Crop Improvement and

Seed Selection
 Plant breeding science, art and business of crop
improvement for human benefit
Goals and objectives of plant breeding higher yields,
improved quality, disease and insect resistance, change in
maturity duration, agronomic characteristics,
photoinsensitivity, synchronous maturity, nonshattering
characteristics, determinate growth, dormancy, abiotic stress
tolerance, etc.
Activities in plant breeding:
creation of variation generation of variability: domestication,
germplasm collection, introduction, hybridization, mutation, genetic
engineering
selection
evaluation
multiplication
distribution
conservation of germplasm
 Generation of variability
naturally existing variability
domestication process of bringing wild species under human
management
germplasm collection collection of a large number of genotypes of a
crop species and its wild relatives
introduction taking a genotype or a group of genotypes of plants into
new environments where they were not being grown before
creation of new variability
hybridization crossing genetically dissimilar individuals; produces a
hybrid
inbreeding mating of individuals related by ancestry; leads to
production of homozygous individuals
inbred product of inbreeding hence consequently a homozygous individual
selfing mating with oneself; most intense form of inbreeding hence
approach to homozygosity is fastest
full sibbing crossing between members of selected pairs of plants; full
sibs have both parents in common
half sibbing crossing one individual with several identified ones; half sibs
have one common parent or pollen source
 topcross cross between an inbred and an open-pollinated variety
testcross cross between a plant or line and a tester (tester may be an
inbred, hybrid, synthetic or open-pollinated variety)
backcross a cross between a hybrid and one of its parents; also a
breeding method based on repeated backcrossing of the F1 (first
generation offspring of a cross) and the subsequent generations to the
recurrent parent usually to transfer a major trait controlled by one or a
few genes from the donor (as the non-recurrent parent) and the
recipient (as the recurrent parent)
polycross open pollination in isolation among a number of selected
genotypes arranged in a manner that promotes random mating
reciprocal cross mating of two individuals in which each is used as
the male parent in one cross and as the female parent in the other
intraspecific cross crossing individuals belonging to the same
species, e. variety x variety cross
wide or distant cross crossing distantly related individuals
interspecific crossing individuals belonging to different species
intergeneric crossing individuals belonging to different genera
introgressive hybridization repeatedly backcrossing interspecific
hybrids to one of the parental species leading to the transfer of some
genes from one species to another
 heterosis or hybrid vigor; superiority of the F1 hybrid over its
parents; maybe positive or negative; ex. positive heterosis
for yield and negative heterosis for days to maturity
mid-parent heterosis increase or decrease in performance of
the hybrid in comparison with the mid-parent value or average
performance of the two parents
heterobeltiosis the increase or decrease in the performance
of the hybrid in comparison with the better parent of the cross
combination
standard heterosis the increase or decrease in the
performance of a hybrid in comparison with the standard check
variety of the region; type of heterosis practically important to
breeders
theories to support heterosis:
dominance hypothesis that heterosis is due to the
accumulation of favorable dominant genes from the two parents
in the hybrid
overdominance hypothesis that heterozygotes are more
vigorous and productive than either homozygotes
heterosis is expected to be high when inbreds used in
producing the hybrids have high combining abilities
 combining ability the ability of a genotype
(inbred, pureline, or synthetic) to transfer its
desirable traits to its progeny
general combining ability (GCA) average
performance of a strain in a series of crosses;
estimated using testers of broad genetic base and
identifies mainly additive genetic effects
specific combining ability (SCA) deviation from
performance predicted on the basis of general
combining ability of parental lines; estimated by
using testers of narrow genetic base and identifies
both additive and non-additive gene action
inbreeding depression loss in vigor due to
inbreeding
 Mechanisms promoting self pollination
cleistogamy flowers do not open at all ensuring complete self-
pollination
chasmogamy flowers open but only after pollination has taken
place
stigmas closely surrounded by anthers
flowers open but stamen and stigma are hidden by other floral
organs
stigma when receptive elongate through staminal columns
Mechanisms promoting cross pollination
dicliny or unisexuality flowers are either staminate (male) or
pistillate (female)
monoecy staminate and pistillate flowers occur in the same plant either
in the same or in different inflorescences
dioecy male and female flowers are present on different plants, the
plants in such species are either male or female
dichogamy stamens and pistils of hermphrodite (perfect, bisexual)
flowers may mature at different times facilitating cross pollination
protogyny pistils mature before stamens
protandry stamens mature before pistils
stigmas are covered with waxy film
self-incompatibility
male sterility
 Systems of pollen control
emasculation removal of immature anthers (or
androecium) from a hermaphrodite flower using clip, hot
water or suction/vacuum methods
male sterility systems male gametes nonfunctional but
female gametes are fertile
cytoplasmic male sterility genes for male sterility residing in
the cytoplasm particularly in the mitochondrion
genetic male sterility sterility controlled by a nuclear gene,
usually recessive
cytoplasmic-genetic male sterility controlled by interaction
between genetic factors present in the cytoplasm and
nucleus; presence of a male sterility gene in the cytoplasm
and a restorer gene in the nucleus results in the latter
overcoming the effect of the former to restore fertility
environment-sensitive genetic male sterility (EGMS)
genetic male sterility system conditioned by environmental
factors
 photoperiod sensitive genic male sterility (PGMS0 responds to
photoperiod or duration of daylength for expression of pollen
sterility and fertility
thermosensitive genic male sterility (TGMS) male sterility/fertility
alteration conditioned by different temperature regimes
photothermosensitive genic male sterility (PTGMS) conditioned
by both photoperiod and temperature
chemically induced male sterility use of chemical hybridizing
agents or gametocides like ethrel, monosodium methyl
arsenate and sodium methyl arsenate
self-incompatibility systems failure of pollen from a flower
to fertilize the same flower or other flowers on the same
plant
heteromorphic system flowers of different incompatibility
groups are different in morphology, ex. Pin and thrum flowers
in Primula
homomorphic system incompatibility is not associated with
morphological differences among flowers; incompatibility
reaction of pollen may be controlled by the genotype of the
plant on which it is produced (sporophytic control; haplo-diplo
system) or by its own genotype (gametophytic control; haplo-
haplo system)
 Mutation
heritable change in an organism
spontaneous mutations occurring in natural populations
induced mutations artificially produced by treatment with certain
physical or chemical agents or mutagens
physical mutagens rays, rays, fast and thermal
neutrons, x-rays and rays , UV radiation
chemical mutagens alkylating agents, acridine dyes, base
analogues, etc.
chimera an individual with one genotype in some of its
parts and another genotype in the other parts
periclinal chimera when the entire outer (outer periclinal) or inner
(inner periclinal) layer of shoot apical meristem is affected
Outer layer gives rise to the dermal system and part of mesophyll while
the inner layer produces the rest of the plant.
sectorial chimera only a part of the outer (outer sectorial) or inner
(inner sectorial) layer is affected
 polyploidization increasing ploidy level to more than two identical or
distinct genomes; types of polyploids
euploidy change in chromosome number involving one or more
complete genomes; chromosome number is an exact multiple of the
basic or genomic number, ex. Triploids, tetraploids, pentaploids, etc.
autopolyploid when all the genomes present in a polyploid species are
identical
allopolyploid two or more distinct genomes are present
amphidiploid an allopolyploid that has two copies of each genome
present in it; have regular meiosis
segmental allopolyploid contains two or more genomes which are
identical with each other, except for some minor differences
aneuploidy change in chromosome number involving one or a few
chromosomes of the genome; nullisomics, monosomics, trisomics,
etc.
somaclonal variation heritable variation for both qualitative and
quantitative traits shown by plants regenerated from tissue and cell
cultures
gametoclonal variation heritable variation shown by plants
regenerated from pollen or anther culture
Genetic engineering
production of transgenic plants
changing the genetic makeup of plants by direct
introduction of genes (transgenes) from microorganisms,
animals or other plant species; done when sexual
hybridization between the recipient and donor is
impossible
steps:
identification of genes, construction of vectors
in vitro plant regeneration system

gene introduction methods

molecular analysis

gene expression assays

stability and transmission analysis
Selection with hygromycin Selection with glyphosate herbicide
Biolistic PDS-
1000/He unit

pressure
chamber
The Ti plasmid structure and function

The Ti plasmid is about 200kb while the T-DNA is about 13kb

 Selection
identification of individuals or lines that are more desirable
than others in a heterogeneous population
natural selection change in gene frequencies from one generation to
another because of differences in survival and reproductive abilities of
parental genotypes in natural populations
artificial selection change in gene frequencies brought about by man
as is done in plant breeding where certain individuals or genotypes are
not used as parents of the next generation
modes of selection
stabilizing or normalizing selection when adaptive individuals in the
populations are selected under a constant environment through the
years; keeps the population constant and eliminates the deviants;
reduces the variability present in the population.
directional selection change towards a particular direction due to
changing environments resulting also in change of genetic constitution
of the population; mode observed when breeders do artificial selection
diversifying or disruptive selection opposite of stabilizing selection;
leads to either formation of subpopulations differing in their
characteristics or polymorphism in which each genotype is represented
by a distinct phenotype.
 traits selected for:
qualitative traits monogenic or oligogenic traits; show discrete or non-
continuous variation, controlled by one or few genes, less influenced
by environment
quantitative traits polygenic, metric or measurable traits; show
continuous variation, controlled by many genes, highly influenced by
environment
bases of selection
phenotypic variance sum of genotypic variance, environmental
variance and GxE variance
genotypic variance sum of additive and non-additive types of gene
action
non-additive due to intralocus and interlocus interactions
additive due to individual effects of genes
Intralocus interaction dominance interactions; interaction between
alleles in the same locus.
complete dominance heterozygote is equal to the dominant homozygote
in value
partial dominance value of the heterozygote is between the average of
the two homozygotes and the value of the dominant homozygote
overdominance if the heterozygote has a value outside the range of the
two homozygotes
Interlocus interaction epistasis; interaction among alleles of different
loci
environmental variance effect of environment on the phenotype and
estimated by measuring variation in a genotypically uniform population
grown in a certain location
GxE interaction change in ranking and/or performance of genotypes
when grown in different environments; estimated by computing
variances of genotypes when grown in a number of locations which are
environmentally diverse.
heritability portion of the phenotypic variation among individuals
that is due to genetic differences among them
broad-sense heritability is estimated from the ratio of the total
genotypic variance to the phenotypic variance
narrow-sense heritability is estimated from the ratio of the additive
portion of the genotypic variance to the genotypic variance
selection intensity the percentage of individuals selected in a
population
selection differential difference between the mean performance
of genotypes selected from a population and the overall population
mean
gain from selection increase in mean performance of a population
that is realized with each cycle of selection
 Methods of selection
self-pollinated crops
mass selection plants are chosen and harvested on the basis of
phenotype and the seeds composited without progeny testing;
appropriate for qualitative characters with simple genetic inheritance
pureline selection procedure for isolating purelines from a mixed
population
Pureline progeny from self pollination of a single homozygous plant
pedigree selection selection for plants with the desired combination
of characters is started in the F2 generation and continued in
succeeding generations until genetic purity is reached; requires
detailed record keeping (pedigree records); suited to individual plant
selections
bulk method seeds harvested in the F2 and succeeding generations
are bulked and grown, with selection delayed until the F5 or F6 at which
time the segregation will have virtually ceased
single-seed descent progenies of the F2 plants are advanced rapidly
through succeeding generations from single seeds; selection done at
F5 and later generations
doubled haploid haploid plants are generated from anthers or F1
plants, or by other means, and the chromosomes of the haploid plants
are doubled with colchicine to produce homozygous diploid plants;
selection may start in early generations
 cross-pollinated crops
Population improvement approach increasing the frequency of
genes in the population for the desired breeding objective
recurrent selection any breeding system designed to increase the
frequency of desired alleles for particular quantitatively inherited
character by repeated cycles of selection
mass selection individual plants are chosen visually for their
desirable traits and the seeds harvested from the selected plants are
bulked to grow the following generation without any form of progeny
evaluation
half-sib family selection

full-sib family selection

S1 progeny selection

S1 is the progeny following self-pollination of plants in an open-pollinated

population of in the F2 following a cross
reciprocal recurrent selection improves two populations
simultaneously; plants are selected in each of two populations, with
the selected plants of one population being selfed and outcrossed as
the tester to the selected plants in the other population; remnant seed
from the plants with superior testcross progenies are grown and
intercrossed to reconstitute the two populations
 Evaluation
process of assessing performance of newly developed lines
of a crop through appropriate multilocational trials and tests
sequence in the conduct of yield tests:
observational yield test may test separate groups of
experimental lines; uses incomplete block design or triple
lattice design with 2-3 replications in one location
preliminary yield test evaluation including a check variety
using incomplete block design with 2-3 replications in at least 2
locations
general yield test uses randomized complete block design
with 3 replications in at least 3 locations
advanced yield test elite lines from general yield tests
evaluated using randomized complete block design with 4
replications in 6-10 locations
superior lines are approved to be released as varieties by the
National Seed Industry Council (NSIC; previously the Philippine
Seedboard); the variety must have passed the tests for
distinctiveness (D), uniformity (U) and stability (S) or the DUS test
 Multiplication
seed multiplication of an entry after it has been identified for release;
the seed produced by the breeder after a strain is identified but
before it is released as a variety is termed as the stock seed. The
stock seed is known as breeder seed once the identified strain is
released and notified
seed seed or any other propagating material used for raising a crop
seed multiplication involves:
seed production should observe proper isolation procedures to
maintain genetic purity of the variety
Isolation separation of a population of plants from other genotypes
with which they are capable of mating
temporal isolation isolation by differences in growth stages

spatial isolation isolation by distance

seed processing drying, cleaning and grading, testing (purity,

viability and moisture content determination), treating (disinfectants
and protectants), bagging and labelling
 Types of varieties
hybrids first generation offspring of a cross between two individuals
differing in one or more genes
synthetics seed mixture of strains, clones, inbreds, or hybrids
maintained by open-pollination for a specified number of generations;
the component units are propagated and the synthetic reconstituted at
regular intervals
composites mixture of genotypes from several sources, maintained
by natural pollination
inbreds a pureline originating by self-pollination and selection
multilines or blends; composite of isolines
Isolines lines that are genetically similar except for one gene
open-pollinated variety variety maintained by natural cross
pollination
landraces farmer-selected cultivated forms
Hybrid seed production
3-line system male sterile line (A), maintainer line (B) and restorer
line
2-line system male sterile line, the expression of which is
influenced by environment and any inbred variety as pollen parent
1-line system use of apomixis to produce the F1 seeds and to
maintain the genotype of the F1
Distribution
classes of seeds
breeder seeds controlled by the originating plant
breeder; starting point of all the subsequent classes of
seeds; seeds obtained from uniform panicles by
breeders; 100% pure; carry a white tag
foundation seeds seeds produced from breeders
seeds; source of registered and/or certified seeds; 98%
pure with at least 85% germination rate; carry a red tag
registered seeds produced from foundation or
registered seeds and carry a green tag
certified seeds produced from foundation, registered
or certified seeds and carry a blue tag
good seeds produced from elite lines not yet
approved by NSIC
Conservation of germplasm
germplasm the sum total of hereditary material or genes
present in a species
plant germplasm genetic source material used by plant
breeders to develop new cultivars (cultivated variety)
centers of diversity where extensive genetic variability of
cultivated species could be found; also believed by Vavilov
to be centers of origin
primary centers where domestication occurred

secondary centers where variation continued after

domestication
germplasm storage
as seeds in cold/refrigerated rooms

maintained as living plants in field or through slow growth

in vitro
cryopreservation or freeze-preservation