Q.60 An RFLP marker shows sequence polymorphism in two ecotypes ( X and Y ) of a plant. In ecotype X,
the marker contains one GAATTC site in its sequence, whereas in Y it has the sequence GAAATC at the
same site. The rest of the sequence is identical in both ecotypes. In a genotyping experiment, the marker
was PCR amplified from four different seedlings ( 𝐏, 𝐐,𝐑, 𝐒 ), completely digested with EcoRI and the
products were analyzed by electrophoresis. The diagram below shows the band patterns obtained. Based
on the information provided, which of the following statements is correct?
(A) Seedling Q belongs to ecotype Y
(B) Seedling Q belongs to ecotype X
(C) Seedling P belongs to ecotype Y
(D) Seedling R belongs to ecotype Y

Introduction

Restriction Fragment Length Polymorphism (RFLP) markers are widely used to detect sequence variation based on the presence or absence of restriction enzyme recognition sites. In this problem, an EcoRI-based RFLP marker is used to distinguish between two plant ecotypes (X and Y) by analyzing banding patterns after PCR amplification and restriction digestion.

Key Concept Behind the Question

EcoRI Recognition Site

EcoRI recognizes and cuts the palindromic sequence:

• Ecotype X: Contains the GAATTC site → EcoRI cuts

• Ecotype Y: Has GAAATC (one base mismatch) → EcoRI does not cut

Expected Banding Patterns After EcoRI Digestion

Analysis of the Given Gel Pattern

From the electrophoresis image:

• Seedling P → Two bands

• Seedling Q → One band

• Seedling R → Three bands

• Seedling S → Three bands

Interpretation

• P is homozygous ecotype X

• Q is homozygous ecotype Y

• R and S are heterozygous (X/Y)

Correct Answer

✅ (A) Seedling Q belongs to ecotype Y

Explanation of All Options

Option (A): Seedling Q belongs to ecotype Y ✅ Correct

• Q shows only one band

• Indicates no EcoRI cut

• Confirms absence of GAATTC

• Therefore, Q is ecotype Y

Option (B): Seedling Q belongs to ecotype X ❌ Incorrect

• Ecotype X must show two bands

• Q shows only one band → no digestion

Option (C): Seedling P belongs to ecotype Y ❌ Incorrect

• P shows two bands

• Indicates EcoRI digestion

• Therefore, P is ecotype X, not Y

Option (D): Seedling R belongs to ecotype Y ❌ Incorrect

• R shows three bands

• This is characteristic of a heterozygote (X/Y), not homozygous Y

Final Summary

• EcoRI digestion differentiates ecotypes based on a single-base polymorphism

• One band = no cut = ecotype Y

• Two bands = cut = ecotype X

• Three bands = heterozygous (X/Y)

👉 Seedling Q is ecotype Y