Dissecting the Genotypic and Environmental Factors Underpinning the Quantitative Trait Variation in a Set of Wild Tomato (Solanum habrochaites LA1777) Introgression Lines

Exotic libraries have proven a powerful tool for the exploitation of wild relatives and quantitative trait loci (QTLs) detection in crop species. In early 2000, an introgression line (IL) population of the wild tomato Solanum habrochaites (SH) acc. LA1777 was developed and made publicly available. Despite the potentiality of the donor parent, so far, these lines have been poorly explored for their agronomic performance and for the identification of genomic regions underlying the variation of quantitative traits (QTLs). Here, we report the evaluation of 19 morpho-agronomic and chemical traits on a set of 39 ILs grown in three consecutive field seasons with the aim to: (a) Determine the overall phenotypic performances of the studied collection, (b) estimate the influence of the genotype (G) and the year of cultivation (Y) and their interaction on the traits analyzed, (c) investigate the plasticity of the traits, and (d) identify whole-genome QTLs in the wild SH background. The ILs showed lower productivity compared to the control genotype, while no major effects were found for the morphological fruit-related traits. Instead, a general increase in the soluble solids content was observed. The combined analysis of G × Y highlighted a major effect of the genotype on trait variation, although yield-related traits were more influenced by environmental factors. In total, 75 associations for 17 traits were detected. Major QTLs increasing soluble solids, pericarp thickness, and trichome density were respectively found on chromosomes 1, 5, and 11 with a percentage variation (PV) of 24.01%, 32.49%, and 200%. Furthermore, different QTLs increasing the color intensity and fruit shape were detected. These results suggest that SH could be a potential source of favorable alleles for qualitative traits despite its inferior phenotype compared to the cultivated parent. The evaluated set of SH LA1777 ILs is a potential for novel allele discovery in wild tomatoes and for breeding purposes towards the exploitation of the available introgressions and for the pyramiding of traits.

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Identification of Quantitative Trait Loci for Fruit Weight, Soluble Solids Content, and Plant Morphology Using an Introgression Line Population of Solanum pennellii in a Fresh Market Tomato Inbred Line

Horticultural Plant Journal ◽

10.1016/j.hpj.2016.02.007 ◽

2016 ◽

Vol 2 (1) ◽

pp. 26-34 ◽

Cited By ~ 3

Author(s):

Hui Zhou ◽

Xiaoxuan Wang ◽

Zejun Huang ◽

Jianchang Gao ◽

Yanmei Guo ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Plant Morphology ◽

Introgression Line ◽

Fruit Weight ◽

Soluble Solids ◽

Soluble Solids Content ◽

Fresh Market ◽

Solanum Pennellii ◽

Solids Content

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Conservation of Gene Function in the Solanaceae as Revealed by Comparative Mapping of Domestication Traits in Eggplant

Genetics ◽

10.1093/genetics/161.4.1713 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1713-1726 ◽

Cited By ~ 3

Author(s):

Sami Doganlar ◽

Anne Frary ◽

Marie-Christine Daunay ◽

Richard N Lester ◽

Steven D Tanksley

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Morphological Diversity ◽

Fruit Shape ◽

Fruit Weight ◽

Crop Species ◽

Phenotypic Differences ◽

F2 Population ◽

Trait Loci ◽

Genomic Locations

Abstract Quantitative trait loci (QTL) for domestication-related traits were identified in an interspecific F2 population of eggplant (Solanum linnaeanum × S. melongena). Although 62 quantitative trait loci (QTL) were identified in two locations, most of the dramatic phenotypic differences in fruit weight, shape, color, and plant prickliness that distinguish cultivated eggplant from its wild relative could be attributed to six loci with major effects. Comparison of the genomic locations of the eggplant fruit weight, fruit shape, and color QTL with the positions of similar loci in tomato, potato, and pepper revealed that 40% of the different loci have putative orthologous counterparts in at least one of these other crop species. Overall, the results suggest that domestication of the Solanaceae has been driven by mutations in a very limited number of target loci with major phenotypic effects, that selection pressures were exerted on the same loci despite the crops' independent domestications on different continents, and that the morphological diversity of these four crops can be explained by divergent mutations at these loci.

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Trait Diversity and Potential for Selection Indices Based on Variation Among Regionally Adapted Processing Tomato Germplasm

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.137.6.427 ◽

2012 ◽

Vol 137 (6) ◽

pp. 427-437 ◽

Cited By ~ 33

Author(s):

Heather L. Merk ◽

Shawn C. Yarnes ◽

Allen Van Deynze ◽

Nankui Tong ◽

Naama Menda ◽

...

Keyword(s):

Environmental Influence ◽

Fruit Size ◽

Fruit Shape ◽

Soluble Solids ◽

Phenotypic Variance ◽

Trait Variation ◽

Flat File ◽

Horticultural Crops ◽

Processing Tomato ◽

Selection Indices

For many horticultural crops, selection is based on quality as well as yield. To investigate the distribution of trait variation and identify those attributes appropriate for developing selection indices, we collected and organized information related to fruit size, shape, color, soluble solids, acid, and yield traits for 143 processing tomato (Solanum lycopersicum L.) lines from North America. Evaluation of the germplasm panel was conducted in a multiyear, multilocation trial. Data were stored in a flat-file format and in a trait ontology database, providing a public archive. We estimated variance components and proportion of variance resulting from genetics for each trait. Genetic variance was low to moderate (range, 0.03–0.51) for most traits, indicating high environmental influence on trait expression and/or complex genetic architecture. Phenotypic values for each line were estimated across environments as best linear unbiased predictors (BLUPs). Principal components (PC) analysis using the trait BLUPs provided a means to assess which traits explained variation in the germplasm. The first two PCs explained 28.0% and 16.2% of the variance and were heavily weighted by measures of fruit shape and size. The third PC explained 12.9% of the phenotypic variance and was determined by fruit color and yield components. Trait BLUPs and the first three PCs were also used to explore the relationship between phenotypes and the origin of the accessions. We were able to differentiate germplasm for fruit size, fruit shape, yield, soluble solids, and color based on origin, indicating regional breeding programs provide a source of trait variation. These analyses suggest that multitrait selection indices could be established that encompass quality traits in addition to yield. However, such indices will need to balance trait correlations and be consistent with market valuation.

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Estimating the Genetic Architecture of Fruit Quality Traits in Melon Using a Genomic Library of Near Isogenic Lines

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.132.1.80 ◽

2007 ◽

Vol 132 (1) ◽

pp. 80-89 ◽

Cited By ~ 68

Author(s):

Iban Eduardo ◽

Pere Arús ◽

Antonio José Monforte ◽

Javier Obando ◽

Juan Pablo Fernández-Trujillo ◽

...

Keyword(s):

Fruit Quality ◽

Quantitative Trait ◽

Genomic Library ◽

Shape Index ◽

Fruit Shape ◽

Fruit Weight ◽

Soluble Solids ◽

Isogenic Line ◽

Soluble Solids Content ◽

Solids Content

A melon (Cucumis melo L.) genomic library of near-isogenic lines derived from the cross between the Spanish cultivar Piel de Sapo and the exotic accession PI 161375 has been evaluated for fruit quality traits in four different locations. Traits evaluated were fruit weight, soluble solids content, maximum fruit diameter, fruit length, fruit shape index, ovary shape index, external color, and flesh color. Among these traits, soluble solids content showed the highest genotype × environment interaction, whereas genotype × environment interactions for fruit shape and fruit weight were low. Heritability was high for all traits except soluble solids content, with the highest value for fruit shape and ovary shape. Ten to 15 quantitative trait loci were detected for soluble solids content, fruit diameter, fruit length, and fruit shape; and four to five for ovary shape, external color, and flesh color. Depending on the trait, between 13% and 40% of the detected quantitative trait alleles from PI 161375 increased the trait, and between 60% and 87% of them decreased it, resulting in some PI 161375 alleles of interest for breeding. Most of the quantitative trait loci detected in previous experiments could be verified with the near-isogenic line population. Future studies with the melon near-isogenic line genomic library will provide a better understanding of the genetic control of melon fruit quality in a wider context related to agronomy, genetics, genomics and metabolomics studies.

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