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Highly efficient genomics-assisted development of a library of introgression lines of Solanum pimpinellifolium

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Abstract

The Solanum pimpinellifolium L. accession TO-937 is resistant to pests due to the presence of type IV glandular trichomes and also has the potential to increase fruit quality traits in tomato cultivars. This accession was selected to develop a genomic library of introgression lines (IL) in the genetic background of tomato cultivar “Moneymaker.” In order to increase the accuracy and speed of the IL development process, high-throughput single-nucleotide polymorphism (SNP) genotyping steps were performed in early backcross generations. Five to seven generations were needed to complete the final set of 53 ILs that were characterized with the 8K SNP SOLCAP Infinium array, which demonstrated that the introgressions present in the IL set covered 94 % of the donor genome and that each IL contained an average of 4.25 % (25 Mb) of the donor genome, defining 71 bins of about 10 Mb on average. Additionally, 37 previously undetected, unwanted introgressions were also detected, and most of them very small (<2 Mb), probably due to double recombination events among the markers used during IL development. Compared to other IL collections recently characterized with high-throughput SNP technologies, the current IL collection contains a significantly lower number of smaller-sized, non-selected introgressions. The combination of several steps of high-throughput genotyping at early generations and the relatively large population size allowed us to construct a collection of ILs with an extraordinary genetic background isogenicity in a relatively short period of time.

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Abbreviations

AB-QTL:

Advanced backcross quantitative trait locus

BC:

Backcross

BIL:

Backcross inbred line

BLAST:

Basic local alignment search tool

cM:

Centimorgan

DS:

Distorted segregation

HRM:

High-resolution melting

IL:

Introgression line

MAS:

Marker-assisted selection

Mb:

Megabases

NGS:

Next-generation sequencing

QTL:

Quantitative trait loci

S:

Selection differential

SGN:

Sol Genomics Network

SNP:

Single-nucleotide polymorphism

SL :

Solanum lycopersicum L.

SP :

Solanum pimpinellifolium accession TO-937

SSD:

Single-seed descent

SOLCAP:

Solanaceae Coordinated Agricultural Project

TYLCV:

Tomato yellow leaf curl virus

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Acknowledgments

The authors wish to thank S. Casal and J. Añó and the technical staff at the greenhouse of IBMCP-UPV for their technical assistance. This work was funded in part by Grants AGL2012-40130-C02-02 from the MICINN, and co-funded by FEDER to AJM and P10-AGR-6784 by the Junta de Andalucía to RF-M. WB was supported by a fellowship granted by the Universidad de Costa Rica and CSIC-Spain by way of a collaboration agreement between CSIC/UCR. GL-C was supported by a JAEDoc contract by CSIC co-funded by the European Social Fund (ESF).

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  1. Walter Barrantes

    Present address: Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, Apartado Postal 183-4050, La Garita-Alajuela, Costa Rica

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  1. Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ingeniero Fausto Elio s/n, 46022, Valencia, Spain

    Walter Barrantes, Asunción Fernández-del-Carmen, Antonio Granell & Antonio J. Monforte

  2. Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga Consejo Superior de Investigaciones Científicas, 29750, Algarrobo-Costa, Málaga, Spain

    Gloria López-Casado, María Ángeles González-Sánchez & Rafael Fernández-Muñoz

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  4. María Ángeles González-Sánchez
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Corresponding author

Correspondence to Antonio J. Monforte.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 891 kb): genetic map including the SNP markers used to genotype the BC2 population

11032_2014_141_MOESM2_ESM.ppt

Supplementary material 2 (PPT 217 kb): neighbor-joining dendrogram of S. pimpinellifolium accessions calculated from Nei (1983) genetic distance based on 8K SNP SOLCAP Infinium array genotyping. Data from all accessions except from TO-937 were obtained from Sim et al. (2012) and Blanca et al. (2012). TO-937, LA1589, and LA2093 accessions (the latter two have also been used in other works for several QTL analyses) are highlighted in red. The origin of the accessions is indicated by the colors green for Ecuador, and black for Peru

11032_2014_141_MOESM3_ESM.ppt

Supplementary material 3 (PPT 146 kb): graphical genotypes of unselected (A) and selected (B) BC2 population that have been characterized with the 665 polymorphic SNP markers indicated in the Online Resource 1. Blue and red areas indicate regions that are heterozygous and homozygous for cv. “Moneymaker,” respectively

Supplementary material 4 (PPT 907 kb): genetic map of the SNP markers used to genotype the BC3 population

11032_2014_141_MOESM5_ESM.ppt

Supplementary material 5 (PPT 151 kb): graphical genotypes of unselected (A) and selected (B) BC3 population that have been characterized with 96 SNP markers (Illumina Veracode array). Blue and red regions indicate heterozygous or homozygous for the recurrent parent cv. “Moneymaker,” respectively

11032_2014_141_MOESM6_ESM.ppt

Supplementary material 6 (PPT 512 kb): primers designed to genotype the BC3 and subsequent generations by high-resolution melting to develop the introgression lines. The chromosome and physical position of each locus according to solgenomics.net are also shown

11032_2014_141_MOESM7_ESM.xls

Supplementary material 7 (XLS 39 kb): SNP data generated from genotyping of the definitive ILs using 8 K SNP SOLCAP Infinium array showing only the polymorphic informative markers. The columns reflect the SNP_ID, scaffold name, chromosome number, segment, and physical position according to the information provided with the SOLCAP array. The order of chromosome 3 segments was according to Online Resource 8

11032_2014_141_MOESM8_ESM.ppt

Supplementary material 8 (PPT 285 kb): assembly of the chromosome segments of chromosome 3 according to the SL2.40 genome build on the left, and according to bin mapping with the current introgression lines on the right

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Barrantes, W., Fernández-del-Carmen, A., López-Casado, G. et al. Highly efficient genomics-assisted development of a library of introgression lines of Solanum pimpinellifolium . Mol Breeding 34, 1817–1831 (2014). https://doi.org/10.1007/s11032-014-0141-0

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  • DOI: https://doi.org/10.1007/s11032-014-0141-0

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