Characterizing the main and epistatic effects and interactions of germination-related quantitative trait loci of tomato using a backcross inbred line population and near-isogenic lines

Rapid germination and early establishment of seedlings under unfavorable environmental conditions are desirable traits for seedling production. Quantitative trait locus (QTL) analysis of germination speed was conducted at 15 and 25 degrees C using a backcross inbred line family. Final germination percentage (FGP), days to 50 % and 90 % of FGP (GT(50) and GT(90), respectively), mean germination time (MGT), and covariance of germination time were determined. The results indicated 11 additive germination-related QTLs on chromosomes 1-3, and 11. GT(50), GT(90), and MGT QTLs detected on chromosomes 1-3 were co-located, of which, gt(50)1, gt(90)1, and mgt1 had positive additive effects. A single epistatic QTL was detected, but no QTL with additive effect was found on chromosome 4 in the present study, which was not consistent with the results of previous studies. To reexamine the effect of QTLs on chromosomes 1 and 4, we constructed one and three near-isogenic lines (NILs) carrying a substituted chromosome segment from Solanum pimpinellifolium (SP) in which putative QTLs were detected on chromosomes 1 and 4. NIL experiment results indicated that a chromosomal segment from SP between TGS0308 and C2_At5g49480 markers on chromosome 1 shortened and prolonged germination time at 15 degrees C and 25 degrees C, respectively, due to QTL-by-environmental interactions. However, the substituted segment between SSR603 and TGS0411 markers on chromosome 4 did not affect seed germination. In conclusion, the QTL on chromosome 1 is useful for breeding cultivars that are able to germinate at low temperatures.