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Standardized phenotyping is being used in tomato (Solanum lycopersicum) and potato (S. tuberosum) as part of the USDA-funded Solanaceae coordinated agricultural project (SolCAP). In tomato, a panel of 480 lines, 144 fresh market, 144 processing, 44 vintage lines, 48 landraces, and 101 related Solanum species accessions, are being grown over two seasons at multiple locations. These tomato genotypes will also be screened for over 7600 single nucleotide polymorphism markers that are being developed. Characters being phenotyped are hypocotyl color, plant habit, inflorescence (simple or compound), flower fasciation, flowering time, time to maturity, size of blossom scar, and pedicel type (jointless or jointed). Transverse and equatorial cross-sections of fruit are also being scanned to obtain measures of fruit shape and color by tomato analyzer computer software. Other fruit characters being measured are pH, titratable acidity, and soluble solids. Some useful information may come from this phenotyping and genotyping effort. However, in this author's opinion, the value of measuring some of the traits is very limited in the face of much more important breeding traits that are difficult to fit into a standardized phenotyping format. For instance, proper assessment of several fruit disorders is not being attempted, but such data might yield some invaluable marker information. Part of this is the result of funding limitations for the phenotyping effort. However, a major benefit of the SolCAP analysis will be the development of markers that will differentiate the lines being studied, because there is a present lack of polymorphisms in tomato germplasm where wild species introgressions are minimal or distant in time. This will allow breeders to proactively select for recurrent parent backgrounds in backcrossing projects and may aid in the identification of associations of markers with important characteristics. As one looks to the future of standardized phenotyping, there are some important traits that will be difficult to phenotype such as tomato flavor, which is quite subjective and for which there are no good objective measures.
Resistance to begomoviruses tomato mottle virus (ToMoV) and tomato yellow leaf curl virus (TYLCV) has been introgressed to tomato (Lycopersicon esculentum) from L. chilense accessions LA 1932, LA 2779, and LA 1938. Resistance genes have been mapped to three regions on chromosome 6 using randomly amplified polymorphic DNA (RAPD) markers. We call these regions 1, 2, and 3. To facilitate breeding by marker assisted selection, advanced breeding lines with resistance from the above sources were assayed for the presence of RAPD markers to determine which were most tightly linked to begomovirus resistance. The best RAPD markers were then converted to sequence characterized amplified region (SCAR) markers or cleaved amplified polymorphic sequence (CAPS) markers. In addition, selected restriction fragment length polymorphism (RFLP) markers near the three regions were converted into CAPS markers, which were tested for association with the advanced breeding lines. Only LA 2779 derivatives have the L. chilense introgression in region 1, which is near the location of the Ty-1 gene and spans across CAPS markers 32.5Cla and TG118. Two region 1 RAPD markers UBC197 and UBC621 were converted co-dominant SCAR or CAPS markers, which were present in all 16 resistant breeding lines tested. Derivatives from all three accessions have introgressions in region 2. Further assays with more markers in this region are under way to determine the lengths and locations of the introgressions. No tightly linked RAPD markers have been found for the resistance gene from LA 1932 in region 3. RFLP and CAPS markers are being used to more precisely locate the region 3 gene.