UPHESC Assistant Professor Genetics & Plant Breeding PYQs

Concept: Selection differential S = mean of selected – population mean = i·σ_P, where i (k) = selection intensity in standard units and σ_P = phenotypic standard deviation.

1. Genetic advance GA = k·σ_P·h² (Johnson et al., 1955).
2. At 5% selection k = 2.06.

Short trick: S = k × σ_P; GA = k σ_P h².

Concept: Kearsey and Jinks (1968) extended North Carolina Design III by adding the F₁ as a third tester: each F₂ (or other) individual is crossed to P₁, P₂ and F₁.

1. NCD-III uses only the two parents as testers.
2. The TTC additionally detects epistasis and gives unbiased D and H.

Short trick: NCD III + F₁ tester = Triple Test Cross.

Concept: The full six-parameter model (Hayman 1958; Jinks & Jones) has m, d, h, i, j, l. The five-parameter model m, d, h, i, j omits l – the dominance × dominance interaction.

1. d = additive, h = dominance, i = additive × additive, j = additive × dominance, l = dominance × dominance.
2. Same sign of h and l → complementary epistasis; opposite → duplicate.

Short trick: Drop the last letter 'l' (D × D) → five parameters.

Concept: In Hayman's diallel analysis, $(H_1/D{)}^{1/2}$ is the mean degree of dominance.

1. = 0 → no dominance.
2. between 0 and 1 → partial dominance.
3. = 1 → complete dominance.
4. > 1 → overdominance.

Short trick: Ratio 1 = complete; >1 = over; <1 = partial.

Concept: Simple interval mapping, using a pair of flanking markers and maximum-likelihood LOD scores, was proposed by Eric Lander and David Botstein (Genetics, 1989) – implemented in MAPMAKER/QTL.

1. Single-marker analysis came earlier (Sax 1923; Soller et al.).
2. Composite interval mapping: Zeng (1993, 1994); Jansen (1993).

Short trick: 1989 Lander–Botstein → SIM; 1994 Zeng → CIM.

Concept: Non-allelic interaction (epistasis) in generation-mean analysis is detected by scaling tests.

1. Mather's (1949) individual scaling tests A, B, C, D (e.g. A = 2B₁ − P₁ − F₁): if any scale differs significantly from zero, epistasis is present – so 'Scaling test' (D) is correct.
2. The joint scaling test (Cavalli, 1952) fits the additive–dominance model (m, [d], [h]) to all generation means together and tests the fit by χ²; a significant χ² shows that non-allelic interaction is present – so 'Joint scaling test' (B) also determines the presence or absence of epistasis.
3. Test cross (genotype/linkage testing) and scale effect (a property of the measurement scale) do not.
4. Since two options (B and D) both fit the description, the question has no single answer as printed.

Short trick: Both Mather's A-B-C-D scales and Cavalli's joint scaling χ² test for epistasis.

Concept: Additive and additive × additive gene effects are fixable – they are retained in homozygous lines after selfing, so such heterosis can be fixed in pure lines.

1. Dominance, additive × dominance and dominance × dominance effects depend on heterozygosity and decline on inbreeding – non-fixable.
2. Hence hybrids are needed when heterosis is due to dominance/overdominance.

Short trick: Fixable = A + A×A; non-fixable = anything with 'D'.

Concept: In a double cross (A × B) × (C × D) the related inbreds are placed in the same single cross, so that the two single crosses are genetically unrelated and give maximum heterosis.

1. The performance of the double cross itself is predicted from the four non-parental single crosses (Jenkins, 1934).
2. Parental single-cross performance and inbred yield are used for seed-production convenience, not to fix the order.

Short trick: Related inbreds together; unrelated single crosses across.

Concept: Second-cycle inbreds (from crosses among elite first-cycle inbreds, i.e. pedigree selection) are mainly superior in their own (per se) vigour and yield.

1. Their combining ability and hybrid performance are generally not much better than those of the first-cycle lines, because both cycles sample similar germplasm.
2. Improved per se yield makes seed production of hybrids cheaper.

Short trick: 2nd-cycle inbreds = stronger lines themselves, not necessarily better combiners.

Concept: Single-gene heterosis (Hull 1945: heterozygote a₁a₂ superior to both homozygotes at one locus) is the overdominance explanation – a genetic basis of heterosis.

1. Genetic theories: dominance (Davenport; Bruce; Jones), overdominance/single-gene heterosis (Shull, East, Hull), epistasis.
2. Biochemical/physiological theories deal with enzymes, growth rates, mitochondrial complementation.

Short trick: Single gene → genetic (overdominance) theory.

Concept: Mariani et al. (1990, 1992) expressed the barnase (RNase from Bacillus amyloliquefaciens) gene under the tapetum-specific TA29 promoter in tobacco and oilseed rape; the barstar inhibitor gene restores fertility in F₁.

1. The system (Plant Genetic Systems, Belgium) is used commercially in canola/rapeseed hybrids; in India, GM mustard DMH-11 uses barnase–barstar.
2. Cotton, maize and bajra hybrids mainly use CMS or GMS.

Short trick: Barnase kills tapetum, Barstar rescues – tobacco & Brassica.

Concept: Reverse breeding (Dirks et al., 2009) suppresses meiotic crossing over in an elite heterozygous plant, recovers non-recombinant spores as doubled haploids, and selects complementary pairs that, when crossed, recreate the original hybrid – i.e. the parental lines are regenerated.

1. Polycross – testing GCA of clones.
2. Shuttle breeding – two generations a year at contrasting sites (Borlaug).
3. Inbreeding – selfing to homozygosity, not reconstruction of parents.

Short trick: Reverse breeding: hybrid → its parents.

Concept: Average degree of dominance $\sqrt{H_1/D}$ > 1 indicates overdominance.

1. 0 → no dominance; 0–1 → partial; = 1 → complete; > 1 → over-dominance.
2. (Here the printed ratio means $\sqrt{H_1/D}$.)

Short trick: > 1 = Over.

Concept: H. G. Khorana's group (1970) made the 77-bp yeast alanine-tRNA gene – the first artificial gene – by chemically synthesising short oligonucleotides by the phosphodiester method and then joining them with DNA ligase.

1. Phosphotriester method came in the 1970s (Letsinger, Reese); phosphite-triester/phosphoramidite (Caruthers, 1981) is used in modern automated synthesisers.
2. Ligation was only the joining step; the approach is known as the phosphodiester approach.

Short trick: Khorana 1970 → phosphodiester; Caruthers 1981 → phosphoramidite.

Concept: M13 is a filamentous single-stranded DNA phage; its vectors (M13mp series, Messing) give single-stranded template DNA directly – ideal for Sanger dideoxy sequencing.

1. λ and cosmid vectors – for large inserts/genomic libraries.
2. Plasmids need denaturation to give template.

Short trick: Single-stranded M13 = sequencing template.

Concept: Escherichia coli (strains like K-12 derivatives DH5α, JM109) is the most widely used cloning host: fast growth, simple genetics, easy transformation and many compatible vectors.

1. Bacillus subtilis and yeast are used for secretion/eukaryotic expression but less commonly.

Short trick: Cloning workhorse = E. coli.

Concept: Microsatellites are tandem repeats of 1–6 bp motifs; PCR with flanking primers gives Simple Sequence Repeat (SSR) markers – co-dominant and highly polymorphic.

1. CAPS – PCR + restriction digestion.
2. RAPD – random 10-mer primers, dominant.
3. RFLP – restriction + Southern hybridisation.

Short trick: Microsatellite = SSR = STR.

Concept: Chromosome walking moves from a known marker to a target gene through overlapping genomic clones; large-insert libraries (cosmid ~35–45 kb, later BAC/YAC) are used so that each 'step' covers a long stretch.

1. An end fragment of one clone is used as probe to pick the next overlapping clone, and so on.
2. Cosmid libraries were the classical choice because inserts are much larger than in plasmid or λ libraries.

Short trick: Long steps need long inserts → cosmid (BAC/YAC).

Concept: Flavr Savr (Calgene, USA, 1994) – the first commercial GM food – carried an antisense copy of the polygalacturonase (PG) gene, which blocked PG synthesis and delayed fruit softening.

1. Antisense RNA pairs with PG mRNA and prevents its translation.
2. Barnase–barstar is for male sterility; ribozymes cleave RNA catalytically.

Short trick: Flavr Savr = antisense PG.

Concept: Genomic selection (Meuwissen, Hayes and Goddard, 2001) uses genome-wide dense markers (SNPs) simultaneously to predict genomic estimated breeding values (GEBVs) of candidates.

1. A training population (genotyped + phenotyped) builds the prediction model; the breeding population is then selected on GEBV alone.
2. Unlike MAS, it does not need significant QTL first.

Short trick: Whole-genome markers → GEBV → Genomic selection.