Question

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.

Answer 1

Tomato is considered as one of the most widely used horticrop across the world. The crop productivity is mainly affected by a number of biotic and abiotic stress factors, both internally and externally to the plant. An increase in the atmospheric temperature results in a huge decrease in crop productivity since high temperature is one of the major abiotic stress factors that affect tomato production. A decrease in crop production is also depends to the quality of the crop variety selected. but most importantly, selecting the crop variety with the most adaptable traits with the corresponding cultivating land is also important.

Tomato is a crop plant, which is highly sensitive to heat stress, resulting in a heavy amount of heat loss. For the fast track development of new farmer-friendly tomato varieties, genomic selection and adaptations new breeding techniques which involve genome editing is highly preferred.

1) To verify that heat tolerance and fruit size will respond to a selective breeding program

the best way to exploit the variability of heat tolerance and fruit size in the non-cultivated varieties of tomato varieties is the implementation of advanced backcrossing lines and chromosome segments substitution lines.

A meta quantitative trait loci (MQTL) analysis should be performed to analyze the QTLs co-localized and associated with the selected traits, here it is fruit size and heat tolerance. The analysis will reveal the number of QTLs associated with the following traits. Statistical analysis of the linkage data obtained from the analysis helps to select the suitable trait associated QTLs for further breeding purposes.

2) Markers most suitable for marker-selected breeding of heat tolerance and fruit size.

From the studies to determine the candidate gene markers used to regulate heat tolerance in tomato, a total of 91 genes were found in the major QTLs qHII-1-1, qHII-1-2, qHII-1-3, qHII-2-1 and qCC-1-5 (qREC-1-3) till date. varified through thorough Rt-PCR protocols, a number of four genes were selected as markers against the traits of interest.- cathepsin B-like protease 2 (SlCathB2), glutathione S-transferase zeta class-like isoform X1 (SlGST), ubiquitin-conjugating enzyme E2–23 kDa (SlUBC5) and arginase 1 (SlARG1).

Considering the fruit size, a total of four genes where identified, from chromosome 2 and 11. They are SSR095 (Chr 1), SSR032 (Chr 2), IND6.0468, and IND6.3717 (Chr 6), IND11.0017, and SG036 (Chr 11).

Thus, understanding the genetic basis of these traits (heat tolerance) through the combination of linkage and population mapping helps to improve the mapping of heat tolerance traits.