A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis

Cl, Wijnen; Botet, R; J, van de Belt; Deurhof, Laurens; H, de Jong; Snoo, de; Dirks, R.; Boer, Martin P.; Fa, van Eeuwijk; Wijnker, Erik; Jj, Keurentjes

doi:10.1101/436154

Cited by 8 publications

(9 citation statements)

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“…The use of reverse breeding offspring has further advantages. DH0s are also CSLs, a type of mapping population useful to dissect epistasis (Nadeau et al, 2000;Spiezio et al, 2012;Ziolkowski et al, 2017;Wijnen et al, 2018). CSLs can also be used as donor lines for single or entire sets of R genes; crossing CSLs to an existing breeding line allows the sequential introduction of desirable R genes into that background (Figure 4B).…”

Section: Reverse Breeding Application To Hybrid Necrosis and Heterosismentioning

confidence: 99%

Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances

2021

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Hybridization is a core element in modern rice breeding as beneficial combinations of two parental genomes often result in the expression of heterosis. On the contrary, genetic incompatibility between parents can manifest as hybrid necrosis, which leads to tissue necrosis accompanied by compromised growth and/or reduced reproductive success. Genetic and molecular studies of hybrid necrosis in numerous plant species revealed that such self-destructing symptoms in most cases are attributed to autoimmunity: plant immune responses are inadvertently activated in the absence of pathogenic invasion. Autoimmunity in hybrids predominantly occurs due to a conflict involving a member of the major plant immune receptor family, the nucleotide-binding domain and leucine-rich repeat containing protein (NLR; formerly known as NBS-LRR). NLR genes are associated with disease resistance traits, and recent population datasets reveal tremendous diversity in this class of immune receptors. Cases of hybrid necrosis involving highly polymorphic NLRs as major causes suggest that diversified R gene repertoires found in different lineages would require a compatible immune match for hybridization, which is a prerequisite to ensure increased fitness in the resulting hybrids. In this review, we overview recent genetic and molecular findings on hybrid necrosis in multiple plant species to provide an insight on how the trade-off between growth and immunity is equilibrated to affect hybrid performances. We also revisit the cases of hybrid weakness in which immune system components are found or implicated to play a causative role. Based on our understanding on the trade-off, we propose that the immune system incompatibility in plants might play an opposite force to restrict the expression of heterosis in hybrids. The antagonism is illustrated under the plant fitness equilibrium, in which the two extremes lead to either hybrid necrosis or heterosis. Practical proposition from the equilibrium model is that breeding efforts for combining enhanced disease resistance and high yield shall be achieved by balancing the two forces. Reverse breeding toward utilizing genomic data centered on immune components is proposed as a strategy to generate elite hybrids with balanced immunity and growth.

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Section: Reverse Breeding Application To Hybrid Necrosis and Heterosismentioning

confidence: 99%

Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances

2021

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“…Fuelled by the description of a variety of meiotic mutants in plants, interest has grown for exploring the use of mutant meiotic phenotypes for improving plant breeding strategies (Wijnker and de Jong, 2008;D'Erfurth et al, 2009;Dirks et al, 2009;Wijnker et al, 2012;Mieulet et al, 2016Mieulet et al, , 2018Lambing et al, 2017;Blary et al, 2018;Wang et al, 2019). For example, mutations causing the increase or decrease of recombination can be used to generate mapping populations that consist of either high-recombinant or low-recombinant offspring (Dirks et al, 2009;Crismani et al, 2012;Wijnker et al, 2012Wijnker et al, , 2014S egu ela-Arnaud et al, 2017;Fernandes et al, 2018;Mieulet et al, 2018;Wijnen et al, 2018). As mutations that alter meiotic recombination rates can adversely affect fertility (i.e.…”

Section: Introductionmentioning

confidence: 99%

“…CSLs are outstanding tools for mapping quantitative trait loci (QTLs) in mice and Arabidopsis thaliana, where they have been used to map recombination modifiers (Nadeau et al, 2000;Singer et al, 2004;Spiezio et al, 2012;Ziolkowski et al, 2017). In addition, the generation of a complete CSL population in A. thaliana allowed the systematic detection of two-way and three-way epistatic (non-additive) interactions for different traits (Wijnen et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…Such haploid gametes can be used in backcrosses or can be grown directly into haploid offspring that carry different chromosome combinations of the parental lines. Haploid plants that are derived from gametes carrying non-recombinant chromosomes can then give rise to diploid homozygous lines, known as doubled haploids (DHs), which are also CSLs ( Figure 1a) (Dirks et al, 2009;Wijnker et al, 2012;Wijnen et al, 2018). Direct CO suppression in a hybrid coupled with DH technology can deliver CSLs in just two generations ( Figure 1a).…”

Section: Introductionmentioning

confidence: 99%

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Meiotic crossover reduction by virus‐induced gene silencing enables the efficient generation of chromosome substitution lines and reverse breeding in Arabidopsis thaliana

et al. 2020

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Significance Statement Changing meiotic recombination rates can support plant research and breeding, but is rarely achieved in a transient way (i.e. where offspring fertility is not compromised). Here we show that virus‐induced gene silencing (VIGS) can be used to temporarily downregulate crossover recombination in Arabidopsis thaliana hybrids to facilitate the generation of chromosome substitution lines, reverse breeding and reverse breeding‐like applications.

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“…Due to the low number of segregating loci (chromosomes), such populations are near unparalleled tools to identify QTL and map complex epistatic interactions(Wijnen et al., submitted) 13 . Since in mixed DH 0 /DH 1 populations the number of segregating loci remains near minimal, the detection power of QTLs and epistasis is unlikely to decrease much.…”

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Efficient reverse breeding by VIGS-mediated transient crossover reduction

Calvo‐Baltanás

Wijnen

Lukhovitskaya

et al. 2018

Preprint

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F1 heterozygotes are traditionally generated by crossing homozygous parental lines. The opposite is achieved through reverse breeding, in which parental lines are generated from a heterozygote. Reverse breeding can be used to develop new F1 hybrid varieties without having prior access to homozygous breeding lines. For successful reverse breeding, the heterozygotes’ homologous chromosomes must be divided over two haploid complements, which is achieved by suppression of meiotic crossover (CO) recombination. We here show two innovations that facilitate efficient reverse breeding. Firstly, we demonstrate that downregulation of CO rates can be accomplished using virus-induced gene silencing (VIGS). We obtain transgene-free parental lines for a heterozygote in just two generations. Secondly, we show that incomplete CO suppression opens up several alternative strategies for the preservation of hybrid phenotypes through reverse breeding.

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A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis

Abstract: One sentence summary:Development of a complete panel of chromosome substitution lines enables high power mapping of epistatic interactions in Arabidopsis thaliana.

Cited by 8 publications

References 28 publications

Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances

Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances

Meiotic crossover reduction by virus‐induced gene silencing enables the efficient generation of chromosome substitution lines and reverse breeding in Arabidopsis thaliana

Efficient reverse breeding by VIGS-mediated transient crossover reduction

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