Question

Q1. You are tasked with developing a new variety of tomatoes that can survive high summer temperatures and yet generate large fruit. You are particularly interested in two heirloom varieties, “small hotties” that are reported to thrive in warm climates but make small fruits and “big wimps” that are reputed to start dying when temperatures go above 30 degrees but make lots of large fruits at lower temperatures. The tomato genome is well characterised and you have access to a SNP genotyping protocol that will allow you to genotype 8000 SNPs distributed across the tomato genome in a cost effective manner. Outline an experimental design that will a) verify that heat tolerance and fruit size will respond to a selective breeding program, and b) identify markers most suitable for marker-selected breeding of these traits.

Q2. Using SNP genotyping you have determined that a focal individual is a double heterozygote for two loci, whereby for locus 1 it has the genotype C1T1 and for locus 2 it has the genotype A2G2. Describe an experimental design that will allow you to determine whether that focus individual is C1_A2/T1_G2 or C1_G2/T1_A2. (The corresponding question on the mini test will supply an experiment that is used and give you results but if you understand how to set up the experiment you will be prepared for that question.)

Answer 1

SNP (Single Nucleotide Polymorphism):

Recent advances in genome technology revealed various single nucleotide polymorphisms (SNPs), the most common form of DNA sequence variation between alleles, in several plant species. The discovery and application of SNPs increased our knowledge about genetic diversity and a better understanding on crop improvement. Natural breeding process which takes an agelong time during collecting, cultivating, and domestication has been accelerated by detecting dozens of SNPs on various species using advanced biotechnological techniques such as next-generation sequencing. This will result in the improvement of economically important traits.

If a single nucleotide change is detected by comparing the DNA of different living species, it is evaluated as there is a single nucleotide polymorphism. These changes in a single position are used as an effective genetic marker practically in both animal and the plant species. Single nucleotide polymorphism (SNP) genotyping studies and the rapid progress in the development of genomic tools have led to the development of new powerful approaches in mapping complex features and identifying the causes.