(1) Chromosomal variations such as translocations, inversions, deficiencies, and duplications have been produced in many cereal crops and used to develop genetic maps, locate genes, and manipulate breeding. (2) Techniques like haploid breeding, synthetic polyploids, and alien introgression have also been used to develop improved crop varieties with new traits. (3) Advances in chromosome banding and fluorescence in situ hybridization (FISH) have provided tools to precisely characterize karyotypes and detect introgressed alien segments for crop improvement.

2. Role of chromosomal variation in
crop improvement in cereals
BAJRANG LAL JAKHAR
M.Sc PBG

3. Introduction
• Gregor Mendel (1865) established that heredity is particulate;
alleles exist in two or more alternate forms.
• Mendel's discoveries were ignored from 1865 to 1900.
• A parallelism between Mendel's laws of inheritance and the
behaviour of chromosomes during meiosis laid the foundation of
'cytogenetics '.
• In 1882, Flemming described the process of mitosis. Waldeyer
coined the term chromosome in 1882.
• A large number of cytogenetic stocks have been produced,
characterized and used in construction of genetic maps, gene
location, manipulation of pairing controlling mechanism, alien
introgression and in developing improved germplasm with new
characteristics.

4. • Eg: Development of improved cultivars through haploid breeding in barley
, rice. Tetraploid varieties in rye, synthetic allopolyploids such as Triticale.
• Major advances have been made in chromosome research during the last
three decades particularly in chromosome image analyzing system,
chromosome banding, Fluorescence in situ hybridization (FISH) and GISH
etc.
• These advances have provided new opportunities for precise manipulation
of chromosomes, aimed at the genetic enhancement of crops.

5. Chromosomal Variation
• A chromosome variation, abnormality, aberration,
or mutation is a missing, extra, or irregular portion
of chromosomal DNA.
• It can be from an atypical number of chromosomes
or a structural abnormality in one or more
chromosomes.

6. Structural Variations
 There are two primary ways in which the
structure of chromosomes can be altered
 1. The total amount of genetic information in the
chromosome can change
 Deficiencies/Deletions
 Duplications
 2. The genetic material remains the same, but is
rearranged
 Inversions
 Translocations

7. • Deficiency (or deletion)
The loss of a chromosomal segment
• Duplication
The repetition of a chromosomal segment compared
to the normal parent chromosome
• Inversion
A change in the direction of part of the genetic material
along a single chromosome
• Translocation
A segment of one chromosome becomes attached to
a different chromosome
– Simple translocations
One way transfer
– Reciprocal translocations
Two way transfer

10. Numerical Variations
• Chromosome numbers can vary in two main ways:
– Euploidy
Variation in the number of complete sets of
chromosome.
– Aneuploidy
Variation in the number of particular chromosomes
within a set.
– Euploid variations occur occasionally in animals and
frequently in plants
– Aneuploid variations, on the other hand, are regarded
as abnormal conditions

11. Structural Changes in
Chromosomes
• A large number of cytogenetic stocks involving chromosomal
interchanges (translocations), inversions, deletions and
duplications have been produced in maize, barley, rice etc.
• In barley alone, cytologically defined stocks include over 1000
reciprocal translocations, inversions, deletions and duplications.
• These stocks have been used extensively in establishing linkage
group and mapping of genes in barley, maize and other crops.

12. (1.) Translocations: Among the different types of structural aberrations,
translocations have been extensively employed in genetic analysis of traits
and in mapping of genes in maize and barley.
• Translocations have been used for duplication of defined segments of
chromosomes 6 and 7 in barley, which seem to be promising for
enhanced yield (Hagberg and Hagberg, 1987).
• Translocations are being used for producing duplications in the short
arm of chromosome 5 and 6, which carry genes for mildew resistance
and alpha-amylase activity, respectively .
• A-B Translocations: The deficiency duplication created by the A-B
translocations has been used to map genes in rye and maize.

13. (2.) Inversion in Plant Breeding Evolution
• In Barley, a trisomic plant (2n=15) was found with pericentric inversions
and deletion in the extra chromosome 6.
• The extra pair of chromosome was entirely different from chromosome
no. 6 and resulted from inversion.
• In the selfed progeny of this trisomic, a 16 chromosomal plant could be
observed.
• But the new plant had reduced fertility.

14. Autoploid Breeding
• Autotetraploids show reduced seed fertility due to genic imbalance and
multivalent formation at meiosis.
• However, subsequent selection can improve seed fertility and reduce
multivalent formation .
• Inspite of many efforts to improve fertility, autotetraploids are not
popular in crops where seed is the commercial product.
• In seed crops, a few tetraploid rye varieties have been released such as
Tetra Petkus, Fourex, Dubbel Stahl and Steel have been released in
Germany, Sweden, and USA.
• The tetraploid rye has larger kernel size, superior ability to emerge
under adverse conditions and possesses higher protein content.
• The seed sterility in autotriploids has been used as an advantage in crops
where seedlessness is a desirable character. The example of triploid
"seedless" watermelons is well-known.

15. Synthetic Amphiploids
• A number of crop plants such as wheat, cotton, Brassica , oats are natural
allopolyploids.
• Numerous amphiploids have been produced by intercrossing two or more
distantly related taxa followed by chromosome doubling to restore the
chromosomal balance.
• In many cases, such amphiploids show varying levels of fertility.
• Triticale (AABBDDRR) is an amphiploid of Triticum spp (AABBDD), and
Secale cereale (RR).
• It combines good agronomic traits of S. cereale which are lacking in T.
aestivum and enable its cultivation in non-traditional wheat areas .
• However, triticale is still not very popular, as it has poor grain
characteristics and also suffers from infertility despite the fact that it has
a perfect chromosome balance.

16. • None of the synthetic amphiploids produced in the past such as
Raphanobrassica, B. campestris x B. nigra , B. campestris X B. oleracia,
have shown promise.
• However, such synthetic amphiploids have been used successfully in
crosses with the natural diploids or polyploids to extract desirable
alloploids.
Seed of wheat Seed of rye Seed of triticale

17. Synthesis of Triticale

18. Extracted Alloploids
• Incorporation of a complete alien genome may bring in several
undesirable characteristics.
• Thus, the alternative approach is to extract stable alloploids from crosses
of synthetic amphiploids with natural allopolyploids or related wild
relatives .
• Triticale is the classical example for demonstrating the usefulness of
extracted alloploids. Hexaploid triticales are comparatively better in
terms of meiotic stability and seed yield.
• The extracted triticales derived from the progenies:
(1) octaploid triticale x hexaploid triticale and,
(2) hexaploid wheat x hexaploid triticale are much better.
• They are superior to the primary triticales in meiotic stability, grain yield,
and grain quality.

19. • According to Gupta (1984), 29 out of 41 released varieties of triticale have
R/D chromosome substitution. The most popular hexaploid triticale are
"Armadillo" strains carrying 2R-2D chromosome substitution .
• Crosses of 8x triticale with Armadillo resulted in the production of Maya 2.
Armadillo from which Mapache was selected and released as Cananea-79
in Mexico.
• The Vavilov Institute has developed a series of 42-chromosome
amphiploids by crossing 4x wheat with Eincorn wheats and doubling the
chromosome number of F1s. Over 30 allopolyploids were intercrossed with
common wheat cultivars and promising lines were extracted.
• A number of genes for disease and insect resistance and tolerance to
abiotic stresses and improved quality character have been introgressed
into crops through crosses with wild relatives.
• Numerous examples on introgression of alien genes are available in wheat,
rice, barley (Brar and Khush, 1986; Khush and Brar, 1989; Brar and Khush,
1997 Friebe et al.,1999).

20. Cananea-79
(Triticale variety)

21. Evolution of wheat

22. Brassica triangle

23. Evolution of Raphanobrassica

24. Evolution of gossypium hirsutum

25. Aneuploid Breeding
• A large number of aneuploid stocks such as monosomics, nullisomics,
primary trisomics, secondary trisomics, tertiary trisomics and
compensating trisomics have been produced.
• These stocks have been characterized and employed in genetic
analysis for mapping major genes as well as genes governing
quantitatively inherited traits (Khush, 1973 Singh 1993, Gupta 1999).
(a.) Monosomics (2n-l): Monosomics have been reported in several
polyploid plant species such as wheat, oats, Nicotiana, cotton, etc .
• These have been extensively studied in wheat.

26. • Sears (1954) was the first to discover that 21 different chromosomes of
wheat fall into seven homoeologous groups of three distinct genomes.
• This was based primarily on the ability of each tetrasome to compensate
for the nullisome of each of the other two chromosomes of the same
group.
• Using monosomics, numerous genes have been mapped in wheat and
chromosome substitution lines developed.
• Due to lack of survival in diploid species, use of monosomics is mainly
restricted to polyploid species.
(b.) Primary Trisomics (2n+l): Primary trisomics have one extra intact
chromosome in addition to the normal diploid chromosome complement.
 Primary trisomics are one of the most extensively studied aneuploids in
assigning genes to specific chromosomes in diploid species such as
Datura, maize, barley, tomato, and rice. These have also been used to
construct molecular map in rice (MeCouch et al., 1988).

27. (c.) Secondary and Telo-Trisomics: In these trisomics, the extra
chromosome is isochromosome for one of the chromosome arms of the
complement.
• Secondary trisomics or telo-trisomics have been reported in maize,
barley, tomato, and rice .
• These trisomics have been used to map only a few genes on specific
arms of barley, tomato and rice chromosomes.
(d.) Telo-trisomics: Rhoades (1936) discovered the first telotrisomic in
Zea mays. Since then , telotrisomics have been developed in a number of
species including Triticum, Secale, and rice.
• Singh et al. (1996) used secondary and telotrisomics for mapping of
centromeres on the genetic map of rice.
• Cheng et al. (2001) reported a complete set of telotrisomics in rice
covering all the 24 chromosome arms .
• A rice centromere BAC clone was used as a marker probe in FISH
analysis to verify the telocentric nature of extra chromosome in
telotrisomic stocks of rice .

28. (e.) Tertiary Trisomics: In tertiary trisomics, extra chromosome
consists of two arms of two non-homologous chromosomes.
• Tertiary trisomics have been used to map a few genes on chromosome
arms of barley and tomato.

30. Balanced Tertiary Trisomics and
Hybrid Barley Production
• Ramage (1965) produced balanced tertiary trisomics for the
production of F1 hybrid barley.
• A pair of recessive male sterility alleles are present on normal
chromosome, while the extra chromosome (interchanged
chromosome) carried a dominant allele linked to the
translocation point.
• A variety of barley - Hembar, was released using such trisomics
derived from the segmental interchange T2-7d induced by X-rays
in Bonus barley .
• The system avoids the need for fertility restorer genes in the
pollen parent as in wheat.
• However, the balanced tertiary trisomics are generally weak and
do not produce sufficient pollen to pollinate the male-sterile
diploids for increasing the seed of male-sterile parent.
• Hence, the system could not be used on commercial scale for
practical barley breeding.

33. Haploid Breeding
• Haploids are important to develop homozygous lines from a
segregating population much faster than by any other technique.
• They serve as mapping populations to locate genes governing economic
traits.
• There are many methods used to produce haploids-
1. Isolation of haploids from natural
populations-
a number of genetic stocks have been found to give increased frequency
of haploids. Such genetic stocks have been extensively used to isolate
haploids in corn , flax, Brassica, etc.
2. Anther culture- has been extensively used
worldwide to produce haploids in several plant species. A number of
promising cultivars in tobacco, rice, wheat, and Brassica have been
released using anther culture derived dihaploids.

34. 3. Interspecific crosses- has proved to be an
important procedure to produce haploids in barley, wheat, and
potato. Hagberg and Hagberg (1980) reported a mutant gene 'hap'
that could produce haploids in barley. Plants homozygous for the hap
gene produce progeny that includes 10-14 % haploids.
 Alien cytoplasm (Aegilops caudata x T. aestivum) can result into
high frequency (30 %) of haploids

35. Haploid via Chromosome
Elimination
• In certain interspecific crosses chromosomes of one parent get
selectively eliminated after fertilization, resulting into the production of
haploid plants.
Eg: 1. Elimination of bulbosum chromosomes in the cross of
H. vulgare x H. bulbosum;
2. Elimination of maize chromosomes in wheat x maize
3. Oat x Maize crosses.
• Haploids from such crosses can be produced through sexual hybridization
followed by embryo rescue.
• Ho and Kasha (1975) made crosses of primary trisomics of barley with
tetraploid bulbosum and located genes governing chromosome
elimination on chromosomes 2 and 3.
• Some high yielding varieties (Mingo, Rodeo, Gwylan) have been released
through bulbosum method.

37. • Thus, this method seems to have good potential in barley breeding.
• Haploids have also been produced from crosses of T. durum x maize.
• Jauhar et al. (2000) observed seed set on synthetic haploids of durum
wheat produced from the crosses of durum wheat x maize . The durum
cultivars had Ph1 gene, their haploids mostly formed univalents and had
irregular meiosis. However, some haploids (2.75 seeds) set viable seeds.
• Dogramaci and Jauhar (2001) reported durum wheat substitution
haploids from crosses of durum x maize.
• These findings on production of haploids from diverse cross-combinations
indicate that mechanism of chromosome elimination should be operative
in other crops as well.

40. Chromosome Banding for Characterization
of Karyotypes and Alien Introgression
• The development of chromosome banding techniques has provided
additional tool to identify individual chromosomes.
• Giesma C-banding has been used in chromosome identification and
in analyzing the evolutionary relationships and to detect
introgressed alien chromosome segments.
• The banding techniques are used for identification of chromosome
segments that consist of either GC or AT rich regions, or for
constitutive heterochromatin.
• In barley, all chromosomes can be identified by using C- or N-
banding techniques, which reveal blocks of heterochromatin as dark
staining regions.

41. In Situ Hybridization: Karyotypic
Changes and Alien Introgression
• Classical cytogenetic techniques in combination with molecular markers
and FISH have enhanced the precision on characterization of changes in
karyotype, determining: structural differences in chromosomes,
differentiation among distant genomes and detection of introgressed
alien genes and chromosome segments.
• Both mitotic and meiotic chromosomes have been used in In situ
hybridization analysis.
• In situ hybridization involves hybridization of DNA or RNA probes to the
cytological preparation and allows the visualization of specific
nucleotide sequences directly on chromosomes.
• The method was developed by Gall and Pardue (1969). Since then,
isotopic probes were used extensively to map both repetitive and low
copy DNA sequences.

42. • FISH offers the advantage to precisely characterize pairing among and
within genomes.
• This is particularly useful when chromosomes of parents are of similar
size and lack diagnostic cytological markers.

44. Using Th. intermedium and Ps. spicata genomic DNA as the probe and
“Chinese Spring” genomic DNA as the competitor DNA, the alien
chromosomes in TAi-27 (wheat addition line) were identified (Figure a).
The results showed that strong hybridization signals were uniformly
distributed on two pair of chromosomes, of which one pair of
chromosomes were the smallest in TAi-27.

45.  The results suggested that chromosome painting could be useful in
detecting chromosome variation and repetitive sequence
distribution in different genomes of plants, which is helpful for
understanding the evolution of different genomes in polyploid
plants.
Achievement in cereal crops
• For Fusarium head blight resistance Hungarian winter wheat monosomic line
‘U136.1’and the highly susceptible cultivar ‘Hobbit sib’
H. Buerstmayr et al.
• The chromosome 5A has been shown to be the one which carries the major
allelic differences that distinguish wheat varieties Chinese Spring, Rannyaya
12 and Mironovskaya 808 for frost resistance.
J. Sutka et al.

47. Triticale variety
Country Variety
Australia Dua, satu
Canada Rosner
India TL 419, TL 2942, DT 46
Kenya T 50, T 65
USA Siskiyou