g. Simple sequence repeats or SSRs - short sequences of 1-5bp tandemly repeated AKA Microsatellites

6. Polyploidy Plants are much more diverse in terms of ploidy level than animals. Almost half of angiosperms (flowering plants) are polyploid. Diploid gametes can be formed without meiosis, or tetraploid tissue is formed when cells fail to divide after replication in mitosis. Triploids (3n) are not uncommon but are generally sterile e.g. commercial banana. Tetraploids (4n) are usually healthy and fertile e.g. durum wheat. Pentaploids (5n) are sterile Hexaploids (6n) are Ok e.g. bread wheat . . Several hundred ploid (n = 100s) do exist Polyploidy is very important in evolution. Commonly, the extra copies of chromosomes are not needed, and undergo rapid mutations and rearrangements. After several generations, the tetraploid is more like a diploid with lots of ‘junk’ DNA.

7. Chloroplast Genome 100-220kb 20-100 copies per chloroplast 500-10,000 copies per cell Up to 20% of the cells DNA 120-140 Genes Evolved from Prochloron-like cyanobacteria MATERNALLY INHERITED

8. Mitochondrial Genome About 60 genes Mitochondial genome bigger in plants than animals or yeast, but variable (16kb in animals, 100-2,000kb in plants). Structure is poorly understood because it appears to be unstable. It appears to be present as subgenomic fragments, sometimes linear and sometimes circular. Also variable amounts within a plant cells. Trans-splicing Cytoplasmic male sterility MATERNALLY INHERITED

9. Reproduction Strategies and Plant Breeding Many plants reproduce asexually Fragmentation (clonal growth, tillering, suckers) e.g. Aspen, Willow Apomixis - production of seed identical to mother e.g. Rubus sps. Most plant species out-cross Self-incompatibility - mechanisms to prevent selfing Some plants are monoecious (separate male and female flowers) e.g. maize Some plants are dioecious (male and female plants) e.g. holly, marijuana and these have X and Y chromosomes like animals

10. Reproduction Strategies and Plant Breeding Self crossing is common- (40% of plants)andit is common in crops Inbreeding crops- Outbreeding crops- Inbreeding Crops Outbreeding Crops (self-pollinators) (cross-pollinators) Wheat Maize Barley Rye Oats Brassicas (cabbage, swedes, rapes) Rice Sunflower Tomato Potato Peach Beets- sugar beet Cotton Carrot Peas and beans Mango Coffee Rubber Pepper Banana

11. Selfing P1 P2 F1 F2 F3 F4 F5 Performance (height) Increasing homozygousity • Inbreeding depression • Self-crossing is much more common in plants than animals. • The reason many plants can inbreed may be due the relative importance of the gametophyte generation. • The superior performance of an F1 from inbred parents is call Hybrid Vigour. It is very important in crop production.

12. Stigma Pollination Pollen Style Pollen tube Ovary Ovule • Self-incompatibility- • A mechanism to prevent selfing • Genetically controlled by S locus alleles. • In self-incompatible species there are many S alleles (up to 200) • These allow the identification of ‘self’ and ‘non-self’ • The male and female have 2 alleles (if they are diploid) • There are two types of incompatibility- • GAMETOPHYTIC and SPOROPHYTIC

13. Pollen S1 S3 S1 S3 S1 S3 Female Parent S1S2 S2S3 S2S4 GAMETOPHYTIC Self-incompatibility In gametophytic, it is the single S allele of the pollen that determines pollination. If the S allele of the pollen grain matches either of the female alleles, there is no germination

14. Pollen S1 S3 S1 S3 S1 S3 Female Parent S1S2 S2S3 S2S4 SPOROPHYTIC Self-incompatibility In sporophytic, it is the combined S alleles of the all pollen that determines pollination (i.e. it is the alleles of the male plant). If the S allele of any pollen grains matches the female, no pollination

15. Cytoplasmic male sterility (CMS) Important in breeding of hybrid seed since the seeds of a male sterile plant must be hybrids. CMS is maternally inherited because it is partially dependent on mitochondrial DNA A mitochondrial gene disrupts pollen development. Nuclear genes can restore pollen development. RESTORER genes. For example, T-type CMS in maize is caused by a constitutive mitochondrial gene T-urf13 which produces a protein located on the mitochondrial membranes in all tissues. This protein prevents pollen development but it is not known how. Two nuclear restorer genes, Rf1 and Rf2, are needed for male fertility. RF1 reduced T-urf13 expression by 80%. RF2 codes a mitochondrial aldehyde of unknown function.

16. Other important differences between • Plants and Animals • Totipotency • Gametophyte generation is very important (in simple plants like mosses and liverworts it is the dominant generation). • Inbreeding is common • Cytosine methylation more common in plants • Introns generally smaller in plants • Many plant genes lack the AAUAAA-like polyadenylation signal • Mitochondria, while similar, are probably of a different origin (a different symbiotic relationship) to animals