G.Y. Lin

RFLP mapping of QTLs conferring cold tolerance during seed germination in an interspecific cross of tomato

Most cultivars of tomato, Lycopersicon esculentum, are sensitive to low (chilling) temperatures (0–15 °C) during seed germination; however, genetic sources of cold (chilling) tolerance have been identified within the related wild species. The purpose of this study was to identify quantitative trait loci (QTLs) that contribute to cold tolerance during germination in tomato using a backcross population of an interspecific cross between a cold-sensitive tomato line (NC84173, recurrent parent) and a L. pimpinellifolium accession (LA722) that germinates rapidly under low temperatures. A total of 119 BC1 individuals were genotyped for 151 restriction fragment length polymorphism (RFLP) markers and a genetic linkage map was constructed. The parental lines and 119 BC1S1 families (self-pollinated progeny of the BC1 individuals) were evaluated for germination at a low temperature (11±0.5 °C). Germination was scored visually as radicle protrusion at 8 h intervals for 28 consecutive days. Germination response was analyzed by the survival analysis and the times to 25, 50 and 75% germination were calculated. In addition, a germination index (GI) was calculated as the weighted mean of the time from imbibition to germination for each family/line. Two QTL mapping techniques, interval mapping (using MAPMAKER/QTL) and single-point analysis (using QGENE), were used to identify QTLs. The results of both methods were similar and two chromosomal locations (3–5 putative QTLs) with significant effects on low temperature germination were identified. The L. pimpinellifolium accession had favorable QTL alleles on chromosomes 1 and NC84173 had favorable QTL alleles on chromosome 4. The percentage of phenotypic variation explained (PVE) by individual QTLs ranged from 11.9% to 33.4%. Multilocus analysis indicated that the cumulative action of all significant QTLs accounted for 43.8% of the total phenotypic variance. Digenic epistatic interactions were evident between two of the QTL-linked markers and two unlinked markers. Transgressive phenotypes were observed in the direction of cold sensitivity. The results indicate that low temperature germination of tomato seed can be improved by marker-assisted selection.

Identification of QTLs for early blight ( Alternaria solani) resistance in tomato using backcross populations of a Lycopersicon esculentum x L. hirsutum cross.

Abstract.Most commercial cultivars of tomato, Lycopersicon esculentum Mill., are susceptible to early blight (EB), a devastating fungal (Alternaria solani Sorauer) disease of tomato in the northern and eastern parts of the U.S. and elsewhere in the world. The disease causes plant defoliation, which reduces yield and fruit quality, and contributes to significant crop loss. Sources of resistance have been identified within related wild species of tomato. The purpose of this study was to identify and validate quantitative trait loci (QTLs) for EB resistance in backcross populations of a cross between a susceptible tomato breeding line (NC84173; maternal and recurrent parent) and a resistant Lycopersicon hirsutum Humb. and Bonpl. accession (PI126445). Sixteen hundred BC1 plants were grown to maturity in a field in 1998. Plants that were self-incompatible, indeterminant in growth habit, and/or extremely late in maturity, were discarded in order to eliminate confounding effects of these factors on disease evaluation, QTL mapping, and future breeding research. The remaining 145 plants (referred to as the BC1 population) were genotyped for 141 restriction fragment length polymorphism (RFLP) markers and 23 resistance gene analogs (RGAs), and a genetic linkage map was constructed. BC1 plants were evaluated for disease symptoms throughout the season, and the area under the disease progress curve (AUDPC) and the final percent defoliation (disease severity) were determined for each plant. BC1 plants were self-pollinated and produced BC1S1 seed. The BC1S1 population, consisting of 145 BC1S1 families, was grown and evaluated for disease symptoms in replicated field trials in two subsequent years (1999 and 2000) and AUDPC and/or final percent defoliation were determined for each family in each year. Two QTL mapping approaches, simple interval mapping (SIM) and composite interval mapping (CIM), were used to identify QTLs for EB resistance in the BC1 and BC1S1 populations. QTL results were highly consistent across generations, years and mapping approaches. Approximately ten significant QTLs (LOD ≥ 2.4, P ≤ 0.001) were identified (and validated) for EB resistance, with individual effects ranging from 8.4% to 25.9% and with combined effects of >57% of the total phenotypic variation. All QTLs had the positive alleles from the disease-resistant parent. The good agreement between results of the BC1 and 2 years of the BC1S1 generations indicated the stability of the identified QTLs and their potential usefulness for improving tomato EB resistance using marker-assisted selection (MAS). Further inspections using SIM and CIM indicated that six of the ten QTLs had independent additive effects and together could account for up to 56.4% of the total phenotypic variation. These complementary QTLs, which were identified in two generations and 3 years, should be the most useful QTLs for MAS and improvement of tomato EB resistance using PI126445 as a gene resource. Furthermore, the chromosomal locations of 10 of the 23 RGAs coincided with the locations of three QTLs, suggesting possible involvement of these RGAs with EB resistance and a potential for identifying and cloning genes which confer EB resistance in tomato.

Mapping QTLs conferring early blight (Alternaria solani) resistance in a Lycopersicon esculentum×L. hirsutum cross by selective genotyping

Most commercial cultivars of tomato, Lycopersicon esculentum Mill., are susceptible to early blight (EB), a devastating fungal (Alternaria solani Sorauer) disease of tomato in the U.S. and elsewhere in the world. Currently, sanitation, long crop rotation, and routine application of fungicides are the most common disease control measures. Although no source of genetic resistance is known within the cultivated species of tomato, resistant resources have been identified within related wild species. The purpose of this study was to identify and validate quantitative trait loci (QTLs) conferring EB resistance in an accession (PI126445) of the tomato wild species L. hirsutum Humb. and Bonpl. by using a selective genotyping approach. A total of 820 BC1 plants of a cross between an EB susceptible tomato breeding line (NC84173; maternal and recurrent parent) and PI126445 were grown in a greenhouse. During late seedling stage, plants were inoculated with mixed isolates of A. solani and subsequently evaluated for EB symptoms. The most resistant (75 plants = 9.1%) and most susceptible (80 = 9.8%) plants were selected and subsequently transplanted into a field where natural infestation of EB was severe. Plants were grown to maturity and evaluated for final disease severity. From among the 75 resistant plants, 46 (5.6% of the total) that exhibited the highest resistance, and from among the 80 susceptible plants, 30 (3.7% of the total) that exhibited the highest susceptibility, were selected. The 76 selected plants, representing the two extreme tails of the response distribution, were genotyped for 145 restriction fragment length polymorphism (RFLP) markers and 34 resistance gene analogs (RGAs). A genetic linkage map, spanning approximately 1298 cM of the 12 tomato chromosomes with an average marker distance of 7.3 cM, was constructed. A trait-based marker analysis (TBA), which measures differences in marker allele frequencies between extreme tails of a population, detected seven QTLs for EB resistance, one on each of chromosomes 3, 4, 5, 6, 8, 10 and 11. Of these, all but the QTL on chromosome 3 were contributed from the resistant wild parent, PI126445. The standardized effects of the QTLs ranged from 0.45 to 0.81 phenotypic standard deviations. Four of the seven QTLs were previously identified in a study where different populations and mapping strategy were used. The high level of correspondence between the two studies indicated the reliability of the detected QTLs and their potential use for marker-assisted breeding for EB resistance. The location of several RGAs coincided with locations of EB QTLs or known tomato resistance genes (R genes), suggesting that these RGAs could be associated with disease resistance. Furthermore, similar to that for many R gene families, several RGA loci were identified in clusters, suggesting their potential evolutionary relationship with R genes.

Genetic analysis of cold tolerance during vegetative growth in tomato, Lycopersicon esculentum Mill.

The genetic basis of cold tolerance (CT) during vegetative growth in tomato was investigated by evaluating plants of a cold-tolerant primitive cultivar (PI120256) and a cold-sensitive breeding line (UCT5) and their reciprocal F1, F2, F3, BC1P1 and BC1P2 progeny under two temperature regimes of 15/10 °C (cold stress) and 25/15 °C (control). Plants were evaluated for shoot dry weight (DW) under cold stress and by a tolerance index (TI) measured as the ratio of DW under cold stress (DWs) to DW under control (DWc) conditions. Shoot DW was reduced in all genotypes in response to cold stress. However, PI120256 exhibited the highest CT (TI = 90.5%) and UCT5 the lowest (TI = 38.9%). The TIs of the filial and backcross progeny were intermediate to the parents. Across generations, there was a positive correlation (r = 0.76, p < 0.01) between DWs and DWc indicating that growth under cold stress was influenced by plant vigor. However, the absence of a significant correlation (r=0.47, p >0.05) between DWc and the TI and, in contrast, the presence of a significant correlation (r =0.92, p <0.01) between DWs and the TI suggest that plant vigor was not a determining factor in the expression of CT in PI120256 and its progeny. Generation means analyses of DWs and TI indicated that the variation among generations was genetically controlled, with additive effects accounting for most of the variation. There were no significant dominance effects, and epistatic effects were minor and involved only additive × additive interactions. The results suggest that the inherent CT of PI120256 should be useful for improving CT of commercial cultivars of tomato.

Genetic relationships among cold, salt and drought tolerance during seed germination in an interspecific cross of tomato

Seed of BC1 progeny of an interspecific cross between a slow germinating Lycopersicon esculentum breeding line(NC84173; maternal and recurrent parent) and a fast germinating L.pimpinellifolium accession (LA722) were evaluated for germination under cold stress, salt stress and drought stress, and in each treatment the most rapidly germinating seeds (first 2%) were selected. Selected individuals were grown to maturity and self-pollinated to produce BC1S1 progeny families. The selected BC1S1 progeny from each experiment were evaluated for germination rate in each of a non stress (control),cold-, salt- and drought-stress treatment, and their performances were compared with those of a non selected BC1S1population in the same treatments. Results indicated that selection for rapid seed germination in each of the three stress treatments was effective and significantly improved progeny germination rate under all three stress conditions. The results support the suggestion that same genes might control the rate of seed germination under cold, salt and drought stress. Furthermore, selection in each of the three stress treatments resulted in improved progeny seed germination rate under nonstress conditions, suggesting that genetic mechanisms that facilitate rapid seed germination under stress conditions might also contribute to rapid germination under nonstress conditions. In practice, therefore, selection for rapid seed germination under a single stress environment may result in progeny with improved seed germination under a wide range of environmental conditions. Furthermore, to improve germination rate under nonstress conditions, it might be more efficient to make selections under stress conditions.