Domestication syndrome in crop plants

Seminar
on
Domestication syndrome in crop
plants
16-Dec-17 1PG seminar
Anilkumar, C.
PALB 5062
PhD scholar

Introduction
Domestication genes
Methods to identify
Genetic bottleneck
Case studies
In this session----
16-Dec-17 2PG seminar

• Neolithic revolution/Agriculture
revolution: 12000 to 10000 years
ago
• Changes:
– The transition from hunting-
gathering to plant agriculture
– The formation of villages
– One of the key technological
elements of the transition to
agriculture was DOMESTICATION.
Introduction

16-Dec-17 PG seminar 4
 Plant domestication is the genetic
modification of a wild species to create a
new form of a plant altered to meet human
needs(Doebley et al., 2006)
 The process by which humans actively
interfere with and direct crop evolution.
What is domestication..?
 Continuum of increasing codependence
between plants and people

Incidental- Didn’t happen on purpose. Hunter/gatherers dropped
seeds, scared off natural herbivores, disrupted natural environments
so that plants could grow.
Directed- Humans and plants became dependent on each other, so
better plants helped people get healthier, planting more (and maybe
improved) plants, etc.
Types of Domestication
Agriculture- Human intervention in crop
Husbandry, Cultivation and Selection.

Where did it happen….??
(Balter, 2007)
Africa
Meso-America
Near East China
South-America
South-East Asia
Gepts, P., 2004
6

How did it happen…???
Is Artificial Selection
Analogous to Natural
Selection?
Unconscious selection: ‘‘that which
follows from men naturally preserving
the most valued and destroying the less
valued individuals, without any thought
of altering the breed.’’ (Darwin, 1868)
It was no different from natural selection
Humans change the conditions in which cultivated species live
and reproduce,
The phenotypic changes associated with domestication are
likely to have arisen via unconscious selection
(Harlan, 1992)
Natural
selection
Domestication

Theories of domestication

Few examples here..

What made domesticates to differed from wild….??
• There is a common suite of traits that
distinguishes most seed and fruit crops
from their progenitors (Hammer, 1984)
These distinct suite of traits later termed the
“domestication syndrome” would likely be
selected for during the initial stages of
domestication (Harlan et al., 1973)
Domestication syndrome:
It is the subset of traits that collectively
form the morphological and
physiological differences between crops
and their wild progenitors.

‘Domestication Syndrome’ traits
A variety of physiological
changes are also involved.
a loss of seed dormancy,
a decrease in bitter
substances in edible
structures
 changes in photoperiod
sensitivity
synchronized flowering
Compared to their progenitors,
food crops typically have
larger fruits or grains,
more robust plants
more determinate growth or
increased apical dominance
a loss of natural seed dispersal
often have fewer (although
larger) fruits or grains per plant
than their progenitors.

Domestication v/s improvement

Superheroes and masterminds

Diversification genes ..
 ‘Diversification’ genes are the target of selection for phenotypic variation
among varieties of a crop, such as different types of starch or flavor
 Glutinous or sticky phenotype of cooked cereal grains, reflecting the
absence (or near absence) of the starch amylose in the endosperm - the
glutinous phenotype is favored in select varieties of rice (primarily a subset
of japonica varieties of O. sativa), maize and foxtail millet, and is
controlled by unique mutations at the Waxy gene in all these crops.
 Rice BADH2 gene (2-Acetyi 1-Pyrrlione) - the aromatic phenotype has also
been generated via a variety of mutations at the same gene
(Gross and Olsen, 2010)

Methods for identifying domestication genes
 Biparental QTL mapping
 Association Mapping Using Unrelated Individuals
 QTL Mapping Using Advanced Intercross
Populations
 Genomic scans
 Genome Resequencing and Screening for
Selection Signatures

Classical Examples…
Teosinte branched 1 (tb1) QTL of maize controls the difference in apical dominance in maize
and teosinte
tb1, it acts as transcriptional regulators, a class of genes involved in the transcriptional
regulation of cell cycle
Teosinte glume architecture1 (tga1) was identified as a QTL controlling the formation of the
casing that surrounds the kernels of the maize ancestor, teosinte
tga1 is a member of the squamosa-promoter binding protein (SBP) family of transcriptional
regulators
Fruitweight2.2 (fw2.2) was identified as a large effect QTL controlling 30% of the difference
in fruit mass between wild and cultivated tomato
fw2.2 acts as a negative regulator of cell division in the fruit, perhaps via some role in cell-to-
cell communication
Q is a major gene involved in wheat domestication that affects a suite of traits, including
The tendency of the spike (ear) to shatter,
The tenacity of the chaff surrounding the grain, and
The spike is elongated as in wild wheat or compact like the cultivated forms

shattering4 (sh4) is a major QTL controlling whether the seed fall off the plant
(shatter) as in wild rice or adhere to the plant as in cultivated rice
sh4 encodes a gene with homology to Myb3 transcription factors.
A single amino acid change in the predicted DNA binding domain converts plants
from shattering to non-shattering
Rc is a domestication-related gene required for red pericarp in rice
Two independent genetic stocks of Rc revealed that the dominant red allele differed
from the recessive white allele by a 14-bp deletion within exon 6 - originated in
japonica cultivar and spread into indica cultivars.

Super-domestication
 The processes that lead to a domesticate with dramatically increased yield that
could not be selected in natural environments without new technologies.
 The array of genome manipulations enable barriers to gene exchange to be
overcome and have lead to super-domesticates with
– dramatically increased yields,
– resistances to biotic and abiotic stresses, and with
– new characters for the marketplace.
 Hybrid rice can be considered a super-domesticate
 Conversion of a crop from C3 to C4 photosynthesis
would certainly be a super-domesticate.
(Vaughan et al. 2007)
PLANT
BREEDERS
GENOMIC
SCIENTISTS
SUPER
DOMESTICATION
leads to

Effect of selection during domestication
 Selection is expected to reduce diversity at domestication related genes and
tightly linked loci
 One common feature of the domesticated genomes is the reduction of
genetic diversity in crops relative to the wild progenitors
 This reduction has two causes:
 Genetic bottleneck
 Selective sweep
(Tang et al., 2010)

 It depends on
 The bottleneck population size
 The duration of bottleneck
The loss in diversity was not experienced equally by all genes in the genome
(Tang et al., 2010)

Effect of Artificial Selection on Genetic Diversity of
Maize Genes.
Bottleneck
effect
(Yamasaki et al., 2005)

 A selective sweep is the reduction or elimination of variation among
the nucleotides in neighboring DNA of a mutation as the result of recent and
strong positive natural selection
 A strong selective sweep results in a region of the genome where the
positively selected haplotype (the mutated allele and its neighbours) is
essentially the only one that exists in the population, resulting in a large
reduction of the total genetic variation in that chromosome region.
Selective sweep
Size of
selective
sweep
Time of selection
Strength of selection
Recombination rates
(Tang et al., 2010)

Case study:1
Aim of the study:
• Attempt identify gene responsible for prostrate growth
and erect growth habit
• Mapping the gene on to chromosome

O. rufipogon
O. sativa

Teqing (indica cultivar) × YJCWR (O. rufipogon)
F1 ×
IL Named it as YIL18

Linkage analysis : F2 derived from cross between YIL 18 and Teqing showed that
prostrate growth was completely controlled by a single semi-dominant gene, PROG1
(PROSTATE GROWTH 1), located between SSR markers RM298 and RM481 on
short arm of chromosome 7
Output of the study
Positional cloning study: demonstrate that in the O. rufipogon genome was a
key gene (PROG1) controlling prostrate growth.
Tissue specificity study: they followed GUS reporter gene method
• detected GUS expression in the tiller base, leaf-sheath pulvinus and lamina
joint, but not in the root, leaf blade and culm

Case study:2
Preamble:
Why did a crop domestication gene hinder breeding with a
modern breeding gene responsible for the beneficial ‘‘jointless’’ trait
in tomato, and how can this genetic interaction be overcome and
exploited?

fresh-market hybrid breeding

Understanding crop domestication- Implications
 Up- and down-regulation of transcription factors
 Application of selection screens to identify genes contributing
to the success of best varieties
 QTL cloning for key agronomic genes
 Screening wild relatives and unimproved varieties to recover
superior alleles (allele mining) that failed to pass through the
domestication and improvement bottlenecks

Domestication syndrome in crop plants

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