Genome evolution,

chromosome and super

domestication
Farrukh Amjad
12-Arid-203
M.Sc.(Hons.) PBG
3rd Semester
Genome Evolution

• Genome evolution a process by which a genome changes in structure (sequence)

or size over time.
• The study of genome evolution involves multiple fields such as
 structural analysis of the genome
 the study of genomic parasites
 gene and ancient genome duplications
 polyploidy
 comparative genomics.
Causes of genome evolution

• mutations
• duplications
• exon shuffling
• transposable elements
• pseudogenes
Key points of genomic evolution
• Gene and whole genome duplications have contributed accumulations that have
contributed to genome evolution.
• Mutations are constantly occurring in an organism’s genome and can cause either a
negative effect, positive effect or no effect at all; however, it will still result in changes to
the genome.
• Transposable elements are regions of DNA that can be inserted into the genetic code and
will causes changes within the genome.
• Pseudogenes are dysfunctional genes derived from previously functional gene relatives
and will become a pseudogene by deletion or insertion of one or multiple nucleotides.
• Exon shuffling occurs when two or more exons from different genes are combined
together or when exons are duplicated, and will result in new genes.
• Species can also exhibit genome reduction when subsets of their genes are not needed
anymore.
Cont...

• Genome evolution is a constantly changing and evolving field due to the steadily
growing number of sequenced genomes, both prokaryotic and eukaryotic,
available to the scientific community and the public at large.
Chromosome

• is a DNA molecule with part or all of the genetic material (genome) of an

organism.

• Chromosomes are normally visible under a light microscope only when the cell is
undergoing the metaphase of cell division.
Genome Evolution of Brassica

• Brassica junecia (2n=36) is an amphidiplooid species derived from interspecific

cross between brassica nigra (2n=18 )and B.rapa campestris (2n=20)

• Many theories about origin but most accepted is middle east.

• Brassica species belong to the Brassicaceae (¼ Cruciferae) family and some of

them are widely used in human diet mainly as an important source of vegetables,
condiments, and edible oils.
Cont...

• The relationship among the different Brassica species started to be explained by

Morinaga (1934) and Nagaharu U(1935) with the already-cited U-triangle .

• According to them, the diploid species B. rapa (AA-genome), B. nigra (BB-

genome), and B. oleracea (CC-genome) originated along the same time as the
allotetraploid species B. juncea (AABB), B. napus (AACC), and B. carinata
(BBCC).
The triangle of U
• The triangle of U is a theory about the evolution and relationships between members of
the plant genus Brassica.

• The theory states that the genomes of three ancestral species of Brassica combined to
create three of the common modern vegetables and oilseed crop species.

• The theory was first published in 1935 by Nagaharu U . It shows how three of the
Brassica species were derived from three ancestral genomes, denoted by the letters AA,
BB, or CC. Alone, each of these diploid genomes produces a common Brassica species.

• AA – 2n=2x=20 – Brassica rapa (syn. Brassica campestris) – turnip, Chinese cabbage

• BB – 2n=2x=16 – Brassica nigra – black mustard
• CC – 2n=2x=18 – Brassica oleracea – cabbage, kale, broccoli, Brussels sprouts,
cauliflower, kohlrabi
Cont...

• Cultivated species of Brassica

• AABB – 2n=4x=36 – Brassica juncea – Indian mustard

• AACC – 2n=4x=38 – Brassica napus – rapeseed, rutabaga
• BBCC – 2n=4x=34 – Brassica carinata – Ethiopian mustard
The "triangle of U" diagram, showing the genetic relationships between six species
of the genus Brassica. Chromosomes from each of the genomes A, B and C are
represented by different colours.
Cont...
• These three species exist as separate species, but because they are
closely related, it was possible for them to interbreed. Unfortunately
inbreeding within the species does not produce genomes that are
resistant to unregulated contamination.
• This interspecific breeding allowed for the creation of three new
species of tetraploid Brassica. Because they are derived from the
genomes of two different species, these hybrid plants are said to be
allotetraploid (contain four genomes, derived from two different
ancestral species).
• More specifically, they are amphidiploid, i.e., containing one diploid
genome from each of the two different Brassica species. Data from
molecular studies indicate the three diploid species are themselves
paleopolyploids.
Genome Evolution of Wheat
• Modern Bread Wheat ( T. aestivum )
• Hexaploid ( AABBDD ) 2n=6x=42
• Genome Size of 17 GB
• >80 % repeats, 2% coding sequence
• High sequence similarity within sub genomes - A/B/D
• IWGSC
The Source of the A-Genome
• The hybrid among diploid Tetraploid , hexaploid wheat were used for
meiotic study by kihara 1924 .
• Three group genome
 AA T.monococcum
 AABB T.dicoccum
 AABBDD T.aestivum
Cont...

• Einkorn wheat ( T.monococcum ) is diploid (AA, two complements of

seven chromosome, 2n=14 ).
• Most tetraploid wheats ( e.g emmer and durum wheat ) are derived
from wild emmer, T. dicoccoides.
• Wild emmer is itself the result of a hybridization between two diploid
wild grasses.
• The hybridization that formed wild emmer (AABB) occured in the wild
long before domestication and was driven by natural selection.
Cont...

• Hexaploid wheats evolved in farmers fields. Either domesticated emmer or durm

wheat hybridized with yet another wild diploid grass ( Aegilops tauschii ) to make
the hexaploid wheats, spelt wheat and bread wheat.

• These have three sets of paired chromosomes, three times as many as in diploid
wheat.
Triticum monoccocum × Aegilops speltoid
2n=14, AA 2n=14, BB

Natural hybridization

Triticum dicoccum Triticum taushii

×
2n=28, AABB 2n=14, DD

Natural hybridization

Triticum aestivum
2n=42, AABBDD
Super domestication

• Vaughn et al 2007 first used the term super domestication.

• The process that lead to domesticate with dramatically increased yield that could
not be selected in natural enviornments from naturally occurring variation
without recourse to new technologies.

• super domestication can be constructed with knowledge led approaches based on

current needs using the range of new technologies now available.
Tools of super domestication

• The major tools to support super-domestication are:

1. Efficient utilization of the existing diversity; by crossing two

varieties/species/genera, Genome manipulations, producing Cell fusion hybrids etc.
2. Chromosome manipulation: Alien line development (Alien addition and
substitution), ploidy manipulation.
3. Generate recombinants: Chromosome recombination.
4. Utilizing the technique like genomics, proteomics, metabolomics, transcriptomics
and other omic techniques.
Applications of Genomic tools in Super Domestication

• Genome sequencing
• Genome wide association studies GWAS
• Next generation sequencing NGS
• Genome editing
Genome sequencing

• Potential methods of sequencing

• Clone by clone approach
• whole genome shotgun approach
• combination of the two methods
GWAS

• It is a study design in which mny markers spread across a genome, are genotyped
and test a statistical association with a phenotype are performed locally along the
genome.
• It is also an examination of many common genetic variants in different individuals
to see if any variant is assocaited with a trait.
• Uses in successfully studying maize, sorghum and barley
• Cannot be utilized generally because it needs large population size.
• GWAS identify rare alleles more precisely.
NGS

• Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop
domestication.
• Re-sequencing of domesticated species can identify low diversity
regions resulting from selection during domestication.
• To identify gene-specific sequences to aid the cloning of homologues
of key domestication genes from wild relatives.
• Useful strategy to analysis the chloroplast genome sequence from
whole-genome shot-gun sequencing.
Genome editing

• Meganucleases
• ZFMs -Zink finger motifs
• TALENs - TRanscription activator like effector nucleases
• CRISPR/ CAS-9 Clustered interspaced short palindromic repeats
Superdomestication in brassica

• The domestication process of Brassica oleracea L. has not been fully clarified,
either regarding its initial location or the progenitor species involved. Two
alternative hypotheses proposed so far point to either a northwest European or a
Mediterranean location.

• These must have differentiated under human selection, starting from a simple
leafy type (leafy kale, var. viridis L.) into various highly valued modification
involving arrested development and enlargement of the inflorescences in broccoli
(var. italica L.) and cauliflower (var. botrytis L.), folding of the leaves into ‘heads’
in cabbage (var. capitata L.), enlargement of the basal stem in kohlrabi (var.
gongylodes L.), thickened stems in marrow-stem kale (var. medullosa Thell.),
proliferation of heading buds in Brussels sprouts.
Superdomestication in wheat

• The development of agriculture is closely associated with the domestication of

wheat, one of the earliest crop species.
• One gene believed to be such a domestication gene is NAM-B1, affecting both
nutritional quality and yield but with opposite effects.
• A null mutation, first arisen in emmer wheat, decreases the nutritional quality but
delays maturity and increases grain size; previously the ancestral allele was
believed lost during the domestication of durum and bread wheat by indirect
selection for larger grain.
Cont...

• Grain size increased early in domestication through alterations both in grain width
and length, followed at later stages by further modifications in grain shape largely
through changes in grain length.

• In addition, the decrease in phenotypic diversity in grain morphology in modern

commercial wheat is shown to be the result of a relatively recent and severe
bottleneck that may have occurred either during the transition from hulled wheat
to the modern nonhulled varieties.
 Chrom. Species that acquired
Trait Gene arm mutation to domestic
form (ploidy)

Br13B T. turgidum ssp.

3AS
dicoccum (4 × )
The three Br13A
3BS
T. turgidum ssp.
principal traits Brittle dicoccum (4 × )
rachis Br13D T. aestivum ssp.
affected by 3DS
aestivum (6 × )
mutation leading Br23D T. aestivum ssp.
to wheat 3DL
aestivum (6 × )
domestication and
their associated T. aestivum ssp.
Tg12D 2DS aestivum (6 × )
genetic loci . Tenaciou
T. turgidum ssp.
s glume
Tg22B 2BS parvicoccum (4 × )
a

T. turgidum ssp.
Free- parvicoccum (4 × )
threshin Q5A 5AL a
g or T. aestivum ssp.
aestivum (6 × )
Cont...
• The main differences between the wild forms of wheat and domesticated wheat
are that domesticated forms have larger seeds with hulls and a non-shattering
rachis.

• When wild wheat is ripe, the rachis--the stem that keeps the wheat shafts together-
-shatters so that the seeds can disperse themselves.

• Of course, if farmers harvest wheat when they believe it is ready, they only get the
wheat that remains on the rachis: that wheat is what the farmers plant and in the
process selected wheats with rachis that didn't become brittle at harvest time.

• Other traits apparently selected for include spike size, growing season, plant
height, and grain size.
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Cont...

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