Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitive Trait Loci Detection

Authors: GONDA, ITAY - Boyce Thompson Institute; ASHRAFI, HAMID - North Carolina State University; LYON, SUSAN - Boyce Thompson Institute; STRICKLER, SUSAN - Boyce Thompson Institute; Hulse-Kemp, Amanda; MA, QIYUE - Boyce Thompson Institute; SUN, HONGHE - Boyce Thompson Institute; STOFFEL, KEVIN - Uc Davis Medical Center; POWELL, ADRIAN - Boyce Thompson Institute; FUTRELL, STEPHANIE - Boyce Thompson Institute; Thannhauser, Theodore - Ted; FEI, ZHANGJUN - Boyce Thompson Institute; VAN DEYNZE, ALLEN - Uc Davis Medical Center; MUELLER, LUKAS - Cornell University; Giovannoni, James; FOOLAD, MAJID - University Of Pennsylvania

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/17/2018
Publication Date: 12/13/2018
Citation: Gonda, I., Ashrafi, H., Lyon, S., Strickler, S., Hulse-Kemp, A.M., Thannhauser, T.W., Mueller, L., Fei, Z., Foolad, M., Giovannoni, J.J., Ma, Q., Sun, H., Stoffel, K., Powell, A., Futrell, S., Van Deynze, A. 2018. A GBS-based high-density genetic map of a tomato RIL population facilitating high resolution QTL mapping and candidate gene identification. The Plant Genome. 12:1. https://doi.org/10.3835/plantgenome2018.02.0010.
DOI: https://doi.org/10.3835/plantgenome2018.02.0010

Interpretive Summary: Recombinant inbred line (RIL) populations are powerful tools for plant genetic studies. RILs are usually derived from a cross between two inbred parents, followed by a series of self-pollinations. Each resulting RIL displays a unique genetic structure that is a mosaic of the two parental lines in both genotypic and phenotypic characteristics. The permanent, immortal nature of a RIL population provides ample opportunities for the population to be evaluated under different conditions for various traits contrasting in the two parental lines. A linkage map of a RIL population allows genetic investigation of the contrasting traits under different conditions. Here we not only confirmed several previously-identified QTLs, but also identification of most probable candidate genes underlying major fruit quality traits. The RIL population as well as the high-resolution genetic map and SNP markers are available to all interested researchers.

Technical Abstract: Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato recombinant inbred line (RIL) population, derived from a cross between Solanum lycopersicum cv. NC EBR-1 and S. pimpinellifolium accession LA2093. A pipeline was developed to convert single nucleotide polymorphism (SNP) data into genomic bins, which could be used for fine mapping of quantitative trait loci (QTLs) and identification of candidate genes. The pipeline, implemented in a python script named SNPbinner, adopts a hidden Markov model approach for calculation of recombination breakpoints followed by genomic bins construction. The total length of the newly developed high-resolution genetic map was 1.2-fold larger than previously estimated based on RFLP and PCR-based markers. The map was used to verify and refine QTLs previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene (LYC) content. Two well-described FW QTLs (fw2.2 and fw3.2) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by 2-10-fold. A major QTL for LYC content (Lyc12.1) was verified at high resolution and its underlying causative gene was determined to be beta-carotene isomerase (SlZISO). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available.