Comparative fine mapping of fruit quality QTLs on chromosome 4 introgressions derived from two wild tomato species

Yates, Heather E.; Frary, Anne; Doğanlar, Sami; Frampton, Anna; Eannetta, Nancy T.; Uhlig, John; Tanksley, Steven D.

doi:10.1023/b:euph.0000013314.04488.87

Cited by 43 publications

(26 citation statements)

References 19 publications

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“…As previously mentioned, this has been reported for fruit shape and weight QTL on tomato chromosome 2 (Eshed and Zamir 1995; Grandillo et al 1999;Lippman and Tanksley 2001). Similar QTL clusters are observed on tomato chromosome 4 (Monforte et al 2001;Yates et al 2004). Several strategies have been used to discriminate whether traits associated with clustered QTL are controlled by a single pleiotropic gene or two (or more) tightly-linked genes.…”

Section: Discussionsupporting

confidence: 78%

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

Frary

Daunay

et al. 2014

Euphytica

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Fifty-eight F 2 individuals derived from an interspecific cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, were phenotyped for 42 plant, leaf, flower, and fruit traits. Composite interval mapping analysis using genotypic data from 736 molecular markers revealed the positions of 71 statistically significant (P B 0.05) quantitative trait loci (QTL) influencing 32 of the morphological traits. Although most QTL were location-specific, QTL governing three traits (leaf lobing, leaf prickles and prickle anthocyanin) were detected in both experimental locations. Analysis of three additional traits (stem prickles, fruit calyx prickles and fruit length) in both locations yielded QTL in similar but non-overlapping map positions. The majority (69 %) of the QTL corresponded closely with those detected in previous analyses of this data set. However the increased resolution of the linkage map combined with advances in QTL mapping permitted more precise localization, such that the average interval length of these QTL was reduced by 93 %. Thirty-one percent of the QTL were novel, suggesting that simple linear regression with a low density linkage map (the method used in previous studies of this population) missed a substantial portion of significant QTL. Hotspots of QTL affecting plant hairiness, prickliness, and pigmentation were identified on chromosomes 3, 6, and 10, respectively, and may reflect the pleiotropic activity of single structural or regulatory genes at these positions. Based on synteny between the eggplant, tomato, potato and pepper genomes, putative orthologs were identified for 35 % of the QTL suggesting strong conservation of gene function within the Solanaceae. These results should make itThe localization of QTL for 32 morphological traits on the high-resolution map of the eggplant genome has allowed hotspots and putative orthologs with other solanaceous species to be identified. 123 Euphytica (2014) 197:211-228 DOI 10.1007/s10681-013-1060 easier to target particular loci for map-based cloning and marker-assisted selection studies.

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Section: Discussionsupporting

confidence: 78%

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

Frary

Daunay

et al. 2014

Euphytica

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“…These results suggest that co-localization of QTLs in these chromosomal regions is caused by gene linkage rather than pleiotropic effects, given that if the phenomenon of pleiotropy was the main reason, a constant epistasis between epistatic QTLs controlling various traits would be constant throughout the traits. Similar results, though between the content of soluble solids and weight of fruits, have been observed in F 2 populations of sub NILs derived from the cross between S. lycopersicum with S. hirsutum and S. peruvianum, where Yates et al (2004) found that high co-localization of QTLs controlling fruit weight and soluble solids content in the region of chromosome 4 was caused by strong genetic linkage. Additionally Monforte and Tanksley (2000) concluded that high co-localization of QTLs controlling different fruit variables in the terminal part of chromosome 1 was not caused by pleiotropic effects but by gene linkage.…”

Section: Genetic Variation In Truss Production Over Time Is Affected supporting

confidence: 83%

“…The co-localization of QTLs associated with days to flowering of the first truss and fruit size on chromosomes 1, 4 and 6 has revealed a number of causes of the positive association identified in several types of mapping populations (e.g., F 2 , inbred backcross lines, near isogenic lines and recombinant inbred lines) (Grandillo and Tanksley, 1996;Doganlar et al, 2002;Monforte and Tanksley, 2000;Yates et al, 2004;Sumugat et al, 2010). However, it is not clear if the cause is due to pleiotropic effects or to gene linkage.…”

Section: Introductionmentioning

confidence: 99%

Quantitative trait locus mapping associated with earliness and fruit weight in tomato

Hernández-Bautista¹,

Lobato-Ortíz²,

García-Zavala³

et al. 2016

Sci. agric. (Piracicaba, Braz.)

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The flowering time is regarded as an important factor that affects yield in various crops. In order to understand how the molecular basis controlling main components of earliness in tomato (Solanum lycopersicum L.), and to deduce whether the correlation between fruit weight, days to flowering and seed weight, is caused by pleiotropic effects or genetic linkage, a QTLs analysis was carried out using an F 2 interspecific population derived from the cross of S. lycopersicum and S. pimpinellifolium. The analysis revealed that most of the components related to earliness were independent due to the absence of phenotypic correlation and lack of co-localization of their QTLs. QTLs affecting the flowering time showed considerable variation over time in values of explained phenotypic variation and average effects, which suggested dominance becomes more evident over time. The path analysis showed that traits such as days to flowering, seed weight, and length of the first leaf had a significant effect on the expression of fruit weight, confirming that their correlations were due to linkage. This result was also confirmed in two genomic regions located on chromosomes 1 and 4, where despite showing high colocalization of QTLs associated to days to flowering, seed weight and fruit weight, the presence and absence of epistasis in dfft1.1 × dftt4.1 and fw1.1 × fw4.1, suggested that the linkage was the main cause of the co-localization.

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“…The most probable candidate was 2534_1 that we inferred to map within 1 cM of Tm-2 a (Labate and Baldo, 2005). Tm-2 a was recorded to have been introgressed into line TA496 for improved disease resistance (Tanksley et al, 1998;Yates et al, 2004). Therefore, we hypothesized that locus 2534_1 contained an introgression as a consequence of linkage drag.…”

Section: Diversity Patternsmentioning

confidence: 93%

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

Labate¹,

Robertson²,

Baldo³

2009

Heredity

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Limited genetic variation has been observed within tomato (Solanum lycopersicum L.), although no studies have extensively surveyed single nucleotide polymorphism (SNP) diversity among tomato landraces. We estimated intraspecific DNA sequence variation by analyzing 50 gene fragments (23.2 kb) per plant in a 31 plant diversity panel. The majority of loci (80%) were polymorphic with the minor allele at a frequency of 10% or less for most (141 of 155) SNPs. Mean diversity as estimated by y and p was approximately 1.5 SNPs per kb. Significant linkage disequilibrium was observed between 19% of locus pairs, and withinlocus population recombination estimates were negligible. We also sequenced 43 gene fragments from wild tomato Solanum arcanum Peralta as an outgroup. Various statistical tests rejected a neutral equilibrium model of molecular evolution at 10 of 50 loci. Rare, highly diverged alleles were observed, involving at least seven tomato lines and five loci. Some of these may represent introgressions that originated both from natural hybridization with Solanum pimpinellifolium L. and from crosses with S. pimpinellifolium and additional wild relatives for crop improvement. The former was reported from classical field studies carried out by CM Rick; the latter has been extensively documented in the crop, particularly for transfer of disease resistance alleles. Extensive introgression and frequent bottlenecks within S. lycopersicum will pose a challenge to reconstructing the genetic bases of domestication and selection using methods that rely on patterns of molecular polymorphism.

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Comparative fine mapping of fruit quality QTLs on chromosome 4 introgressions derived from two wild tomato species

Cited by 43 publications

References 19 publications

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

Quantitative trait locus mapping associated with earliness and fruit weight in tomato

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

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