CRISPR/Cas inactivation of RECQ4 increases homeologous crossovers in an interspecific tomato hybrid

Ruud A. de Maagd, Annelies Loonen, Jihed Chouaref, Alexandre Pelé, Fien Meijer-Dekens, Paul Fransz, Yuling Bai*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Abstract

Crossover formation during meiosis in plants is required for proper chromosome segregation and is essential for crop breeding as it allows an (optimal) combination of traits by mixing parental alleles on each chromosome. Crossover formation commences with the production of a large number of DNA double-strand breaks, of which only a few result in crossovers. A small number of genes, which drive the resolution of DNA crossover intermediate structures towards non-crossovers, have been identified in Arabidopisis thaliana. In order to explore the potential of modification of these genes in interspecific hybrids between crops and their wild relatives towards increased production of crossovers, we have used CRISPR/Cas9-mutagenesis in an interspecific tomato hybrid to knockout RecQ4. A biallelic recq4 mutant was obtained in the F1 hybrid of Solanum lycopersicum and S. pimpinellifolium. Compared with the wild-type F1 hybrid, the F1 recq4 mutant was shown to have a significant increase in crossovers: a 1.53-fold increase when directly observing ring bivalents in male meiocytes microscopically and a 1.8-fold extension of the genetic map when measured by analysing SNP markers in the progeny (F2) plants. This is one of the first demonstrations of increasing crossover frequency in interspecific hybrids by manipulating genes in crossover intermediate resolution pathways and the first to do so by directed mutagenesis. Significance statement: Increasing crossover frequency during meiosis can speed up or simplify crop breeding that relies on meiotic crossovers to introduce favourable alleles controlling important traits from wild relatives into crops. Here we show for the first time that knocking out an inhibitor of crossovers in an interspecific hybrid between tomato and its relative wild species using CRISPR/Cas9-mutagenesis results in increased recombination between the two genomes.

Original languageEnglish
Pages (from-to)805-813
JournalPlant Biotechnology Journal
Volume18
Issue number3
Early online date4 Sep 2019
DOIs
Publication statusE-pub ahead of print - 4 Sep 2019

Fingerprint

Clustered Regularly Interspaced Short Palindromic Repeats
Lycopersicon esculentum
inactivation
tomatoes
wild relatives
mutagenesis
Mutagenesis
Meiosis
plant breeding
meiosis
Breeding
Alleles
Genes
alleles
mutants
Chromosome Segregation
chromosome segregation
genes
Double-Stranded DNA Breaks
Solanum lycopersicum

Keywords

  • class II crossover pathway
  • interspecific crosses
  • introgression breeding
  • meiosis
  • RECQ4

Cite this

@article{1539e14eed6d4bc3b7b51bbd91ee1a83,
title = "CRISPR/Cas inactivation of RECQ4 increases homeologous crossovers in an interspecific tomato hybrid",
abstract = "Crossover formation during meiosis in plants is required for proper chromosome segregation and is essential for crop breeding as it allows an (optimal) combination of traits by mixing parental alleles on each chromosome. Crossover formation commences with the production of a large number of DNA double-strand breaks, of which only a few result in crossovers. A small number of genes, which drive the resolution of DNA crossover intermediate structures towards non-crossovers, have been identified in Arabidopisis thaliana. In order to explore the potential of modification of these genes in interspecific hybrids between crops and their wild relatives towards increased production of crossovers, we have used CRISPR/Cas9-mutagenesis in an interspecific tomato hybrid to knockout RecQ4. A biallelic recq4 mutant was obtained in the F1 hybrid of Solanum lycopersicum and S. pimpinellifolium. Compared with the wild-type F1 hybrid, the F1 recq4 mutant was shown to have a significant increase in crossovers: a 1.53-fold increase when directly observing ring bivalents in male meiocytes microscopically and a 1.8-fold extension of the genetic map when measured by analysing SNP markers in the progeny (F2) plants. This is one of the first demonstrations of increasing crossover frequency in interspecific hybrids by manipulating genes in crossover intermediate resolution pathways and the first to do so by directed mutagenesis. Significance statement: Increasing crossover frequency during meiosis can speed up or simplify crop breeding that relies on meiotic crossovers to introduce favourable alleles controlling important traits from wild relatives into crops. Here we show for the first time that knocking out an inhibitor of crossovers in an interspecific hybrid between tomato and its relative wild species using CRISPR/Cas9-mutagenesis results in increased recombination between the two genomes.",
keywords = "class II crossover pathway, interspecific crosses, introgression breeding, meiosis, RECQ4",
author = "{de Maagd}, {Ruud A.} and Annelies Loonen and Jihed Chouaref and Alexandre Pel{\'e} and Fien Meijer-Dekens and Paul Fransz and Yuling Bai",
year = "2019",
month = "9",
day = "4",
doi = "10.1111/pbi.13248",
language = "English",
volume = "18",
pages = "805--813",
journal = "Plant Biotechnology Journal",
issn = "1467-7644",
publisher = "Wiley",
number = "3",

}

CRISPR/Cas inactivation of RECQ4 increases homeologous crossovers in an interspecific tomato hybrid. / de Maagd, Ruud A.; Loonen, Annelies; Chouaref, Jihed; Pelé, Alexandre; Meijer-Dekens, Fien; Fransz, Paul; Bai, Yuling.

In: Plant Biotechnology Journal, Vol. 18, No. 3, 03.2020, p. 805-813.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - CRISPR/Cas inactivation of RECQ4 increases homeologous crossovers in an interspecific tomato hybrid

AU - de Maagd, Ruud A.

AU - Loonen, Annelies

AU - Chouaref, Jihed

AU - Pelé, Alexandre

AU - Meijer-Dekens, Fien

AU - Fransz, Paul

AU - Bai, Yuling

PY - 2019/9/4

Y1 - 2019/9/4

N2 - Crossover formation during meiosis in plants is required for proper chromosome segregation and is essential for crop breeding as it allows an (optimal) combination of traits by mixing parental alleles on each chromosome. Crossover formation commences with the production of a large number of DNA double-strand breaks, of which only a few result in crossovers. A small number of genes, which drive the resolution of DNA crossover intermediate structures towards non-crossovers, have been identified in Arabidopisis thaliana. In order to explore the potential of modification of these genes in interspecific hybrids between crops and their wild relatives towards increased production of crossovers, we have used CRISPR/Cas9-mutagenesis in an interspecific tomato hybrid to knockout RecQ4. A biallelic recq4 mutant was obtained in the F1 hybrid of Solanum lycopersicum and S. pimpinellifolium. Compared with the wild-type F1 hybrid, the F1 recq4 mutant was shown to have a significant increase in crossovers: a 1.53-fold increase when directly observing ring bivalents in male meiocytes microscopically and a 1.8-fold extension of the genetic map when measured by analysing SNP markers in the progeny (F2) plants. This is one of the first demonstrations of increasing crossover frequency in interspecific hybrids by manipulating genes in crossover intermediate resolution pathways and the first to do so by directed mutagenesis. Significance statement: Increasing crossover frequency during meiosis can speed up or simplify crop breeding that relies on meiotic crossovers to introduce favourable alleles controlling important traits from wild relatives into crops. Here we show for the first time that knocking out an inhibitor of crossovers in an interspecific hybrid between tomato and its relative wild species using CRISPR/Cas9-mutagenesis results in increased recombination between the two genomes.

AB - Crossover formation during meiosis in plants is required for proper chromosome segregation and is essential for crop breeding as it allows an (optimal) combination of traits by mixing parental alleles on each chromosome. Crossover formation commences with the production of a large number of DNA double-strand breaks, of which only a few result in crossovers. A small number of genes, which drive the resolution of DNA crossover intermediate structures towards non-crossovers, have been identified in Arabidopisis thaliana. In order to explore the potential of modification of these genes in interspecific hybrids between crops and their wild relatives towards increased production of crossovers, we have used CRISPR/Cas9-mutagenesis in an interspecific tomato hybrid to knockout RecQ4. A biallelic recq4 mutant was obtained in the F1 hybrid of Solanum lycopersicum and S. pimpinellifolium. Compared with the wild-type F1 hybrid, the F1 recq4 mutant was shown to have a significant increase in crossovers: a 1.53-fold increase when directly observing ring bivalents in male meiocytes microscopically and a 1.8-fold extension of the genetic map when measured by analysing SNP markers in the progeny (F2) plants. This is one of the first demonstrations of increasing crossover frequency in interspecific hybrids by manipulating genes in crossover intermediate resolution pathways and the first to do so by directed mutagenesis. Significance statement: Increasing crossover frequency during meiosis can speed up or simplify crop breeding that relies on meiotic crossovers to introduce favourable alleles controlling important traits from wild relatives into crops. Here we show for the first time that knocking out an inhibitor of crossovers in an interspecific hybrid between tomato and its relative wild species using CRISPR/Cas9-mutagenesis results in increased recombination between the two genomes.

KW - class II crossover pathway

KW - interspecific crosses

KW - introgression breeding

KW - meiosis

KW - RECQ4

U2 - 10.1111/pbi.13248

DO - 10.1111/pbi.13248

M3 - Article

VL - 18

SP - 805

EP - 813

JO - Plant Biotechnology Journal

JF - Plant Biotechnology Journal

SN - 1467-7644

IS - 3

ER -