Multiple QTL for Horticultural Traits and Quantitative Resistance toPhytophthora infestansLinked onSolanum habrochaitesChromosome 11

Abstract

Previously, a Phytophthora infestans resistance QTL from Solanum habrochaites chromosome 11 was introgressed into cultivated tomato (S. lycopersicum). Fine mapping of this resistance QTL using near-isogenic lines (NILs) revealed some co-located QTL with undesirable effects on plant size, canopy density, and fruit size traits. Subsequently, higher-resolution mapping with sub-NILs detected multiple P. infestans resistance QTL within this 9.4-cM region of chromosome 11. In our present study, these same sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over 2 years. The horticultural trait QTL originally detected by fine mapping each fractionated into two or more QTL at higher resolution. A total of 34 QTL were detected across all traits, with 14% exhibiting significant QTL × environment interactions (QTL × E). QTL for many traits were co-located, suggesting either pleiotropic effects or tight linkage among genes controlling these traits. Recombination in the pericentromeric region of the introgression between markers TG147 and At4g10050 was suppressed to approximately 29.7 Mbp per cM, relative to the genomewide average of 750 kbp per cM. The genetic architecture of many of the horticultural and P. infestans resistance traits that mapped within this chromosome 11 S. habrochaites region is complex. Complicating factors included fractionation of QTL, pleiotropy or tight linkage of QTL for multiple traits, pericentromeric chromosomal location(s), and/or QTL × E. High-resolution mapping of QTL in this region would be needed to determine which specific target QTL could be useful in breeding cultivated tomato.

Quantitative Trait Loci for Water‐Stress Tolerance Traits Localize on Chromosome 9 of Wild Tomato

“…This result suggests the possibility of this trait QTL fractionating into multiple QTL if higher‐resolution mapped with a set of sub‐NILs that represent a larger introgressed region beyond marker T0532 (toward the centromere). Fractionation of QTL has been reported for other traits in tomato, including late blight disease resistance, fruit size, maturity, and plant architecture (Johnson et al, 2012; Haggard et al, 2013, 2015).…”

Complex Relationships among Water Use Efficiency‐Related Traits, Yield, and Maturity in Tomato Lines Subjected to Deficit Irrigation in the Field

“…Fractionation of a QTL can occur in higher resolution mapping studies due to multiple QTL of small phenotypic effect that are closely linked but were not detected in initial global mapping studies (Mackay et al, 2009). QTL fractionation has been reported in both tomato and maize (Haggard et al, 2013; Haggard et al, 2015; Johnson et al, 2012; Studer and Doebley, 2011). Larger effect QTL may sometimes fractionate into multiple smaller effect QTL with both positive and negative phenotypic effects (Haggard et al, 2013; Haggard et al, 2015; Mackay et al, 2009).…”

“…QTL fractionation has been reported in both tomato and maize (Haggard et al, 2013; Haggard et al, 2015; Johnson et al, 2012; Studer and Doebley, 2011). Larger effect QTL may sometimes fractionate into multiple smaller effect QTL with both positive and negative phenotypic effects (Haggard et al, 2013; Haggard et al, 2015; Mackay et al, 2009). Alternatively, coincident QTL for different traits may suggest tight linkage and/or pleiotropy (Mackay et al, 2009; Alonso‐Blanco and Méndez‐Vigo, 2014).…”

“…Alternatively, coincident QTL for different traits may suggest tight linkage and/or pleiotropy (Mackay et al, 2009; Alonso‐Blanco and Méndez‐Vigo, 2014). If coincident QTL result from close linkage of the gene(s) controlling each of the traits, QTL for different traits may be linked in repulsion, requiring a large segregating population to break negative linkages to obtain desirable recombinants (Haggard et al, 2013; Haggard et al, 2015; Mackay et al, 2009). Collectively, our results imply that the coincident QTL identified by Lounsbery et al (2016) were the result of close linkage of gene(s) underlying QTL for the seven primary traits.…”

Development of an in vitro protocol to screen Clavibacter michiganensis subsp. michiganensis pathogenicity in different Solanum species

“…Examples are Solanum pimpinellifolium (Thyr, ; Sen et al ., ), Solanum habrochaites (Vulkova & Sotirova, ; Francis et al ., ), S. lycopersicum (Elenkov, ) and Solanum arcanum (Lindhout & Purimahua, ; Vulkova & Sotirova, ). To broaden the genetic variation of cultivated varieties, parts of the genome of wild tomatoes can be introgressed (Haggard et al ., ). Previous studies have shown that the best source of tolerance is S. arcanum LA2157 (van Heusden et al ., ).…”