Extrachromosomal Inheritance (Non-Mendelian Inheritance)

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kamlesh kumar chandel

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Extrachromosomal Inheritance:

Extrachromosomal Inheritance Department of Genetics & Plant Breeding Junagadh Agricultural University Junagadh 362 001 (GUJARAT) Kamlesh Kumar Chandel (Genetics & Plant Breeding) JAU, Junagadh 2

EXTRACROMOSOMAL INHERITANCE:

EXTRACROMOSOMAL INHERITANCE The genes governing cytoplasmic inheritance are called "plasma genes", " cytoplasmic genes", " cytogenes " or " extranuclear genes", while the sum total of the extrachromosomal genetic material is known as plasmon and occurs this type inheritance is known as extra-chromosomal inheritance. Siemens in 1921 suggested that the term ideotype should be used to denote the sum total of nuclear genes (genotype), while the extrachromosomal genes should be called plasmatype 3

Rules of Extrachromosome Inheritance:

Rules of Extrachromosome Inheritance Extranuclear genes display Non- mendelian Inheritance , which has four characteristics: a. Typical Mendelian ratios do not occur, because meiosis-based segregation is not involved. b. Reciprocal crosses usually show uniparental inheritance, with all progeny having the phenotype of one parent, generally the mother because the zygote receives nearly all of its cytoplasm (including organelles) from the ovum. c. Extranuclear genes cannot be mapped to chromosomes in the nucleus. d. If a nucleus with a different genotype is substituted, non- Mendelian inheritance is unaffected. 4

Important features :

Important features Reciprocal Differences Maternal Effects Mappability Non- Mendelian Segregation Somatic Segregation Infection like Transmission Governed by Plasma genes 5

Basis of the Extranuclear Inheritance:

Basis of the Extranuclear Inheritance In early 1960's, DNA was discovered in certain cell organelles viz., - Chloroplasts - Mitochondria This DNA is the basis of cytoplasmic inheritance. It has been demonstrated that these organelles have their own system of protein synthesis. 6

Organellar DNA:

Organellar DNA Cytoplasmic DNA has been found to be present in cell organelles such as, chloroplast, mitochondria and the mitochondria-like kinetoplasts of some protozoan parasites. The organellar DNA was detected through various techniques like Feulgen staining, autoradiography, electron microscopy, cesium chloride isodensity centrifugation. Organellar DNA is usually circular and differs from the nuclear DNA in several aspects. 7

Nucleoids per Organelle:

Nucleoids per Organelle 8

Chloroplast DNA (cpDNA):

Chloroplast DNA (cpDNA) In 1951, using cytochemical methods, Chiba was the first to demonstrate the presence of nucleic acids in chloroplasts. In 1962, Ris and Plaul showed that the chloroplasts of Chlamydomonas has particles of 150-200A in diameter which resembled ribosomes . 9

Chloroplast DNA (cpDNA):

They also demonstrated the presence of DNA in the form of fibrils of 25-30Aº in thickness which disappeared after a treatment with DNAase . Plastid DNA is naked and circular. In higher plants, its length varies from 39 µm (sweet pea) to 45 µm (pea) and in algae from 40 µm ( Euglena ) to 62 µm ( Chlamydomonas reinhardtii ). The number of cpDNA molecules per chloroplast varies in different organisms. Sweet pea chloroplasts have 34 molecules, whereas those of Chlamydomonas have 70-100 molecules. Molecular weight of cpDNA in Chlamydomonas is 13 x 10 7 daltons . Chloroplast DNA (cpDNA) 10

Chloroplast DNA (cpDNA):

The cpDNA of liverwort (a moss) is 121 kb in size, while the cpDNA of tobacco has 155 kb. In higher plants, the buoyant density of cp DNA obtained by cesium chloride isodensity centrifugation is about 1.696g/cm 3 which is slightly higher than that of nuclear DNA. However, in Euglena and Chlamydomonas , the density of cp DNA is lower than that of nuclear DNA. Chloroplast DNA (cpDNA) 11

The main differences between cpDNA and the nuclear DNA are as follows -:

The main differences between cpDNA and the nuclear DNA are as follows - About 10% of the cytosine residues are methylated as 5-methylcytosine in nuclear DNA of higher plants ; such methylation is absent in cpDNA. Chloroplast DNA is circular while nuclear DNA is linear. Histones and other proteins are complexed with nuclear DNA but not with cpDNA. After denaturation , cpDNA reassociates much more rapidly than nuclear DNA. Chloroplast DNA is smaller in size than nuclear DNA. Replication of chloroplast DNA is accompanied by the formation of "displacement loops" (D-loops) that extend around the DNA circle. Such D-loop (s) are not formed during the replication of nuclear DNA. However, replication of both, cpDNA and nuclear DNA is semiconservative . 12

Mitochondrial DNA (mtDNA):

In 1962, Nass and Nass discovered mitochondrial DNA of embryonic chick tissues. They observed filaments like the DNA component of certain bacteria in the lower electron density areas of the matrix. Mitochondrial DNA ( mtDNA ) 13

Mitochondrial DNA (mtDNA):

The mtDNA is generally circular, except in some cases, e.g., Paramecium aurelia , and Tetrahymena pyriformis etc. Where it is linear. The mtDNA of animals is smaller (generally about 5 jum , having 16kb) than that of plants (8-30 µm in fungi and 30-150 µm in higher plants) and protozoa (10-15 µm). In most organisms, mtDNA is smaller than cpDNA. Due to the unique base composition of mtDNA , its buoyant density differs from that of nuclear DNA. In higher plants and birds, the density values of mtDNA are considerably higher than that of nuclear DNA, while in fungi (yeast, Neurospora , slime mold) the density values for mtDNA are lower than those of nuclear DNA. Mitochondrial DNA ( mtDNA ) 14

Mitochondrial DNA (mtDNA):

In most organisms, mtDNA is smaller than cpDNA. Due to the unique base composition of mtDNA , its buoyant density differs from that of nuclear DNA. In higher plants and birds, the density values of mtDNA are considerably higher than that of nuclear DNA, while in fungi (yeast, Neurospora , slime mold) the density values for mtDNA are lower than those of nuclear DNA. After denaluration , mlDNA can be separated into "heavy" and "light" strands by cesium chloride density centrifugation. Mitochondrial DNA ( mtDNA ) 15

The main differences between mtDNA and nuclear DNA arc as follows -:

With few exceptions, mtDNA is circular, while nuclear DNA is linear. Mitochondrial DNA is not complcxed with histones , whereas nuclear DNA forms typic nucleosomes and chromatin fibers due to its association with histones . After denaturation , mtDNA reassociates more rapidly than nuclear DNA. The buoyant density of mtDNA differs from that of nuclear DNA. It is greater for mtDNA than that of nuclear DNA in higher plants and animals, but is lower for the mtDNA of Chlamydomonas, yeast and Neurospora etc. Replication of mtDNA occurs through the formation of D-loop (displacement loop), while there is no D-loop formation in the case of nuclear DNA. The main differences between mtDNA and nuclear DNA arc as follows - 16

Replication of Mitochondrioal DNA:

Replication of Mitochondrioal DNA Replication of mtDNA is scmiconservative . At the point of origin of replication, a small loop is formed due to the displacement of one strand of the DNA double helix from the other strand. This loop is called displacement loop or D- loop and the displacement is caused by the synthesis of a small DNA fragment of about 500-600 bases. A new heavy strand (complementary to the light strand) is synthesized first. The synthesis of new 'light' strand begins only after the synthesis of the heavy strand has progressed to a considerable extent. The reason for this resides in the fact that the replication initiation points of the two strands are located at different sites . 17

Followings are the main features of replication of mtDNA:

Followings are the main features of replication of mtDNA Replication is initiated at a single point. At the origin point, DNA replication utilizes as template only the light strand of the double helix ; this results in partial synthesis of a new 'heavy strand'. The initially synthesized DNA fragment (heavy strand) is very short, approximately 500-600 nucleotides long ; this fragment displaces the old heavy strand from the mtDNA forming the D-loop. The DNA replication is unidirectional for some time utilizing only the light strand of the mtDNA as template. When about 2/3 or 80% of the strand has been replicated, replication of the second strand (the heavy strand) also begins so that a new light strand is synthesized. The DNA synthesis always proceeds from 5' to 3' direction. The two circular DNA molecules so produced separate even before the completion of replication : replication of one of the two molecules is already complete (due to early initiation), while in the other molecule, there is a short one-stranded gap (due to the delayed start of replication of the heavy strand). This gap is filled through continued replication. It takes about 2 hr for completion of the replication of mtDNA . D 18

Model for mitochondrial DNA replication that involves the formation of a D-loop structure:

Model for mitochondrial DNA replication that involves the formation of a D-loop structure 19

Replication of Chloroplast DNA:

Replication of chloroplast DNA differs from that of mtDNA in that, the replication begins simultaneously at two distinct origin points. At one origin, one of the two strands of cp DNA is replicated, while at the other origin the second strand is replicated, as a consequence two D-loops are formed. In both the D-loops, DNA synthesis proceeds only in 5' -» 3' direction, i.e., it is unidirectional. Therefore, the two loops continue to advance towards each other till they fuse to form a single large D-loop. DNA synthesis now proceeds in both the directions and both the strands of cpDNA are replicated simultaneously. Thus replication of cpDNA is bidirectional, whereas that of mtDNA is unidirectional. Replication of Chloroplast DNA L L H H Initiation of DNA replication of both strands Both D- loops combine together Bi – directional DNA Synthesis 20

Map of Chloroplast DNA :

Map of Chloroplast DNA 21

Map of Chloroplast DNA :

The size of cpDNA varies in different plants. Chloroplast genomes have been mapped by restriction site mapping technique. This technique utilizes various restriction enzymes to cut DNA into pieces and the sites of cleavages by the different enzymes are mapped on the chromosome. Chloroplast DNA has been completely analysed in liverwort (121 kbp ) and tobacco (155 kbp ). In both these plants, the circular chloroplast genome is divided by two inverted repeats, into two regions, one large and one small. In the tobacco cpDNA, each inverted repeat is 25339 bp long while in liverwort (a moss), it is 10058 bp long. The large region (single copy) of the genome is 86,684 bp long in tobacco and 81,095 bp long in liverwort. The short single copy in tobacco is 18,482 bp long, while in liverwort it is 19813 bp . The chloroplast genome possesses genes coding for specific polypeptides, tRNAs and rRNAs . It codes for all the tRNAs (30 types) and rRNA types, utilized in chloroplast protein synthesis. Map of Chloroplast DNA 22

Map of Chloroplast DNA :

The tRNA genes are distributed throughout the cpDNA molecule. About 50 proteins such as, ribosomal proteins (19 types), RNA polymerase (3 types), H+ - ATPase (6 types), photosystem I (2 types), photosystem II (7 types) chtochrome b/f (3 types), ferredoxin (3 types), ribulose-biphosphate carboxylase (1 type), NADH dehydrogenase (6 types) and others are encoded by cpDNA. Many genes code for proteins of the thylakoid membranes. Many of the chloroplast genes are split genes (containing introns ). The genes identified on cpDNA are : 45 genes coding for RNA, 27 coding for proteins related to gene expression, 18 coding for proteins of thylakoid membranes and 10 coding for the function of electron transfer. There are about 30 reading frames the products of which are still unidentified, hence they are called "unidentified reading frames" (URF). Some featuers of the chloroplast genome are similar to the prokaryotic genome, while others arc similar to those of eukaryotic nuclear DNAs. The rRNA genes in cpDNA have operon like arrangement which is reminiscent of prokaryotic genomes. Many genes and ribosomal proteins in this organelle are similar to those of prokaryotes and eukaryotes (nuclear genes). The genes coding for α, ß and ß' subunits of core enzyme of RNA polymerase in chloroplast and E. coli are homologous. Map of Chloroplast DNA 23

Map of Mitochondrial DNA :

Map of Mitochondrial DNA 24

Map of Mitochondrial DNA :

Mapping of mitochondrial genes has been done using restriction fragment analysis, and recombination analysis in organisms like yeast ( Saccharomyces cerevisiae ), human and Xenopus . Human mtDNA is 16,569 bp long. Most of the genes are located on the heavy strand of mtDNA . The mtDNA has 13 protein coding, 2 rRNA and 22 tRNA genes. The proteins coded by mtDNA are : cytochrome b, cytochrome oxidase (COI, COII, COIII), NADH dehydrogenase (ND1, ND2, ND3, ND4, ND4L, ND5, ND6), AtPase 6 and AtPase 8. The tRNA genes are located in between different protein coding genes and rRNA genes of the 22 tRNA genes, 14 are located on the heavy strand while 8 are located on the light strand. Ribosomal RNA genes are of two types (16S rRNA and 12S rRNA ), and both are located in the heavy strand. The 14 tRNA genes in the heavy strand are expressed in clockwise direction, but the 8 tRNA genes in the light strand are transcribed in the anticlockwise direction . Map of Mitochondrial DNA 25

Map of Mitochondrial DNA :

The tRNA genes and the protein coding genes are transcribed in the same direction, the gene ND6 being the exception. The human mitochondrial genes have no introns . In sonic cases, there is no separation of genes ; one gene starts just after the other ends. In some other cases, the last base of one gene is the first base of the next gene (single base overlapping). The human and yeast mtDNAs possess some common genes, such as, cytochrome b ( cyt b), three units of cytochrome oxidase (COI, COII and COIII) and one of the subunits of ATPase . But there are several differences in the genetic maps of the two mtDNAs . Map of Mitochondrial DNA 26

Maternal Effects:

Maternal Effects Inheritance pattern for certain nuclear genes. Genotype of mother directly determines phenotype of offspring. Genotype of father and offspring are irrelevant. Explained by the accumulation of gene products mother provides to developing eggs . 27

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First to study an example of maternal effect. Involved morphological features of water snail. Limnea peregra Shell and internal organs can be either right- or left-handed Dextral or sinistral , respectively Determined by cleavage pattern of egg after fertilization Dextral orientation is more common and dominant. A. E. Boycott (1920) 28

Maternal effect in snail:

Maternal effect in snail -One dextral, one sinistral Dextral ♀ x sinistral ♂  dextral offspring Reciprocal cross  sinistral offspring Contradict a Mendelian pattern of inheritance. 29

A. E. Boycott (1920) & Alfred Sturtevant (1923):

Sturtevant proposed that Boycott’s results could be explained by a maternal effect gene Conclusions drawn from F 2 and F 3 generations Dextral ( D ) is dominant to sinistral ( d ) Phenotype of offspring is determined by genotype of mother. A. E. Boycott (1920) & Alfred Sturtevant (1923) 30

Alfred Sturtevant (1923) result:

Alfred Sturtevant (1923) result 31

Inheritance Involving Infective Particales:

Inheritance Involving Infective Particales In paramecin , killer strains contain cytoplasmic particles “Kappa particles” 0.4 mm long contain their own DNA. Gene encodes paramecin toxin. Genes encode resistance to this toxin Kappa particles are infectious. Particles in extract from killer strains can infect non-killer strains. Converted to killer strains. 32

Kappa particles inheritance:

Kappa particles inheritance 33

The [poky] Mutant of Neurospora:

The [ poky ] Mutant of Neurospora 34

Yeast petite Mutants:

Yeast petite Mutants 35

Inheritance in Chlamydomonas:

Inheritance in Chlamydomonas 36

Plastid Inheritance:

Plastid Inheritance Plastids are self replicating organelles present in the cytoplasm. they never originate de novo. They develop from undifferentiated proplastids along a number of developmental paths. Leukoplasts ( leukos = white) develop in roots and other storage organs of higher plants and may accumulate starch ( amyloplasts ), proteins ( proteinoplasts ), or lipids ( lipoplasts ). Oil containing plastids ( elaioplasts ) are found in some epidermal cells of leaves. Some plastids contain pigments ( chromoplasts ) which give colour to fruits and flowers. The plastids containing chlorophylls are called chloroplasts which give the green colour to plants. The chloroplasts of the same plant may be of two kinds : Those having grana are found in mesophyll cells of leaf. Those without grana are present in association with vascular bundle cells. In the absence of light, chlorophylls can not be produced; the poorly developed chloroplasts devoid of chlorophyll are called etioplasts . 37

Plastid inheritance in Mirabilis Jalapa :

Correns in 1909 described the inheritance of plastid variegation in 4’0 clock plant ( Mirabilis jalapa ). In some varieties of this plant, there are three kinds of branches; Those producing only green leaves, Branches producing only white leaves, and those producing variegated leaves. Crosses between flowers produced on the different types of branches yield very different results (Table 1). Plastid inheritance in Mirabilis Jalapa 38

Plastid inheritance in Mirabilis Jalapa :

Plastid inheritance in Mirabilis Jalapa The leaf colour of progeny depended only on which flower was used as the female, while the flower contributing the pollen did not have any influence. The universally accepted view for this inheritance pattern is as follows. It is assumed that the variegation is produced by the plastid itself and not by the nuclear genes. The egg contributes the total cytoplasm present in the zygote, and the sperm is generally devoid of cytoplasm. Since plastids are present in the cytoplasm, only the egg will be able to contribute the plastids. 39

Plastid inheritance in Mirabilis Jalapa :

Plastid inheritance in Mirabilis Jalapa Therefore, the type of plastid (normal green, defective white or both-giving rise to variegation) present in the egg cell will determine the type of progeny recovered from a cross. Several other cases of plastid inheritance have been reported in various plant species, such as, maize, rice, beans and others. 40

Model for the inheritance of shoot color in the four o’clock:

Model for the inheritance of shoot color in the four o’clock 41

Variegation in the four o’clock:

Variegation in the four o’clock 42

Plastid inheritance in Mirabilis Jalapa :

Plastid inheritance in Mirabilis Jalapa Table 1 Cytoplasmic inheritance in plastid colour in Mirabilis jalapa 43 Leaf colour of the branch used as female parent Leaf colour of the branch used as male parent Leaf colour of the progeny Green Green Green White Green Veriegated Green White Green White White White Variegated White Variegated Green Green, white, variegated White Green, white, variegated Variegated Green, white, variegated

Exceptions to Maternal Inheritance :

Exceptions to Maternal Inheritance When the female gamete contributes most of the cytoplasm, maternal inheritance is the usual explanation for extranuclear mutations. However, exceptions occur. Examples: a. PCR analysis shows heteroplasmy in mice, with paternal mtDNA present at a frequency of 10 -4 relative to maternal mtDNA . This heteroplasmy may facilitate recombination between the mtDNAs , creating more diversity in mtDNA than previously believed. b. In plants, the angiosperms show variation in plastid inheritance, with most inheriting only maternal plastids, but others inheriting from both parents, or from the paternal parent. Paternal inheritance is also found in gymnosperms. 44

Importance in Plant Breeding :

Importance in Plant Breeding 45 To develop male sterile line- Genetic Male Sterile Line Discard Selfing Cytoplasmic – genetic male sterility

Some genes responsible for male sterility :

Some genes responsible for male sterility 46

Maternal inheritance for Hybrid seed production:

Maternal inheritance for Hybrid seed production For plant breeding, the observation of heterosis for yield has lead to the development of inbred lines that exhibit a heterotic yield advantage. Corn was the first crop species in which heterosis was exploited. In hybrid corn seed production it required manual detasseling of the female parent. Manual detasseling of corn plants would not be required if male sterile system could be developed The weakness of the genetic systems is F2 were male fertile, and thus a portion of the seed that was developed was not hybrid. The solution of problem is the use of cytoplasmic male sterility ( cms ). Thus all the males that contain the appropriate cytoplasm would be sterile. 47

To developed hybrid seed production:

To developed hybrid seed production 48 Step 3: Commercial hybrid seed production

In sorghum hybrid seed production:

In sorghum hybrid seed production 49

In maize hybrid seed production:

50 In maize hybrid seed production Line A Male fertile F1 X R Line X X R Line Fertile hybrid seed

Morphological characters:

Morphological characters 51 In maize -

Morphological characters:

52 Morphological characters In mustered crop In rice crop

Mitochondrial Disease:

Mitochondrial Disease 53 Examples of Human Mitochondrial Disease

Human Disorders:

Human Disorders Several rare human disorders are produced by mutations to mitochondrial DNA. These primarily impact ATP supply by producing defects in the electron transport chain or ATP synthase . Tissues that require high energy supplies (for example, the nervous system and muscles) may suffer energy deprivation from these defects. Other mitochondrial mutations may contribute to diabetes, heart 54

References:

References Prasad, G. (1998). Introduction to cytogenetics ., Kalyani publishers, New Delhi,(INDIA). Singh. P. (2005). Elementary of genetics., Kalyani publishers, Ludhiana,(INDIA). Google search engine. Wikipedia.org Aurthostream.com 55

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