Solanum pennelliibackcross inbred lines (BILs) link small genomic bins with tomato traits

Abstract

SUMMARYWe present a resource for fine mapping of traits derived from the wild tomato species Solanum pennellii (LA0716). The population of backcross inbred lines (BILs) is composed of 446 lines derived after a few generations of backcrosses of the wild species with cultivated tomato (cultivar M82; LA3475), followed by more than seven generations of self-pollination. The BILs were genotyped using the 10K SOL-CAP single nucleotide polymorphism (SNP) -Chip, and 3700 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs carry, on average, 2.7 introgressions per line, with a mean introgression length of 11.7 Mbp. Whereas the classic 76 introgression lines (ILs) partitioned the genome into 106 mapping bins, the BILs generated 633 bins, thereby enhancing the mapping resolution of traits derived from the wild species. We demonstrate the power of the BILs for rapid fine mapping of simple and complex traits derived from the wild tomato species.

Canalization of Tomato Fruit Metabolism

“…We next sought to validate these putative canalization QTL by analyzing a subset of the independently derived S. pennellii backcrossed introgression lines (BILs) (Ofner et al, 2016), which provide increased resolution of the regions of interest. For this purpose, we focused on the putative canalized primary metabolite QTL on chromosome 10, specifically the hot spot in IL10-1, and were able to confirm 9 (out of 25) cmQTL mapped to chromosome 10, using the BIL population.…”

“…Correlation analysis was also performed across the entire population by means of the Pearson correlation coefficient to determine possible technical artifacts. A gas chromatography-mass spectrometry analysis was also performed on fruit materials harvested in three independent field trials from selected Solanum pennellii BILs (Ofner et al 2016).…”

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

“…S. pennellii is a wild, green-fruited tomato species native to Peru that exhibits beneficial traits such as abiotic stress resistances (Lippman et al, 2007;Koenig et al, 2013). The previously sequenced accession LA716 (Bolger et al, 2014a) has been used to generate a panel of introgression (Eshed and Zamir, 1995) and backcrossed introgression (Ofner et al, 2016) lines that have been used to identify many interesting quantitative trait loci (Alseekh et al, 2015;Fernandez-Moreno et al, 2017), thus complementing large-scale genomic panel studies for tomato (Lin et al, 2014;Tieman et al, 2017). However, the accession LA716 does not perform well in the field and carries the NECROTIC DWARF gene on chromosome 6, which reduces plant vigor when introduced into a Solanum lycopersicum background (Ranjan et al, 2016).…”

Identification of tomato introgression lines with enhanced susceptibility or resistance to infection by parasitic giant dodder (Cuscuta reflexa)

“…An additional two lines have overlapping introgressions on chromosome 1. The tentative conclusion that these overlapping regions contain the loci that confer susceptibility in S. pennellii , or resistance in S. lycopersicum , is supported by the observation that lines from the sub‐IL and BIL‐collections (Alseekh et al , Ofner et al ), which have introgressions in the overlap regions, are also susceptible (Table ).…”

“…In this study, we describe the responses of different tomato lines to an infection by Cuscuta . Our host plant set included S. lycopersicum , S. pennellii , long‐established ILs derived from these two parental lines (Eshed and Zamir ) and selected sub‐ILs and BILs, which became available during the course of the study (Alseekh et al , Ofner et al ). In general, we found that the speed of infection of the tomato species was not as high as in the Cuscuta ‐ Pelargonium interaction, which has been characterized in detail (Johnsen et al , Olsen et al , Olsen and Krause ).…”