63. In 1990, Bhattacharya et al identified that the wrinkled seed character of pea as described by Mendel is caused by a transposon — like insertion in a gene encoding Starch Branching Enzyme (encoded by the R allele). This leads to an RFLP pattern, when genomic DNA of round and wrinkled seed is digested With EcoRI and probed with the cDNA of the R gene product. The following is a representation of the hybridization pattern. Choose the INCORRECT statement?

(1) Lane 3 represents genomic DNA from plant withwrinkled seeds
(2) These DNA markers are codominant in nature
(3) Lane 1 represents genomic DNA from plant with round seeds
(4) If genomic DNA from F2 progeny as obtained in Mendel’s work was analyzed by RFLP, the ratio of progeny with patterns in late 1, 2 and 3 will be 2:1:1

Question recap and concept

In this question, wrinkled seed phenotype in pea (Mendel’s r allele) is due to a transposon-like insertion in the gene encoding starch branching enzyme, the product of the dominant R allele that gives round seeds. EcoRI-digested genomic DNA from round and wrinkled plants is probed with cDNA of the R gene, producing an RFLP pattern. The gel diagram shows three lanes (1, 2, 3) with: lane 1 having one band, lane 3 having a different single band, and lane 2 having both bands (codominant pattern). The task is to identify the incorrect statement among four options.

The correct incorrect option is: (4) If genomic DNA from F2 progeny, as in Mendel’s work, is analyzed by RFLP, the ratio of progeny with patterns in lanes 1, 2 and 3 will be 2:1:1.

Interpreting the RFLP pattern

The R allele encodes an intact starch-branching enzyme gene; the r allele carries a transposon insertion, changing the size of the EcoRI fragment hybridizing to the cDNA probe.​

• RR (homozygous round) will show a single “R-specific” fragment: one band (lane 1 type).

• rr (homozygous wrinkled) will show a single “r-specific” fragment: one band of different size (lane 3 type).

• Rr (heterozygous) will carry both R and r fragments and therefore show two bands (lane 2 type), demonstrating codominance at DNA (marker) level even though the phenotype shows complete dominance.​

Thus:

• Lane 1 = genomic DNA of plant with round seeds, genotype RR.

• Lane 2 = genomic DNA of heterozygous round, genotype Rr (both bands).

• Lane 3 = genomic DNA of plant with wrinkled seeds, genotype rr.

Detailed evaluation of each option

Option (1) Lane 3 represents genomic DNA from plant with wrinkled seeds

Lane 3 shows a single band distinct from lane 1, corresponding to the fragment size produced by EcoRI digestion of the transposon-disrupted r allele. Wrinkled seeds in pea occur when the plant is homozygous rr, which will lack the normal R-fragment and show only the “mutant” fragment.​

Therefore, assigning lane 3 to a wrinkled plant (rr) exactly matches the genetics and the RFLP pattern. Option (1) is correct.

Option (2) These DNA markers are codominant in nature

RFLP bands behave as codominant markers because both alleles can be visualized independently in a heterozygote.

Here, the heterozygote Rr (lane 2) simultaneously shows the R-specific band and the r-specific band. Presence of both fragments reveals both alleles without dominance masking, fulfilling the definition of codominant molecular markers. Thus, option (2) is correct.

Option (3) Lane 1 represents genomic DNA from plant with round seeds

Round seeds occur in genotypes RR or Rr. In the gel, lane 1 has only the R-specific fragment, so it must be RR, a homozygous round plant.​

Hence, saying that lane 1 represents genomic DNA from a plant with round seeds is true (even though it is specifically RR). Option (3) is correct.

Option (4) F2 RFLP pattern ratio will be 2:1:1 (INCORRECT)

From a classical Mendelian cross:

• P: RR (round) × rr (wrinkled)

• F1: all Rr (round, lane 2 pattern).

• F2 from selfing F1 (Rr × Rr) gives genotypic ratio 1 RR : 2 Rr : 1 rr.

Mapping these genotypes to RFLP patterns:

• RR → lane 1 pattern (single R band) → frequency 1

• Rr → lane 2 pattern (both bands) → frequency 2

• rr → lane 3 pattern (single r band) → frequency 1

So the expected RFLP band pattern ratio among F2 plants is 1 (lane 1) : 2 (lane 2) : 1 (lane 3), not 2:1:1. The student must recognize that the F2 genotypic ratio projects directly onto the codominant marker phenotype ratio.

Therefore, option (4) is the incorrect statement and is the required answer.