Question

2) (10 point question) Many people love colorful and tasty tomatoes and an ambitious student in horticulture wants to breed such a tomato variety. He searched all the available tomato genetic resources, and found the two inbred lines he needed. One line produces the tomatoes with a colorful red-green-yellow mosaic pattern (rrTT), and the other strain is 'very tasty' (RRtt).

When the student crossed the two strains together, he made the following observations:

In the F1 generation, all the ripe tomatoes have a regular red color and a regular flavor. The student tasted tomatoes from over 40 individual plants, and was sick with regular tasting tomatoes.

In the F2 progeny, the student sampled 1000 tomato plants: 498 had red-color tomatoes with normal taste, 248 colorful tomatoes with normal taste, and 254 red-color tomatoes with great taste. He was disappointed not to find any colorful tomatoes with great taste. He then sampled another 2000 F2 plants: 998 had red-color tomatoes with normal taste, 511 colorful tomatoes with normal taste, 488 red-color tomatoes with great taste, and 3 colorful tomatoes with great taste; he was so happy to find what he wanted!!!

Based on these experimental results, he realized that the alleles he needs are recessive and the two genes are linked.

A) (4 points) How closely linked are the r and t genes? Please explain your strategy to calculate the distance.

B) (2 points) A testcross with the F1 can be used to further define the genetic distance between the two genes. Indicate the ratio of progeny phenotypes that you'd expect (describe phenotypes) from this cross based on the map distance you propose for part a).

C) (2 points) The tomato genome has now been sequenced and genes on the chromosome are in the following order OPQRSTU. The respective physical distances on the chromosome between these seven genes are very similar. But we now know that there is a 'cold spot' between genes RT and 'hot spots' between PQ and TU. Draw a representation of the genetic map relative to the physical map (both maps are needed here) for this part of the tomato genome. Show the relative (approximate) locations of the genes on the two maps.

D) (2 points) What can you predict about the chromosome chromatin structure between the R and T genes?

Answer 1

A) To determine distance between r and t genes, their recombination frequency has to be determined. A 1% recombination frequency (RF) corresponds to 1 map unit or 1 centimorgan.

Out of sampling 2000 tomatoes, 3 were very tasty and colourful, so these had genes r and t (recessive alleles)

So RF = 3/2000 = 0.0015 = 0.15% or 0.15 centimorgan

B) The genes r and t are very closely linked. F1 is RrTt is with all red and regular tasting tomatoes. The ratio of genotype rrtt would be very less. Since a test cross is with a recessive individual (rrtt)

	rt	rt	rt	rt
Rt	Rrtt	Rrtt	Rrtt	Rrtt
Rt	Rrtt	Rrtt	Rrtt	Rrtt
RT	RrTt	RrTt	RrTt	RrTt
rT	rrtt	rrtt	rrtt	rrtt

Here 1/4th of the progeny would have colourful and tasty phenotype. But since r and t genes are very close, they are likely to not segregate independently.

C) Presence of a cold spot between RT genes indicates there is a heterochromatin like structure which lowers recombination rate , these regions are also near the centromeres.

D) Region between R & T genes is likely to be highly dense,tightky packed, different than other parts of the chromosome, a heterochromatin like formation.