(a) Explain the types of variations found in the structure of chromosomes and discuss their importance and significance. 10 (b)…

(a) Structural changes in chromosomes: types and significance

Structural changes alter the arrangement of genes on a chromosome without changing the chromosome number. They arise from breaks, followed by wrong rejoining or by unequal crossing over. There are four types.

• Deletion (deficiency): a terminal or interstitial segment is lost. In a heterozygote the normal homologue forms an unpaired loop at pachytene. Large deletions are usually lethal. Small ones cause "pseudodominance", where recessive alleles on the normal homologue are expressed, which was used to map genes in maize and Drosophila. Example: cri-du-chat syndrome (5p−).
• Duplication: a segment is repeated, in tandem or reversed. The Bar eye of Drosophila is a duplication of region 16A, created by unequal crossing over (Sturtevant). Duplicated genes can diverge into new functions; the globin and rRNA gene families arose this way.
• Inversion: a segment is turned through 180°. It is paracentric if it excludes the centromere and pericentric if it includes it. Heterozygotes form an inversion loop. A crossover inside the loop gives a dicentric bridge and an acentric fragment (paracentric), or duplication–deletion gametes (pericentric), so recombinants are not recovered. Inversions therefore keep blocks of genes together; the inversion polymorphism of Drosophila pseudoobscura was studied by Dobzhansky.
• Translocation: segments move between non-homologous chromosomes. It may be reciprocal or Robertsonian (fusion of two acrocentrics). Heterozygotes pair as a cross-shaped quadrivalent. Adjacent segregation gives unbalanced gametes, so about half the pollen is sterile (semi-sterility). Oenothera lamarckiana carries a ring of 14 chromosomes and breeds true as a permanent heterozygote. In humans, the Philadelphia chromosome t(9;22) creates the BCR–ABL fusion of chronic myeloid leukaemia.

Importance

• Evolution: rearrangements create reproductive barriers and new gene orders. Human chromosome 2 arose by the fusion of two ancestral ape chromosomes.
• Genetic analysis: deletions map genes, and inversion balancers (such as the ClB chromosome) help detect mutations.
• Plant breeding: translocations carry alien genes into crops. Sears (1956) transferred leaf-rust resistance from Aegilops umbellulata to wheat, and the wheat–rye 1BL·1RS translocation brought rust-resistance genes into many wheat varieties.
• Medicine: many syndromes and cancers are caused by structural changes.

(b) Incomplete dominance and polygenic inheritance

Incomplete dominance: the heterozygote is intermediate between the two homozygotes, because one functional allele makes only part of the product.

• Mirabilis jalapa (four o'clock plant; Correns): red (RR) × white (rr) gives pink F1 (Rr). The F2 is 1 red : 2 pink : 1 white.
• Antirrhinum majus (snapdragon): red × white also gives pink F1 and the same 1:2:1 F2.
• Result: the phenotypic ratio equals the genotypic ratio (1:2:1 instead of 3:1). Every genotype can be recognised from its phenotype, and the parental phenotypes reappear in F2, which shows the alleles did not blend. This differs from codominance, where both alleles show fully (for example, the AB blood group).

Polygenic (quantitative) inheritance: several genes, each with a small, additive effect, control one trait, and the environment adds further variation.

• Wheat kernel colour (Nilsson-Ehle, 1909): with two genes (R1R1R2R2 dark red × r1r1r2r2 white), the F1 is intermediate. The F2 falls into five classes in the ratio 1:4:6:4:1, and 1/16 are white (15 coloured : 1 white). With three genes there are seven classes, 1:6:15:20:15:6:1, and only 1/64 are white.
• Maize ear length (East, 1916) and human skin colour are other examples. Yield, height and grain weight in crops behave the same way.
• Result: variation is continuous and bell-shaped rather than in discrete classes, and the extreme parental types become rarer as the number of genes rises. F2 plants can go beyond either parent (transgressive segregation). Such traits are studied with means, variances and heritability rather than simple ratios.

(c) Cell receptors and cell signalling

A receptor is a protein that binds a specific signal molecule (ligand) and changes shape. This converts an outside signal into a change inside the cell (signal transduction). Signals are then usually amplified through second messengers or phosphorylation cascades, so a few ligand molecules can switch whole sets of genes or enzymes on or off.

Types of receptors

Cell-surface receptors: these bind water-soluble ligands.

• G-protein-coupled receptors: they act through cAMP, IP₃ and Ca²⁺.
• Receptor tyrosine kinases: such as the insulin receptor.
• Ion-channel receptors: such as the acetylcholine receptor.
• Plant receptor-like kinases: BRI1 for brassinosteroids, and FLS2, which recognises bacterial flagellin.
• Two-component histidine kinases: ETR1 for ethylene, and CRE1/AHK4 for cytokinin.
• Intracellular receptors: steroid hormone receptors in animals. In plants: TIR1 for auxin, GID1 for gibberellin, PYR/PYL for ABA, and the light receptor phytochrome.

Example: auxin perception by TIR1

1. Without auxin, Aux/IAA proteins bind the transcription factors ARFs and keep auxin-responsive genes off.
2. Auxin enters the nucleus and binds TIR1, the F-box subunit of an SCF ubiquitin ligase. It acts as "molecular glue" between TIR1 and the Aux/IAA protein.
3. The Aux/IAA protein is ubiquitinated and destroyed by the 26S proteasome.
4. ARFs are freed and switch on genes for cell expansion, root initiation and vascular differentiation.
5. Aux/IAA genes are among the genes induced, which provides negative feedback.

Animal example: insulin binds its receptor tyrosine kinase, the receptor autophosphorylates, and the PI3K–Akt pathway moves GLUT4 transporters to the membrane, so glucose is taken up. Faults in this pathway underlie type 2 diabetes.

(d) RNA in the origin and evolution of life

The RNA world hypothesis (the term was coined by Walter Gilbert in 1986) proposes that early life used RNA both to store genetic information and to catalyse reactions, before DNA and proteins took over these jobs.

Evidence

• Ribozymes: Thomas Cech found a self-splicing intron in Tetrahymena rRNA, and Sidney Altman showed that the RNA of RNase P cuts tRNA precursors. They shared the 1989 Nobel Prize.
• The ribosome is a ribozyme: peptide bonds are formed by the 23S rRNA of the large subunit, not by its proteins. The crystal structures that showed this earned the 2009 Nobel Prize (Ramakrishnan, Steitz, Yonath). Protein synthesis itself therefore still runs on RNA.
• "Molecular fossils": coenzymes such as ATP, NAD, FAD and coenzyme A contain ribonucleotides. Deoxyribonucleotides are made from ribonucleotides by ribonucleotide reductase, which suggests DNA came later.

Experiments:

• Spiegelman's Qβ RNA evolved to replicate faster in a test tube.
• In vitro selection has produced ribozymes that copy RNA, and ligase ribozymes that replicate each other (Lincoln and Joyce, 2009).
• Powner, Gerland and Sutherland (2009) showed a plausible prebiotic route to pyrimidine ribonucleotides.

Role in evolution

RNA's instability and high mutation rate gave variation for selection. Later, DNA, which is more stable because it lacks the 2'-OH group and uses thymine, took over storage. Proteins, with 20 amino acids, became the more versatile catalysts. RNA kept the central roles of mRNA, tRNA and rRNA, and gained regulatory roles through siRNA, miRNA and riboswitches. Reverse transcriptase, RNA viruses and viroids are further traces of that earlier world.

(e) Probability and distribution in a breeding programme

Probability: Mendelian segregation is a chance process, so a breeder uses probability to plan how many plants to grow.

• Example: a breeder crosses AAbbCC × aaBBcc and wants the triple homozygote AABBCC. In the F2 its probability is (1/4)³ = 1/64.
• Population size: to be 95% sure of finding at least one such plant, the F2 must have n = ln(0.05)/ln(1 − 1/64), which is about 190 plants. With more genes, the needed population grows very fast. This is why breeders use backcrossing, marker-assisted selection or doubled haploids (a DH line has a 1/8 chance of being AABBCC).
• Backcrossing: recovery of the recurrent parent's genome is 1 − (1/2)ⁿ⁺¹: 75% in BC1, 87.5% in BC2 and about 99% by BC6.
• Testing ratios: the chi-square test checks whether observed classes fit expected ratios, such as 3:1 or 9:3:3:1.

Distribution: quantitative traits like yield follow an approximately normal distribution, described by the mean (μ) and variance (σ²). Only the genetic, and especially the additive, part of the variance responds to selection.

• Selection: the breeder keeps the top fraction of plants. The selection differential S is the mean of the selected plants minus the population mean. The response in the next generation is R = h²S, where h² is the narrow-sense heritability. For example, selecting the top 10% of a wheat F3 population for grain yield with h² = 0.4 raises the mean by only 40% of S.

• Designing trials: the distribution of error also decides how many replications and locations are needed in yield trials, analysed by ANOVA, before a variety can be declared superior.
• Summary: probability tells the breeder how big a population to raise; the distribution tells which plants to keep and how much progress to expect.