The document summarizes the genetic basis of crop domestication. It discusses how early farmers unconsciously selected traits from wild plants like larger seeds and loss of seed dispersal, forming the domestication syndrome. This selection through bottlenecks and selective sweeps reduced genetic diversity in crops compared to their wild ancestors. Various approaches are described to identify genes underlying domesticated traits, like QTL mapping, association studies, and selection scans of genomes. Two case studies on soybean and sunflower domestication are presented, finding genes related to traits like shattering and oil content experienced strong selection. Understanding domestication genetics can aid future crop improvement efforts.

1. SEMINAR TOPIC:
Deciphering The Genetic Basis Of
Crop Domestication
1
Presented by
YENGKHOM LINTHOINGAMBI DEVI
Msc. 2nd year
Adm. No. CAU/CPGS/GPB/M17/05

2.  Neolithic revolution/Agriculture
revolution: 12000 to 10000 years
ago
 Changes:
 The transition from hunting-
gathering to plant agriculture
 Sedentism
 The formation of villages
 One of the key technological
elements of the transition to
agriculture is DOMESTICATION.
Introduction
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3.  Plant domestication is the genetic modification of a wild
species to create a new form of a plant altered to meet
human needs.
 The process by which humans actively interfere with and
direct crop evolution.
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Continuum of increasing codependence
between plants and people

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5. Fully domesticated plants cannot survive on their own in the wild.
The plants are using us!
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One of the best examples -MAIZE,
the husks surrounding the ear and
the tight attachment of kernels to the cob
prevent natural dispersal.
When hundreds of kernels germinate so close to
another unable to obtain adequate light and
nutrients and fail to reproduce.

6.  There is a common suite of
phenotypic traits that distinguishes
most seed and fruit crops from their
progenitors or wild ancestors.
 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)
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Physiological changes 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.

8. Maize
Wild
1. Multiple stalks, long branches
2. Ear has its grains enclosed in
the triangular casing that
comprises the ear
3. Hard glumes
cultivated
1. Single stalk
2. Husk surrounding the ear.
3. Maize ear bears its grain
naked on the surface of the
ear
4. Soft outer glumes
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9. Wild
1. Wild rice has a panicle that
shatters
Cultivated
1. Cultivated rice has a solid panicle
of grains
Rice
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10. Cultivated
1. Massive fruit
Wild
1. Miniscule fruit
Tomato
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11. Wild
1. Wild wheat with recessive allele
q responsible for slender, fragile
spikes
Cultivated
1. Cultivated wheat with the
dominant allele of the Q gene has
a condensed and tough spike
Wheat
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12. Cultivated
1. Cultivated sunflower has a
single large head borne on a
thick stalk
Wild
1. Wild sunflower plants have
many heads borne on multiple
slender stalks
Sunflower
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13. How did it happen…???
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 is natural selection in crop species as a result of human cultivation
practices and of growth in agro-ecological environments.
 The phenotypic changes associated with domestication are likely to have
arisen via unconscious selection
 Humans change the conditions in which cultivated species live and
reproduce, and this change exerts selection on the population even in
the absence of a choice or predetermined goal by the cultivator.
Natural
selection
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Domestication
Artificial
selection

14. Effect of selection during domestication
 Early farmers used only a limited number of individuals of the
progenitor species.
 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
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15.  A population bottleneck (or genetic bottleneck) is an
evolutionary event in which a significant percentage of a
population or species is killed or otherwise prevented from
reproducing.
 Genetic bottleneck usually quantified by factors:
 The bottleneck population size (Nb )
 The duration of bottleneck (d)
Severity of bottleneck is given by coefficient, k = Nb / d
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The loss in diversity was not experienced
equally by all genes in the genome

17.  Neutral gene :
genes that do not influence favoured phenotypes.
 Selected gene :
genes that influence desirable phenotypes – experienced a
more drastic loss of diversity because plants carrying
favoured alleles contributed the most progeny to each
subsequent generation and other alleles were eliminated
from the population
Genetic bottleneck…..
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18. Effect of Artificial Selection on Genetic Diversity
Bottleneck
effect
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19.  It 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.
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Selective sweep

20. SELECTIVE SWEEP
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21. TYPES OF SELECTIVE SWEEP:
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24. APPROACHES TO FIND ADAPTIVE GENE FOR
DOMESTICATION
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25. Biparental QTL Mapping
 One of the first techniques applied to understand the
genetic basis of domestication traits
 Domestication traits can be mapped using populations
derived from wild-by-domesticate crosses
 Identification of QTL regions
 fine mapping,
 cloning,
 functional characterization of underlying genes,
 QTL mapping and fine mapping remain by far the most
common approach for identifying domestication-
related genes and causal mutations.

26.  One interesting demonstration of this phenomenon is the two shattering genes
that have so far been cloned in rice, sh4 and qSH1
Seed shattering
sh4 qSH1
Wild x Crop Japonica × indica
sh4 is a locus that
differentiates wild
from domesticated
rice
qSH1 is QTL controlling
shattering in rice present in
chroosome no 1

27. Association Mapping
 Linkage disequilibrium mapping takes advantage of linkage disequilibrium to
link phenotype to genotypes by using a population of unrelated individuals
 The goal is to statistically associate segregating allelic variation with a
phenotype of interest
 Makes use of the natural history of recombination events in a population
 Tests for associations between phenotypes of interest and genetic markers
 Association mapping offers an advantage compared with any other technique
in potentially identifying a restricted genomic region or even the causal single-
nucleotide polymorphism controlling the trait of interest

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30.  Bottom up approaches begin by assaying genetic diversity in
hundreds of loci, preferably from 100 individuals.
 Use of statistical tests of selection from the genomic data.(
eg. Tajima’s D test) to find the candidate gene
 Observed polymorphism data were compared with historical
coalescent demographic model that included a population
bottleneck.
 Emperical ranking is an otherwise option of demographic
model.
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31. Genomic scans or selection scans
 Diversity at molecular markers in
wild and domesticated populations
is compared to identify reductions in
variation consistent with selection
 In this method, one looks for loci
that show significant reduction of
sequence diversity in domesticated
genotypes compared to wild
samples.
 Relatively high-throughput method,
often identifying a large set of
‘candidate genes’ compared to
conventional QTL mapping which
interrogates only a few loci at a time
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32. Genome resequencing
 High-throughput re-sequencing techniques can offer a complement to the
approaches outlined above
 Genome re-sequencing or SNP genotyping in a diverse population sample
can be used to identify specific genomic regions that bear signatures of
domestication-related selection
 Re-squencing of candidate domestication gene in population level samples
of wild or domesticated species
 used to test for the presence of a selective sweep
 For domesticates that have experienced a severe genetic bottleneck these
re-sequencing surveys can identify regions of high divergence between the
crop and the wild species.
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33.  Several genes were targets of domestication or crop improvement
 The mutations in these genes that were incorporated into crops most likely
occurred naturally in the progenitor plant population
 The form and nature of the genetic mutations associated with transitions
from wild to domesticated plants is highly variable
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Genomic changes associated with the
domestication

34. Deletion in promoter Insertion of TE
Translocation A SNP in PROG1
A SNP at splice siteA SNP in promoter
Leads to non-shattering phenotype Leads to altered shoot
Leads to low shattering Leads to erect growth in Asian rice
Leads to non-shattering phenotype Leads to determinate inflorescences

35. CASE STUDY-1
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36. OBJECTIVE:
 To investigate loss and recovery of genetic diversity in
the course of soybean domestication and breeding.
 Genomic analysis among wild, landraces and elite
soybeans to identify the genes under selection.
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37. MATERIALS AND METHOD:
 25 soybean accessions( 8 landraces ,9 elite cultivar and
5 wild type)
 Integration of 30 re-sequencing data from NCBI Short
Read Archive.
 85 F2 plants were generated by crossing G. max cultivar
E9 and G. soja accession S8
 7 plants in each row were used to extract DNA.
 The extracted DNA is sequenced and alligned with
reference genome and SNPs are identified.
 Phylogenetic tree is constructed.
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38. RESULTS:
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39. Data revealed that 1,661,945 SNPs in wild soybean were not
polymorphic in the landraces
the number of fixed SNPs from landraces to elite cultivar was only
54% of the number of fixed SNPs during domestication.
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43. KEGG database used to find the potential
function of the selected genes.
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44.  To validate footprints of selection during
domestication and genetic improvement, we
compared the genomic region with previously
mapped QTLs.
 A total of 21 candidate domestication regions
including 60 genes were covered by mapped
domestication QTLs and adjacent regions.
 A total of 20 candidate improvement regions including
106 genes were covered by improvement QTLs and
adjacent regions
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45. DISCUSSION:
Genomic diversity was more impacted by domestication than
by genetic improvement.
The number of fixed SNPs from landraces to elite cultivars
was only half to the number of fixed SNPs during
domestication.
The study helps us to construct a large-scale soybean
haplotype map and discover important trait related genes
using genome wide association mapping
Helps in identifying the gene under selection and the
phonotype of the gene can be predicted which helps in
crop improvement.
Comparison of candidate domestication and crop
improvement related genes with previous QTL mapping
results provide information on potential function of genes
under artificial selection.
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46. CASE STUDY 2
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47. Objectives:
 To analyse the genomic change associated with
domestication and improvement in sunflowers based
on transcriptome sequences of early and improve
domesticated sunflower.
 To identify the alleles associated with domestication or
improvement.
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48. Material and Method
 Sequence variation in 80 transcriptomes representing
38 genotypes of wild and cultivated are analyzed.
 RNA extraction ,library preparation and sequencing
using Illumina and 454 sequencing platforms were
carried out
 Reads were alligned against a reference transcriptome
comprised of 16312 contigs.
 Contigs containing one or more outlier SNPs are used
to generate phylogenetic network.
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49. RESULTS:
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53. DISCUSSION:
 Outlier analysis identified 122 and 15 candidates genes
associated with domestication an improvement
respectively.
 The 2 most extreme outlier contigs in the
domestication scan have homology to genes that are
involved in basic metabolism and presumably oil
biosynthesis.
 Improvement of sunflower involved the introduction
of alleles from numerous wild species.
 The transition from landraces to modern inbred line
involved selection for self-compatibility
 Admixture analysis revealed that all the modern
cultivar genome contained one or more introgressions
from wild polulation
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54.  the processes that lead to a domesticate with dramatically increased yield
that could not be selected in natural environments from naturally occurring
variation without recourse to 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
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55.  Knowing the genetic basis of domestication it will help us in finding the
putative candidate genes under seelction.
 It helps in introgression of wild useful genes to the cultivated one to broaden the
genetic diversity
 The bottom-up method of finding adaptive gene is more advantageous as
compare to the top-down model.
 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
that failed to pass through the domestication and improvement bottlenecks
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