Domestication as a method of plant breeding

plant breeding

1. Principals of crop improvement ,
Domestication and introduction

2. CONVENTIONAL METHODS, TECHNIQUES AND PRACTICES IN
PLANT BREEDING
1.1) Plant Introduction and domestication
2.2) Selection
Mass selection
Pureline selection
3) Hybridization:
Pedigree method
Bulk method
Single seed Descent Method
Back cross Method
4) Heterosis and Hybrid Vigor

3. •PLANT INTRODUCTION AND ACCLIMATIZATION
•Plant Introduction is the process of
introduction of plants from their growing locality
to new area.
•The introduction may include the new variety
or wild relative of the crop species.
•Plant introduction includes the introduction of
the new genotype or sub genotype from original
environment or area to a new environment or
area where the plant is not grown previously.
•Introduction of the oil palms from the Malaysia
to Tamilnadu in India is an example of the Plant

4. •Introduction.
•The success of the Plant introduction
depends on the two important processes
Domestication and Acclimatization of the
plants.

5. •Domestication:
•It is a process of bringing wild species under
cultivation by making them change in
behavior suitable for new environment.
•

6. •Acclimatization:
•It is an ability of the crop to become
adapted to change
•climatic and edaphic conditions.
•The process of Acclimatization increase
the frequency of the most adapted
genotypes which depends on the breeding
system, genetic variation, and duration of
the crops.
•Success of the Acclimatization depends
on the Place effect and selection of the
new genotype.

7. •Crop Improvement Method
•# 1. Plant Introduction:
•Plant introduction usually means the introduction
of the plants from places outside the county, may
be of same or another continent. It can be defined
as the“process of introducing plants from their
growing locality to a new locality.”
•
•The introduction of the genotypes from the place
where it is grown to an entirely new area. It is the
easiest or most common method of crop
improvement.

8. OBJECTIVES OF PLANT
INTRODUCTION
•To introduce new plant species to established new plant
based product Industries.
•E.g. Rubber, Oil palm
•To introduce high yielding varieties to fulfill the
requirement of the Food and increase in the production of the
crop plants.
•E.g. Wheat and Rice
•To enrich the germplasm collection and its conservation.
•E.g Legumes, Pulses, Cereals
•To get new source of resistance against the biotic and
abiotic stress causing agents and factors.
•E.g. Bt. Cotton, Bt. Maize

9. •PURPOSE OF THE PLANT INTRODUCTION
•Use in Agriculture, Forestry and Industry:
•New varieties of the crop plants are introduced
from various places for the food, fodder, wood or
medicinal purpose.
•Aesthetic Value: Various Ornamental plants are
introduced for beautification
•Germplasm Conservation: Germplasm collection
and conservation helps conservation of wild
germplasm, clones, new cultivars and mutant lines
•Studying origin and Distribution: Study of the
origin and evolution of the crop plants are
possible.

10. •TYPES OF PLANT INTRODUCTION
•Primary Introduction
Secondary Introduction
•Primary Introduction:
•When introduced crop or variety is well suited to
environment it is directly grown or cultivated
without altering the original genotype this is called
as an primary introduction.
•E.g. Introduction of IR-8, IR-20, IR-34 varieties of
rice in India.

11. •Secondary Introduction:
•If the introduced variety is used for
selection method to isolate superior variety or
used for hybridization programme to transfer
the desirable trait it is called as an Secondary
introduction.
•E.g. In soyabean crop variety EC 39821
introduced from Taiwan and by the selection
method variety C0-1 is developed.

12. •Plant introduction may be of following types:
•(i) Intercontinental plant introduction:
•Plant material is introduced from the country of
another continent e.g., ridley wheat variety from
Austria in India.
•(ii) Intracontinental or Inter-countries plant
introduction:
•Introduction of plant material from another
country within same continent, for e.g., Litchi
and loquat from China.
•

13. •(iii) Interstate plant introduction:
•Introduction of plant material from another state
within the same country, for e.g., N.P. wheat
varieties from Delhi.
•(iv) Intrastate or Inter-district plant
introduction:
•Introduction of plant material into different
states within the country or from another district
within the same state, for e.g., distribution of
state recommended varieties of different crops
from one district to another within the same
state for general cultivation.

14. •Any plant material therefore brought from
another place may be within or outside the
country, may be termed as introduced
material or method of plant introduction.
These introductions are also termed as exotic
collection (EC, Introductions may be from
outside the country) or indigenous collections
(IC, Introduction may be from other parts or
other states of the same country).

15. PROCEDURE OF PLANT
INTRODUCTION
•Procurement of Germplasm:
•Requisition of introduction Plant variety or germplasm submitted to NBPGR(Within
country)or IBPGR(Between the country). Material can be obtained on exchange
basis directly between friendly countries or Associations or through FAO.
•Packaging and dispatch:
The propagules decontaminated first and packaged carefully and
•dispatch to reach destination in viable conditions Entry and plant Quarantine:
•Entry inspection is done for pest and diseases from entering into the country and
to check the spreading further
•Cataloguing:
After quarantine the specimen is given the number regarding species,
•variety and place of origin and data is recorded.
•Evaluation:
•Performance of the variety at different substations and resistance to pest and
pathogens evaluated at different environments.
•Multiplication and Distribution:
•Introduced material propagated, multiplied and released as new variety.

16. PLANT INTRODUCTION
A) Advantages and disadvantages
•It provides new plant species
•It introduce new variety which is high yielding and disease resistant.
•Provide parent material for genetic improvement of the economic crops.
•Enriching the existing germplasm and increase the variability.
•Introduction into new area and environmentsaves plant species
•B) Disadvantages:
•Introduction of new weed. E.g. Argemone mexicana, Parthenium hysteroporous
•Introduction of new disease. E.g Fungal disease like Late blight of Potato from
Europe and Viral disease Bunchy top of Banana from Sri Lanka.
•New Pest Introduction. E.g. Potato Tuber Moth came from Italy
•Ornamental plants become weed. E.g. Lantana camera
•Introduction may cause ecological imbalance. E.g. Eicchornia

17. Argemone mexicana

19. . Eicchornia
water
hyacinth

20. Lantana camara

21. PLANT INTRODUCTION :
ACHIEVEMENTS:
•1) Introduction of New crop species:
•Potato, Chilly, Rubber, Groundnut, Coffee, Maize
•Ornamental plants like Delonix, Salvia, Aster
•2) Introduction of New crop varieties:
•a) Direct Multiplication and released as new varieties:
•Dwarf wheat varieties like Sonora 64, Lerma Rojo
•Dwarf Rice varieties like TN-1, IR-8
•b) Selection of desirable varieties:
•Selection of Kalyan sona and Sonalika after the introduction of the Mexican dwarf
variety.
•c) Introduced variety as a Donor for Hybridization Programme
All the sugarcane varieties with thick stem and sugar content developed
•from the introduction of the Noble cane variety of Saccharum officinarum. d)
Mutation Breeding:
Induction of the mutations by using the Physical and chemical mutagens.
•The Gamma treatment is given to Sonora 64 with red colored grains to produced
Sharbati Sonora with Amber colour grains

25. Delonix, Salvia, Aster

28. •The following points highlight the six
methods of crop improvement. The methods
are:
•1. Plant Introduction
•2. Acclimatization /domestication
•3. Mutant Breeding
•4. Polyploidy
•5. Tissue Culture
•6. Genetic Engineering.
•

29. Domestication
‘Domestication is the process by which humans
actively interfere with and direct crop evolution.’
•It involves a genetic bottleneck:
•Often only few genes are actively selected and account
for large shifts in phenotype.
•Crops exhibit various levels of domestication.

30. •Concept first devised by Vavilov in 1919
•Archaeological evidence suggests that hunter-gatherers independently
began cultivating food plants in 24 regions,….” (Purugannan and Fuller,
2009)
Centres of Plant Domestication

31. What is a domestication syndrome?
A domestication syndrome describes the properties
that distinguish a certain crop from it’s wild progenitor.
Typically such characteristics are:
•larger fruits or grains
•more robust plants
•more determinate growth / increased apical
dominance
•loss of natural seed disperal
•fewer fruits or grains
•decrease in bitter substances in edible structures
•changes in photoperiod sensitivity
•synchronized flowering

32. Tomato -Fewer and Larger Fruits

33. Sunflowers -reduced branching, larger seeds,
increased seed set per head

34. Wheat -reduced seed shattering, increased seed size

35. Squash –larger, fleshier fruits

36. Corn –reduced fruitcase, softer glume, more kernels
per cob, no dispersal, reduced branching, apical
dominance

37. Lettuce –leaf size/shape, fewer secondary compounds

38. Rice –no shattering,
larger grains

39. Crop Improvement Method #3.
Mutation Breeding:
A sudden heritable change in a
characteristic of an organism is called
mutation; function of mutations with the
aid of mutagens is called mutagenesis.
Breeding method utilizing variation
created through mutagenesis is called
mutation breeding. In this method, gamma
rays and X-rays are the most commonly
used physical mutagens, while EMS (ethyl
methane sulphonate), EI (ethylene imine)
and sodium azide are the most commonly
used chemical mutagens.
More than 300 varieties have been
developed through mutagenesis in various
countries. In India, a number of varieties
have been developed by mutation breeding
e.g., BGM 408 (Chick pea), Hans (pea),
JRO 3690 (Jute), Sharbati Sonora,
(Wheat), Jagannath (Rice), Co8152
(sugarcane) etc.

40. Crop Improvement Method #4. Polyploidy:
An organism or individual having more than two basic monoploid sets of
chromosomes is called polyploid (Gr. Polys = many + aploos = one fold + eidos –
form) and such condition is called polyploidy. Polyploidy is of two types –
autopolypoidy and allopolyploidy.
Polyploids which originate by multiplication of the chromosomes of a single species
are known as autopolyploids or autoploids and such situation is called
allopolyploidy Autopolyploids are generally larger in size, have larger cells, stomata,
pollen grains and seeds.
Some of our crops are autopolyploids e.g., potato, coffee, sweet potato, ground nut,
alfa alfa, banana etc. Autopolyploids are produced spontaneously by gamma
irradiation, tissue culture and with treatment of the chemicals like colchicine.
A polyploid organism, which originates by combining complete chromosomes sets
from two or three species is known as alloploid and the condition is known as
allopolyploidy. Some important natural allopolyploid crops are wheat, cotton,
tobacco, mustard, oat etc.

41. The role of polyploidy in domestication

42. Crop Improvement Method
#5. Tissue Culture:
The growth of tissues of living organism in a suitable culture medium (in
vitro)I is called tissue, culture. Plant tissue culture refers to growth of
plant tissues in a suitable culture medium. The plant part which is used in
regeneration is called explants).
It has several useful applications in crop improvement for e.g.,
development of haploids, embryo rescue generation of variability,
selection of disease resistance, selection for salinity and metal toxicity
resistance, selection for drought resistance, micro propagation,
preservation of germplasm, somatic hybridization etc.

44. Crop Improvement Method#6. Genetic Engineering:
Isolation, introduction and expression of foreign DNA in plants and
animals is called genetic engineering. It involves introduction of a
gene by the techniques of recombinant DNA technology and genetic
transformation.
It provides an exciting tool to improve specific traits of inbreeds
provided a transgene is available for this purpose e.g., suitable
version of the cry gene of Bacillus thuringiensis has been
transferred in maize inbreeds and insect resistant commercial
hybrids have been produced using such inbreeds.
Similarly, many transgenes have been shown to generate
resistance to fungal diseases (e.g.. Vacuolar’chitinase, (β-1, 3-
glucanase, groundnut stilbene synthase etc.)
The cry gene transfers have been so far the most successful. Insect
resistant transgenic varieties of maize, soybean, cotton etc.
expressing this gene are being cultivated in U.S. A. In India, efforts
are being made to develop aphid resistant transgenic brassicas by
expressing in them protease inhibitor genes from wheat etc..

47. Domestication is a process
•The distinction ‘domesticated’ or ‘not domesticated’ is an over-
simplification
•Some crops have moved further along this process further than
others.
•We can recognize different levels of domestication
•How can we decide which level?

48. •Different domestication traits were selected for progressively
•Distinction between selection under domestication vs. crop
diversification more targeted, ‘conscious’ selection during
diversification
•‘Slow’ rate of evolution of different domestication traits
despite faster rates suggested by models
•Artificial selection can be “similar across different taxa,
geographical origins and time periods”

49. •Parallel evolution for “sticky glutinous varieties” in rice and
foxtail millets, all through selection at the waxylocus
•Most QTL studies suggest that many domestication traits are
controlled by a few genes of large effect –not though in
sunflower
•Population genomic studies in maize suggest 2 –4% of genes
show evidence of artificial selection

50. Domestication of Maize

51. How often has maize been domesticated?
–Sampling (Matsuoka et al, 2002)

52. How often has maize been domesticated?
–Once. (Matsuoka et al, 2002)

53. Tracking footprints of maize domestication and evidence for a
massive selective sweep on chromosome 10
(Tian et al., 2009 PNAS)

54. Teosinte branched 1 (tb1)
•was identified as a major QTL controlling the difference in apical
dominance between maize and its progenitor, teosinte (Doebley et al.,
1997; Doebley, 2004)
•is a member of the TCP family of transcriptional regulators, a class of
genes involved in the transcriptional regulation of cell-cycle genes.
•Differences in tb1 expression patterns between maize and teosinte indicate
that human selection was targeted at regulatory differences that produced a
higher level of tb1 message in maize.
•Lack of any fixed amino acid differences between maize and teosinte in
the TB1 protein supports this hypothesis.

55. “For maize tb1 … [the selection coefficient] is in the range 0.05
to 0.2, comparable to cases of natural selection.” (Purugannan
and Fuller, 2009)

56. Teosinte glume architecture1 (tga1)
•was identified as a QTL controlling the formation of the casing that
surrounds the kernels of the maize ancestor, teosinte (Wang et al., 2005)
•is a member of the squamosa-promoter binding protein (SBP) family of
transcriptional regulators.
•tga1has phenotypic effects on diverse traits including cell lignification,
silica deposition in cells, three-dimensional organ growth, and organ size
•The difference in function between the maize and teosinte alleles of tga1
appears to be the result of a single amino acid change. The fact that there
are no discernable differences in gene expression supports this
interpretation.

57. Domestication genes in plants

58. Crop Diversification genes in plants

59. The evolution of non-shattering
in the archaeological record

60. The genetic basis of the evolution of non-shattering
Non-shattering is often regarded as the hallmark of
domestication in most seed crops because it renders a
plant species primarily dependent on humans for survival
and propagation:
•rice gene sh4(similar to the genes encoding MYB-
like transcription factors in maize)
•rice quantitative trait locus (QTL) qSH1, which
encodes a homeobox-containing protein
•the wheat gene Q, which is similar to genes of the
AP2family in other plants
•In sunflower likely controlled by multiple genes

61. Domestication genes in plants
•Maize and rice domestication seem to suggest few loci of
large effect are important
•Sunflower domestication seems to suggest many loci of small
to intermediate effect are important
•9 domestication genes in plants so far, as well as 26 other loci
known to underlie crop diversity
•Of the 9 domestication loci, 8 encode transcriptional
activators.
•More than half of crop diversification genes encode enzymes.
Domestication seems to be associated with changes in
transcriptional regulatory networks, whereas crop
diversification involves a larger proportion of enzyme-
encoding loci (lots of them loss-of-function alleles).

63. Towards resolving the genetic
basis of domestication in the
Compositae
Artificial selection
through
domestication
but HOW ?

64. Some fundamental questions in domestication genetics
Whichgenes show strong signs of selection in different
crops?
Can we see common patterns in taxa that have been
domesticated for similar purposes?
Can we see dissimilar categories of genes under
selection in different crop types despite their close
phylogenetic relationship (e.g. sunflower and
jerusalem artichoke)?

65. Bioinformatics pipeline:
Methodological ‘bottom-up’ approach
1.) Input: EST libraries of crop, progenitor
and outgroup
2.) Genes that are orthologous in all taxa
are identified
3.) These genes are scanned for signs of
strong positive selection
4.) Such genes are compared to all known
proteins in Arabidopsis
5.) Functional characteristics of best fits in Arabidopsisgenomic
database (TAIR) are annotated

66. Some preliminary results
Preliminary results from candidate domestication gene search
in Compositae crops:
•Several stress response genes are under selection in leaf
and oil seed crops
•Other interesting candidate domestication genes:
safflower: fatty acid metabolism
sunflower: nitrate assimilation
Jerusalem artichoke: lateral root formation

67. What to do with candidate genes?
Confirm their role underlying traits
-functional analysis (introgression/transgenes)
-expression
-population genetic work
confirm associations with fitness
association mapping with traits of interest

68. What to do with candidate genes?
Applications:
breeding / improvement
conservation of genetic diversity
identification of taxon boundaries
understanding adaptation/domestication
comparative analysis –other taxa

69. Crop improvement
•Phenotype –based selection
–Slow, ineficient but can be effective
•Using genetics to inform breeding
–Marker-assisted selection
–Marker-assisted introgression
•Transformation
–Efficient (if you have the gene) but controversial

70. Transgenics controversy
•Advantages:
–Targeted to specific gene
–Any gene can be changed / introduced from any species
–Fast and efficient
•Disadvantages:
–Safety issues
–Regulations / legal issues
–Requires expertise and technology

71. Transgenics controversy
•Advantages:
–Huge improvements in phenotype of interest possible
–Yield improvements
–Health / nutrition benefits
–Reduce herbicide / pesticide / fertilizer use
–New products –pharmaceuticals, chemicals, etc.
•Disadvantages:
–Little regulation for health/environmental safety
–Loss of genetic diversity
–Reliance on big seed companies