67. The AFLP technique generates polymorphic DNA fragments that are generally scored as dominant markers. However, a pair of DNA fragments (say ‘a’and ‘b’) generate by AFLP can be termed as co dominant, if on analysis of a large progeny of doubted haploids (DH) derived from an F1 (resulting from a cross between two parents one with fragment ‘a’ and the other with it is observed that:
(1) 1.50% of the progeny has both ‘a’ and ‘b’ fragments and the rest have none.
(2) 50% of the progeny has fragment ‘a’ and the remaining have fragment ‘b’
(3) 25% of the progeny has fragment ‘a’, 50% both ‘a’ and ‘b’ and the rest fragment
(4) 75% of the progeny has both the fragments. While 25% has either ‘a’ or ‘b’.

Introduction

Amplified Fragment Length Polymorphism (AFLP) markers are usually scored as dominant, because a band’s presence masks its absence. However, in special situations AFLP fragments can behave as codominant, allowing discrimination between the two parental alleles at a locus. This CSIR NET question uses a doubled haploid (DH) population derived from an F1 to ask under which segregation pattern a pair of AFLP fragments ‘a’ and ‘b’ can be treated as codominant markers.

Set‑up of the question

• Parent 1 has fragment ‘a’ only; Parent 2 has fragment ‘b’ only.

• F1 is heterozygous at that locus and carries both ‘a’ and ‘b’.

• Doubled haploid lines are produced from F1 gametes; each DH line is completely homozygous and represents one F1 gamete doubled.

• For a single locus, codominance in DH lines means that each line shows either the pure ‘a’ allele or the pure ‘b’ allele, and the two types are distinguishable and segregate 1:1.

With this in mind, analyse each option.

Option (1): “1. 50% of the progeny has both ‘a’ and ‘b’ fragments and the rest have none.”

If a DH line has both ‘a’ and ‘b’, that implies it carries both alleles simultaneously, i.e. a heterozygous state. But DH lines are derived from single haploid gametes whose chromosomes are doubled, so they must be homozygous at every locus. Therefore any DH at this locus can carry only ‘a’ or only ‘b’ or neither, but never both together.

• “50% both ‘a’ and ‘b’” is inconsistent with the definition of a doubled haploid.

• The rest having no band at all would mean most F1 gametes carry no allele from either parent, which is impossible if this is the same locus that showed bands in both parents and F1.

Hence, Option (1) cannot describe a single AFLP locus in a true DH population and does not represent codominant inheritance.

Option (2): “50% of the progeny has fragment ‘a’ and the remaining have fragment ‘b’.” (Correct)

Consider locus A with two alternative alleles: Aᵃ (band ‘a’) and Aᵇ (band ‘b’).

• Parent 1: AᵃAᵃ → only band ‘a’.

• Parent 2: AᵇAᵇ → only band ‘b’.

• F1: AᵃAᵇ → carries both ‘a’ and ‘b’.

Gametes produced by F1 at this locus are:

• 50% Aᵃ (produces DH lines with only ‘a’ band),

• 50% Aᵇ (produces DH lines with only ‘b’ band).

After chromosome doubling, each DH is either AᵃAᵃ (band ‘a’) or AᵇAᵇ (band ‘b’), so:

• 50% DH lines show fragment ‘a’.

• 50% DH lines show fragment ‘b’.

• No DH has both fragments, and none lacks both, because the locus is segregating as a single Mendelian locus.

This pattern means:

• Each fragment uniquely identifies a homozygous genotype.

• The locus is fully informative and acts as a codominant marker in the DH population.

Therefore, Option (2) is the correct condition under which the pair ‘a’ and ‘b’ is effectively codominant.

Option (3): “25% of the progeny has fragment ‘a’, 50% both ‘a’ and ‘b’ and the rest fragment ‘b’.”

This resembles a classical diploid F2 ratio for a codominant locus (1 AA : 2 AB : 1 BB) in a normal sexually produced F2 population, not in DH lines. In ordinary diploids:

• 25% homozygous ‘a’,

• 50% heterozygous (both ‘a’ and ‘b’),

• 25% homozygous ‘b’.

But doubled haploid lines cannot be heterozygous, so 50% of lines having both ‘a’ and ‘b’ contradicts the definition of DH. Thus, Option (3) describes segregation in an F2, not in a DH population, and is not valid here.

Option (4): “75% of the progeny has both the fragments, while 25% has either ‘a’ or ‘b’.”

Again, any line with “both fragments” is heterozygous at the locus. In a DH population, heterozygotes are not expected because each DH line derives from a single gamete. A 3:1‑like ratio (75% both, 25% either) is reminiscent of a dominant/recessive pattern in a normal segregating diploid population (e.g. 3 showing the dominant trait, 1 recessive), but:

• It implies most lines are heterozygous, which a DH panel cannot be.

• It does not give two clearly