Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection

Itay Gonda, Hamid Ashrafi, David A. Lyon, Susan R. Strickler, Amanda M. Hulse-Kemp, Qiyue Ma, Honghe Sun, Kevin Stoffel, Adrian F. Powell, Stephanie Futrell, Theodore W. Thannhauser, Zhangjun Fei, Allen E. Van Deynze, Lukas A. Mueller, James J. Giovannoni, Majid R. Foolad

Research output: Contribution to journalArticle

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Abstract

Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato (Solanum lycopersicum L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR-1 and the wild tomato S. pimpinellifolium L. 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 (QTL) 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 restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)–based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well-described FW QTL (fw2.2 and fw3.2) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two- to tenfold. A major QTL for LYC content (Lyc12.1) was verified at high resolution and its underlying causative gene was determined to be z-carotene isomerase (SlZISO). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available.

Original languageEnglish (US)
Article number180010
JournalPlant Genome
Volume12
Issue number1
DOIs
StatePublished - Mar 1 2019

Fingerprint

Quantitative Trait Loci
Lycopersicon esculentum
quantitative trait loci
tomatoes
Fruit
inbred lines
Population
lycopene
genotyping
fruits
Solanum pimpinellifolium
Boidae
genomics
Weights and Measures
Python
Isomerases
Genetic Linkage
genes
isomerases
Solanum lycopersicum

All Science Journal Classification (ASJC) codes

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

Cite this

Gonda, Itay ; Ashrafi, Hamid ; Lyon, David A. ; Strickler, Susan R. ; Hulse-Kemp, Amanda M. ; Ma, Qiyue ; Sun, Honghe ; Stoffel, Kevin ; Powell, Adrian F. ; Futrell, Stephanie ; Thannhauser, Theodore W. ; Fei, Zhangjun ; Van Deynze, Allen E. ; Mueller, Lukas A. ; Giovannoni, James J. ; Foolad, Majid R. / Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection. In: Plant Genome. 2019 ; Vol. 12, No. 1.
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title = "Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection",
abstract = "Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato (Solanum lycopersicum L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR-1 and the wild tomato S. pimpinellifolium L. 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 (QTL) 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 restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)–based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well-described FW QTL (fw2.2 and fw3.2) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two- to tenfold. A major QTL for LYC content (Lyc12.1) was verified at high resolution and its underlying causative gene was determined to be z-carotene isomerase (SlZISO). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available.",
author = "Itay Gonda and Hamid Ashrafi and Lyon, {David A.} and Strickler, {Susan R.} and Hulse-Kemp, {Amanda M.} and Qiyue Ma and Honghe Sun and Kevin Stoffel and Powell, {Adrian F.} and Stephanie Futrell and Thannhauser, {Theodore W.} and Zhangjun Fei and {Van Deynze}, {Allen E.} and Mueller, {Lukas A.} and Giovannoni, {James J.} and Foolad, {Majid R.}",
year = "2019",
month = "3",
day = "1",
doi = "10.3835/plantgenome2018.02.0010",
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Gonda, I, Ashrafi, H, Lyon, DA, Strickler, SR, Hulse-Kemp, AM, Ma, Q, Sun, H, Stoffel, K, Powell, AF, Futrell, S, Thannhauser, TW, Fei, Z, Van Deynze, AE, Mueller, LA, Giovannoni, JJ & Foolad, MR 2019, 'Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection', Plant Genome, vol. 12, no. 1, 180010. https://doi.org/10.3835/plantgenome2018.02.0010

Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection. / Gonda, Itay; Ashrafi, Hamid; Lyon, David A.; Strickler, Susan R.; Hulse-Kemp, Amanda M.; Ma, Qiyue; Sun, Honghe; Stoffel, Kevin; Powell, Adrian F.; Futrell, Stephanie; Thannhauser, Theodore W.; Fei, Zhangjun; Van Deynze, Allen E.; Mueller, Lukas A.; Giovannoni, James J.; Foolad, Majid R.

In: Plant Genome, Vol. 12, No. 1, 180010, 01.03.2019.

Research output: Contribution to journalArticle

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T1 - Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection

AU - Gonda, Itay

AU - Ashrafi, Hamid

AU - Lyon, David A.

AU - Strickler, Susan R.

AU - Hulse-Kemp, Amanda M.

AU - Ma, Qiyue

AU - Sun, Honghe

AU - Stoffel, Kevin

AU - Powell, Adrian F.

AU - Futrell, Stephanie

AU - Thannhauser, Theodore W.

AU - Fei, Zhangjun

AU - Van Deynze, Allen E.

AU - Mueller, Lukas A.

AU - Giovannoni, James J.

AU - Foolad, Majid R.

PY - 2019/3/1

Y1 - 2019/3/1

N2 - Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato (Solanum lycopersicum L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR-1 and the wild tomato S. pimpinellifolium L. 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 (QTL) 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 restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)–based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well-described FW QTL (fw2.2 and fw3.2) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two- to tenfold. A major QTL for LYC content (Lyc12.1) was verified at high resolution and its underlying causative gene was determined to be z-carotene isomerase (SlZISO). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available.

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