Lecture 1 Plant Genetics Overview.
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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. Plants From space, the land is green!!

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Lecture 1 Plant Genetics Overview.

How plants are different from animals?

Variation in quantity of DNA


Mitochondrial Genome

Chloroplast Genome

Crossing Strategies and Plant Breeding

Cytoplasmic Male Sterility


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)

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)

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.

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


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


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.

Chloroplast Genome


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



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.


Cytoplasmic male sterility


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

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













  • 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.





Pollen tube



  • 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-


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

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

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.

  • 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