Download cs 253: principles of plant breeding

CS 253: PRINCIPLES OF
PLANT BREEDING
LECTURERS:
1.Prof.
Richard Akromah [BSc Agric.
(Kumasi),
MSc
(Birmingham),
PhD
(Reading)]
2.Nabila Joshua [ph.D Brooklyn College of
Agriculture]
3.Mr. Alexander Wireko Kena [BSc Agric.
(Kumasi), MSc (Ibadan)]
1
Recommended Text Books
1. Principles of plant genetics and breeding
(2007), by George Acquaah
2. Principles of plant breeding (1960), by R. W.
Allard
3. Principles of cultivar development, vol 1. by
Walter R. Fehr
4. Principles of crop improvement by N. W.
Simmonds
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• “That whoever could make two
ears of corn, or two blades of
grass, to grow on a spot of
ground where one grew before,
would deserve better of mankind
and do more essential services to
his country than the whole race
of politicians put together”.
Jonathan Swift, 1726
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The Role of Plant Breeding in Agriculture
What is Plant Breeding?
 Plant breeding is the art and science of the
genetic improvement of plants (Fehr, 1993)
 Evolution directed
(Vavilov, 1951)
by
the
will of
man
 The genetic adjustment of plants to the
service of man (Frankel, 1958)
 The branch of agriculture that focuses on
manipulating plant heredity to develop new
and improved plant types for use by society
(Acquaah, 2007)
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Plant Breeding and Food Security
Global Population (Billions)
1950 - 2050
10
9
8
7
6
5
4
3
2
1
0
1950
1970
1990
2010
2030
2050
Adapted from http://www.census.gov/population/popclockworld.html
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Urban sprawl encroaches rapidly on farmland
How can we maintain or increase agricultural productivity?
Source: http://www.ars.usda.gov/is/graphics/photos/
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7
Give us this day our daily bread!!
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Objectives of Plant Breeding
• Primary objective is to increase crop yield and
improve quality of crop produce
• Increases in crop productivity come from careful
attention to:
 water
Environment
fertilizer
component
 pest control
crop variety
Genotype
• Phenotype, P= Genotype + Environment + (G*E)
• Plant breeders concentrate on changing the crop
variety (genotype).
10
Fertility Management and Nutrient Runoff
 Nitrogen fertilizers - revolutionized agriculture
 P, K, and micro-nutrient fertilizers
 Liming
Source: http://www.ars.usda.gov/is/graphics/photos/
11
Irrigation
WATER – continues to be the most limiting factor in productivity
Source: http://www.ars.usda.gov/is/graphics/photos/
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Weed Control, Herbicides
Source: http://www.ars.usda.gov/is/graphics/photos/
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Integrated Pest Management
Source: http://www.ars.usda.gov/is/graphics/photos/
14
Plant Breeding
alone contributes
> 50% of
increased USA
Agricultural
productivity
Source: http://www.ars.usda.gov/is/graphics/photos/
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Ancillary Objectives
Resistance
diseases
to
pests
and
Earliness
Tolerance to abiotic stresses
(eg.
Drought,
Nitrogen
deficiency,
mineral
toxicity,
lodging, Photoperiod response)
Adaptability to mechanization
Appearance, taste, nutritional
quality
- Aesthetic appeal
Explain
the
difference
between
productivity
and
production?
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Plant Breeding and Related Disciplines
• Agronomy, horticulture and genetics are the core
disciplines
• Plant pathology and entomology is basic to developing
cultivars for resistance to diseases and insects
• Statistics is fundamental to the evaluation characters
that are subject to variable environmental conditions
• Biochemistry helps in understanding the physiological
and molecular basis of phenomena in plants.
• Botany is important in physiology, morphology and
anatomy of plants.
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Plant breeders need to:
• be observant of differences
• understand the genetics
• have imagination to visualize final
product
• foresight to predict demand for
future plant products
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History of Plant Breeding
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Selected milestones in plant breeding
9000 BC
First evidence of plant domestication in the hills above the
Tigris river
1694
Camerarius first to demonstrate sex in (monoecious) plants and suggested
crossing as a method to obtain new plant types
1714
Mather observed natural crossing in maize
1761-1766 Kohlreuter demonstrated that hybrid offspring
received traits from both parents and were intermediate in
most traits, first scientific hybrid in tobacco
1866
Mendel: Experiments in plant hybridization
1900
Mendel’s laws of heredity rediscovered
1944
Avery, MacLeod, McCarty discovered DNA is hereditary
material
1953
Watson, Crick, Wilkins proposed a model for DNA
structure
1970
Borlaug received Nobel Prize for the Green Revolution
Berg, Cohen, and Boyer introduced the recombinant DNA
technology
1994
‘FlavrSavr’ tomato developed as first GMO
1995
Bt-corn developed
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Evolution of Farming and Cultivated Plants
• Agriculture is about 10,000 years old.
• It’s a man-made construct that is still developing.
• Agriculture provides mankind with foodstuff, feedstuff, fibre and
herbals; which are vital for man’s continued existence on earth.
• The first farmer is believed to be a woman, who lived around
the Neolithic period, somewhere in the tri-boundary of Iraq,
Syria and Turkey (the fertile crescent; Garden of Eden?)
• She abandoned nomadic life as a gatherer of food from the
wild, and settled in a fixed community to cultivate crops, due to
the intermittent imbalance of food supply from the wild.
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• Man began to direct the cause of evolution,leading to the
domestication of few plant species through artificial selection.
• This was made possible through the availability of natural diversity within
plant species.
•
This deliberate effort to alter plants’ morphology, composition,
performance, and consequently, usefulness to mankind through
selection, established the art of plant breeding.
• Through careful selection, seeds of species and individual plants that
could best meet man’s need were obtained and propagated outside their
ecological niche.
• Natural vegetation was cleared to make room for large-scale planting of
the chosen crops.
• The choice of crop plants made by the primitive Plant Breeders for
cultivation still remain as humankind’s most important crops.
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Crop Domestication: Teosinte to Maize
• Domestication actively changes the
genetic
constitution
of
living
organisms to satisfy the needs of
farmers and consumers.
• This reflects in their morphologic
appearance and behaviour.
Teosinte, the progenitor of
maize (top), modern maize • This process is on-going through
(bottom), and a hybrid between
the work of modern Plant Breeders
teosinte and modern maize
who design and construct the
(middle).
genetic architecture of plants.
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Reproduction in Plants
Floral structure
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Terminology
 Reproduction can be asexual (from vegetative
parts--non-gametic/ non-fertilized) or by sexual
(requiring
effective
fertilization/
hybridization
forming botanic seed) methods
 Alternation of sporophytic (2n) and gametophytic
(n) generations
 In order to change from the sporophytic (2n) to
gametophytic (n) generation, meiosis must take
place.
 Among vascular plants, the diploid (2n) phase
dominates the gametophyte (pollen or embryo sac
– n) phase.
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Types of flowers
Complete flowers - have sepals,
petals, stamen, and pistil
Incomplete flowers—lacking one
of the above parts
Perfect
flowers--stamens
and
pistils are in the same floral
structure - wheat
Imperfect flower--stamen and
pistil not in the same floral
structure
Monoecious
("one
house")-stamens and pistils on the same
plant (eg. maize, cassava)
Dioecious
("two
houses")-stamens and pistils on different
plants. Ex. hemp, hops, buffalo
grass, pawpaw, kiwi, nutmeg
Flowers may either be solitary or
may be grouped together to form
an inflorescence
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Gametogenesis
Formation of
higher plants
male and female gametes in
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Pollination and Fertilisation
ANTHESIS: Maturation of the anther accompanied by the
extension of the filament
POLLINATION: Transfer of pollen grains from anther to
stigma.
• Method of transfer varies with crop
• Pollen germinates on the stigma and the pollen tube
enters the ovule via the micropyle
• The generative nucleus divides -----> 2 male germ cells
(gametes). These male gametes enter the embryo sac
FERTILIZATION:
• One male gamete(sperm) fuses with the egg ---> zygote.
The other male gamete unites with the two polar nuclei.
This triple fusion -----> the primary endosperm nucleus.
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Mechanisms that promote Self
Pollination
• Cleistogamy
• Chasmogamy
• Stigma closely surrounded by anthers
• Very few species are completely self
pollinated
• Rice, oats, wheat, barley, cowpea,
soyabean, peanut, tomato, eggplant,
okra etc
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Mechanisms that promote Cross
Pollination
• Dioecy
• Monoecy
• Dichogamy (protoandry and
protogyny)
• Self incompatibility
• Male sterility
• Heterostyly (pin and thrum flowers)
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Plant Breeding Vrs Evolution
Vavilov (1951)
Evolution is a population phenomenon
Populations but not individuals evolve
What is evolution?
Evolution is simply, descent with modification
It concerns the effect of changes in allele frequency within
a genepool of a population, leading to changes in genetic
diversity and the ability of the population to undergo
evolutionary divergence
The term was proposed by Charles Darwin in 1859
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Principles of Evolution
1. Variation
2. Heredity
3. Selection
The core of plant breeding
principles
•
The process of evolution has parallels in plant breeding
•
Darwin’s theory of evolution relies on Natural Selection as
the discriminating force, and Time
•
Plant breeders also employ these same principles in cultivar
development
•
Breeders assemble or create variation and impose artificial
selection to obtain the most desired individuals that meet
their objectives
32
Breeders’ Activity
• The work of the plant breeder can be described using six
simple verbs (Burton, 1966):
– Variate
Intermate
– Isolate
– Evaluate
– Multiplicate
– Disseminate
• The methods of plant breeding are based on the laws of
heredity and the recognition that genes situated on
chromosomes control hereditary differences between
individuals
• The phenomenon of segregation and recombination of genes
in higher plants resulting from sexual reproduction
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Review of Mendelian Genetics
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Mendelian Inheritance
Gregor
Mendel
published a small
work with the title
Experiments in Plant
Hybridization in 1866
Gregor Mendel (1822-1884)
This work remained
obscured, and was
re-discovered
in
1900
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Mendel’s Experiments
1. Mendel developed pure lines of pea
Pure Line - a population that breeds true for a
particular trait e.g., all seeds are either round or
wrinkled, flowers purple or white for many
generations. This was an important innovation
because any non-pure (segregating) generation
would and did confuse the results of genetic
experiments.
2. Counted his results and kept statistical notes
– this is essential for data analysis
36
Mendel had pure parental lines (P) that differed in single characters or
traits
Flower colour: Purple vrs white
Seed colour: Green vrs yellow
Seed shape: Round vrs wrinkled
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Mendel crossed parents differing in these characteristics and obtained
the following in the first offspring (F1 or first filial generation):
P1 = yellow; P2 = green seeds
F1 hybrids = All yellow
P1 = Purple; P2 = white flowers
F1 hybrids = All purple
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The Allele Concept
Allele - one alternative form of a given allelic pair; purple and white are the
alleles for the flower colour of a pea plant; more than two alleles can exist for
any specific gene, but only two of them will be found within any diploid
individual
Allelic pair - the combination of two alleles which comprise the gene pair
Homozygote - an individual which contains only one allele at the allelic pair; for
example DD is homozygous dominant and dd is homozygous recessive; pure
lines are homozygous for the gene of interest
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Dominant - the allele that expresses itself at the expense of an
alternate allele; an allele that determines the phenotype in a
heterozygous condition
Recessive - an allele whose expression is suppressed in the presence
of a dominant allele; the phenotype that disappears in the F1
generation from the cross of two pure lines and reappears in the F2
generation. A recessive allele displays no influence on the phenotype
in heterozygous individuals
Homozygote - an individual which contains the same allele at a gene
locus; for example DD is homozygous dominant and dd is homozygous
recessive; pure lines are homozygous for the gene of interest
Heterozygote - an individual which contains one of each member of the
gene pair; for example the Dd heterozygote
Monohybrid cross - a cross between parents that differ at a single gene
pair (usually AA x aa)
Monohybrid - the offspring of two parents that are homozygous for
alternate alleles of a gene pair
Remember --- a monohybrid cross is not the cross of two monohybrids
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The phenotype is the appearance
of an individual that is based on an
underlying genotype and on the
influence that the environment
exerts
42
Mendel crossed the F1 to themselves (selfed
the F1)
He observed that white flowers that was
absent in the F1 appeared in the F2 in a ratio
of 3 purple flowers to one white flower i.e., a
phenotypic ratio of 3:1
MENDEL's first law is the principle of
segregation. It states that during gamete
formation each member of the allelic pair
separates from the other member to form the
genetic constitution of the gamete.
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Law of Segregation
44
Genotype vs. Phenotype
= appearance
= allele combinatio
45
According to this principle hereditary traits are
determined by discrete factors (now called genes)
that occur in pairs, one of each pair being inherited
from each parent.
This concept of independent traits explains how a
trait can persist from generation to generation
without blending with other traits. It explains, too,
how the trait can seemingly disappear and then
reappear in a later generation.
The
principle
of
segregation
was
consequently of the utmost importance for
understanding both genetics and evolution
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Confirmation of law of segregation
The Testcross
The F1 phenotypic ratios tell whether the dominant phenotype is
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homozygous (no segregation) or heterozygous ( ratio of 1:1)
Mendel’s Second Law
Mendel also performed crosses in which he followed the
segregation of two genes e.g., Yellow and round seeds x Green
and wrinkled seeds.
The dominance relationship between alleles for each trait was
already known to Mendel when he made this cross
Dihybrid cross - a cross between two parents that differ by two
pairs of alleles (GGWW x ggww)
Dihybrid - an individual heterozygous for two pairs of alleles
(GgWw)
Example of dihybrid cross: Yellow, Round Seed x Green,
Wrinkled Seed
F1 Generation: All yellow, round
F2 Generation: 9 Yellow, Round, 3 Yellow, Wrinkled, 3 Green,
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Round, 1 Green, Wrinkled
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Mendel selfed the F1 and obtained individuals as shown in Punett
Square below:
Female Gametes
GW
Gw
Male
Gametes
gW
gw
GW
Gw
gW
gw
GGWW
GGWw
GgWW
GgWw
Yellow,
round
Yellow,
round
Yellow,
round
Yellow,
round
GGWw
GGww
GgWW
Ggww
Yellow,
round
Yellow,
wrinkled
Yellow,
round
Yellow,
wrinkled
GgWW
GgWw
ggWW
ggWw
Yellow,
round
Yellow,
round
Green,
round
Green,
round
GgWw
Ggww
ggWw
ggww
Yellow,
round
Yellow,
wrinkled
Green,
round
Green,
wrinkled
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The phenotypes and general genotypes from this cross can be
represented in the following manner:
Phenotype
General Genotype
9 Yellow, Round
Seed
G_W_
3 Yellow, Wrinkled
Seed
G_ww
3 Green, Round
Seed
ggW_
1 Green, Wrinkled
Seed
ggww
The results of this experiment led Mendel to formulate his second law.
Mendel's Second Law - the law of independent assortment; during
gamete formation the segregation of the alleles of one allelic pair is
independent of the segregation of the alleles of another allelic pair
It does inevitably cover the case that new combinations of genes, that
were not existing before can arise. In MENDEL's experiment these are
the combinations: Yellow wrinkled seeds; Green round seeds
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PUNNETT-Square: The
scheme shows the genotypes
of the P-, F1- and F2generation of a dihybrid
hereditary path.
This kind of representation
was introduced by the British
geneticist R. C. PUNNETT at
the beginning of 20th century
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Law of Independent Assortment
53
Note:
MENDEL's fundamental work was forgotten
for 35 years. It became known in 1900. The
German C. CORRENS, the Dutchman HUGO
de VRIES and the Austrian ERICH von
TSCHERMAK-SEYSENEGG are regarded as
its rediscoverers.
Mendel’s work is today viewed as the
fundament of modern genetics.
The chromosome theory confirmed Mendel’s
work
54
Complications to Mendelian Genetics
1. Gene actions
• Intra-allelic interactions
» Additivity
» Incomplete or partial
dominance
» Dominance
» Over-dominance
•
Inter-allelic interactions
» Epistasis
» Pleiotrophy
2. Linkage
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Incomplete Dominance
Incomplete Dominance is an exception to Mendel’s
general observations. In case of incomplete
dominance, a homozygous dominant trait crossed
with a homozygous recessive trait will produce an
intermediate trait which allows some of the
recessive trait to filter through, incompletely
masked by the dominant trait.
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Dominance
• Dominance is not an inherent property of an
allele
• An allele may be dominant to a second allele,
but co-dominant, incompletely dominant, or
even recessive to a third
57
Epistasis
Epistatic genes override or mask the phenotype of a
second gene.
Epistasis is not dominance.
Compare the definitions:
Epistasis
One gene masks the expression of a different gene
for a different trait
Dominance
One allele masks the expression of another allele
of the same gene
58
Classical Epistatic Ratios
• About 6 different epistatic gene actions
have been observed
1. Complementary gene action (9:7):
also known as duplicate recessive
epistasis
2. Duplicate gene action (15:1): a.k.a
duplicate dominant epistasis
3. Recessive suppressors (13:3): a.k.a
dominant and recessive epistasis
4. Additive gene action (9:6:1)
5. Dominant epistasis (12:3:1)
6. Recessive epistasis (9:3:4)
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Pleiotropy
One gene causes multiple effects on a
phenotype, i.e. the control of two or more
characters by a single gene
Sickle cell anemia: one mutant gene, many symptoms
Single amino acid substitution
in the hemoglobin protein
Pain, stroke, leg ulcers, bone damage, jaundice, gallstones,
lung damage, kidney damage, eye damage, anemia, delayed
growth
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LINKAGE
• T. H. MORGAN’S LAWS (1911):
• Genes occur
chromosomes
• Linked
genes
chromosome
in
a
are
linear
on
order
the
• Genes can be exchanged
chromosomes during meiosis
on
same
between
• The closer genes are located on a
chromosome, the less likely they will
separate and recombine in meiosis
61
Genes on the same chromosome are
linked
Gene loci
Dominant
allele
a
P
P
Genotype:
PP
Homozygous
for the
dominant allele
B
b
a
aa
Homozygous
for the
recessive allele
Recessive
allele
Bb
Heterozygous
Figure 9.9
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GENETIC RECOMBINATION
63
• If two genes are close
together,
they
will
not
independently
enough
assort
• If they are not close together,
recombination or crossing over may
occur to separate them
• Linkage types
– Two possible configurations
• cis:
• trans:
A B // a b
A b // a B
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REVIEW OF MOLECULAR
GENETICS: THE CHEMICAL
BASIS OF HEREDITY
65
Discovery of DNA as the Hereditary Material
• Nucleic Acids (DNA and RNA)
were discovered in 1869 by
Friedrich
Mieschner
as
a
substance contained within cells
• During the ’30s & 40’s proteins
rather than DNA was thought to
hold genetic information
66
What is DNA?
• Deoxyribonucleic acid (DNA) is a Nucleic Acid
• Nucleic acids are polymers of Nucleotides
• A nucleotide consists of three molecules
– A Pentose or 5-carbon sugar
– A nitrogenous base
– Phosphate group
• There are four N-bases in DNA
– Adenine, Guanine, Thymine, Cytosine
67
Structure of DNA by J. Watson & F. Crick
(1953)
• Carbon 1 (C1) is where the base is attached.
• Carbon 2 (C2) tells you if it is a ribose or
deoxyribose. In deoxyribose, oxygen at C2 is
missing.
• Carbon 3 (C3) is the point of attachment for
more nucleotides through a phospho-diesther
bond
• Carbon 4 (C4) completes the ring via an
oxygen (O) which bridges to the carbon 1 (C1).
Carbon 5 (C5) hangs away from the ring and
is the point of attachment for its phosphate(s).
68
• DNA is a double stranded helix
• The two strands are Antiparallel
• Strands are held together
hydrogen bonds between bases
by
• A pairs with T, and C with G
69
Nucleotide Structure
70
DNA is Antiparallel
71
DNA Replication
• Before mitosis and meiosis, all of
the DNA in the cell must be copied
or replicated
• How does this happen?
72
DNA Replication
73
What is a gene?
• A gene is a piece of DNA consisting of coding
(exons) and non-coding (introns) base
sequences with the inherent ability to be
transcribed and translated to produce a
protein
74
• Thus, a gene locus for any character or trait
(eg. Flower colour, seed coat colour, disease
resistance, dwarfism, etc) on any chromosome,
can be viewed as a code of genetic information
written with the four bases; A, C, G, T.
• Alleles actually emanate from differences in
base sequences on homologous chromosomes
caused by mutations, resulting in different
proteins being formed, hence different
phenotypes.
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