Mol. Cells 2017; 40(11): 814-822
Published online November 23, 2017
https://doi.org/10.14348/molcells.2017.0171
© The Korean Society for Molecular and Cellular Biology
Correspondence to : *Correspondence: kyuha@postech.ac.kr
Meiotic homologous recombination generates new combinations of preexisting genetic variation and is a crucial process in plant breeding. Within the last decade, our understanding of plant meiotic recombination and genome diversity has advanced considerably. Innovation in DNA sequencing technology has led to the exploration of high-resolution genetic and epigenetic information in plant genomes, which has helped to accelerate plant breeding practices via high-throughput genotyping, and linkage and association mapping. In addition, great advances toward understanding the genetic and epigenetic control mechanisms of meiotic recombination have enabled the expansion of breeding programs and the unlocking of genetic diversity that can be used for crop improvement. This review highlights the recent literature on plant meiotic recombination and discusses the translation of this knowledge to the manipulation of meiotic recombination frequency and location with regards to crop plant breeding.
Keywords breeding, crossover, epigenetics, meiotic DSBs, meiotic recombination
Meiosis is a specialized cell division process that occurs in sexually-reproducing organisms in which a single round of DNA replication is followed by two successive rounds of chromosome segregation, resulting in gametes that have half the chromosome number (n) of their parental cells (2n). During fertilization, two gametes fuse together to restore the number of chromosomes in the resulting zygote to the same number that the parent cells had prior to meiosis (2n). During meiosis, programmed double-stranded breaks (DSBs) are formed by an evolutionally conserved SPO11 topoisomerase-like complex and are then repaired resulting in either reciprocal crossover, or non-crossovers by using a homologous template. By these processes, gametes are produced with recombined chromosomes (Hunter, 2015; Mercier et al., 2015; Villeneuve et al., 2001). Therefore, meiosis profoundly affects the genetic diversity of populations, and consequently adaptation potential, through meiotic recombination, independent chromosome segregation, and random fertilization (Barton and Charlesworth, 1998). This population genetic diversity also represents an important resource for selection of desirable traits in crop breeding (Bevan et al., 2017; Chaney et al., 2016).
Extensive genomic diversity has been revealed in plants by next-generation sequencing (NGS) technologies and computational analyses. Innovations in DNA sequencing and bioinformatics allow for the detection of genetic variations within plant populations that are used to recombine or map genomic locations of favorable traits by linkage and association mapping (Bevan et al., 2017; Chaney et al., 2016; Soyk et al., 2017). Genomics and computational approaches such as genotyping-by-sequencing and LDhat that is a package of estimating historical recombination by analyzing patterns of linkage disequilibrium (LD) in population have also contributed to the map of fine-scale meiotic crossovers in plant genomes (Choi et al., 2013; Hellsten et al., 2013; Wijnker et al., 2013). Like other eukaryotes, plant meiotic crossover frequency is not uniform along a chromosome, but instead occurs frequently within narrow regions of approximately 1–2 kb called recombination hotspots (Baudat et al., 2013; Choi and Henderson, 2015; Lichten and Goldman, 1995; Mercier et al., 2015). Fine-scale maps show that plant meiotic crossover hotspots occur near gene promoters and terminators in euchromatin while crossovers are suppressed in heterochromatic regions (Choi and Henderson, 2015; Lambing et al., 2017). Importantly, the suppression of crossover formation within heterochromatin is one of main bottlenecks in attempts to recombine favorable traits in the place of unfavorable traits in crop plants such as wheat and barley (Bevan et al., 2017; Choulet et al., 2014; Mayer et al., 2012; Tomato Genome Consortium, 2012). Notably, the heterochromatin of crop genomes is large, covering hundreds of mega base-pairs, and also contains functional genes (Bevan et al., 2017; Choulet et al., 2014; Mayer et al., 2012).
Despite the excessive DSBs that are made during the initiation of meiotic recombination, only one to three DSBs result in crossovers along chromosome after repair. The rest of the DSBs result in either repair by a sister chromatid, or non-crossovers through repair by a different repair pathway, such as synthesis-dependent strand annealing (SDSA) (Gray and Cohen, 2016; Hunter, 2015; Mercier et al., 2015). The limited number of crossovers per chromosome is relatively conserved among species with the exception of a few fungal species that generate more crossovers, although at least one crossover is required to ensure proper chromosomal segregation (Mercier et al., 2015). Enhancing the crossover frequency in both euchromatin and heterochromatin should help breeders acquire desirable traits or remove undesirable traits along chromosomes in crop plant genomes, as both the resolution of genetic mapping and the recombination of desirable trait variations are dependent on meiotic crossover rates and locations (Bevan et al., 2017).
This review describes the recent advances in understanding and control of plant meiotic recombination in Arabidopsis, including meiotic DSBs as well as the genetic and epigenetic factors that contribute to crossovers. This is followed by a discussion of the application of these advances to crop breeding using the CRISPR (clustered regularly interspace palindromic repeats) system.
In Arabidopsis, SPO11-1 and SPO11-2 are homologs of the archaeal DNA topoisomerase TOPOVI subunit A (TOPOVIA) that interact with MEIOTIC TOPOISOMERASE VIB-LIKE (MTOPVIB) to form a DNA topoisomerase VI-like heterotetrameric complex that catalyzes DSBs to initiate meiotic recombination (Fig. 1A) (Grelon et al., 2001; Hartung et al., 2007; Vrielynck et al., 2016). During DSB formation, the catalytically active tyrosine residue of SPO11 is covalently attached to 5′ end of the DNA by a phosphodiester bond. Subsequent endo- and exonuclease activities of the MRNS (MRE11, RAD50, NBS1/XRS2, SAE2/COM1) complex with EXOI process the 3′ region near the SPO11 attachment site, which releases SPO11 protein-oligonucleotide as a complex from the DNA (Fig. 1A) (Cannavo and Cejka, 2014; Choi et al., 2017; Garcia et al., 2011; Lam and Keeney, 2014; Neale et al., 2005; Pan et al., 2011). Accordingly, purified SPO11-associated oligonucleotides (~20–40 nucleotide) have been sequenced and used to generate high resolution genome-wide maps of meiotic recombination initiation sites in fungi and mice (Fowler et al., 2014; Lam and Keeney, 2014, 2015; Lange et al., 2016; Pan et al., 2011). The first plant meiotic DSB map was developed by sequencing Arabidopsis SPO11-1 oligonucleotides (30–50 nt) and revealed both conserved and plant-specific features compared with fungal and mammalian maps (Choi et al., 2017).
As in yeasts, meiotic DSB location and frequency in plants are mainly determined by nucleosome occupancy (Fig. 1B–1C) (Choi et al., 2017; Fowler et al., 2014; Pan et al., 2011). In mammals, the PRDM9 protein directs meiotic DSBs to specific DNA sequences (Baudat et al., 2013; Clément and de Massy, 2017; Lange et al., 2016). Since plants and yeasts do not have PRDM9, the nucleosome-depleted gene promoters are the highest DSB hotspots (Choi et al., 2017). Notably, plant gene terminators and introns are also DSB hotspots with low nucleosome occupancy (Fig. 1C), yet gene terminators are not DSB hotspots in yeast, even though they also have lower nucleosome occupancy (Choi et al., 2017; Pan et al., 2011). The DSB hotspots that were identified in Arabidopsis gene terminators are consistent with the occurrence of crossover hotspots in Arabidopsis and monkey flower plants (Choi et al., 2013; 2016; Hellsten et al., 2013; Wijnker et al., 2013). Bird genomes also display crossover hotspots in both gene promoters and terminators, implying that a similar pattern of recombination hotspots is present in plants and birds (Singhal et al., 2015).
Strikingly, Arabidopsis DSB hotspots occur within specific DNA transposon families (such as Helitron, Tc1/mariner, and pogo) that are nucleosome-depleted, while retrotransposons and nucleosome-occupied DNA transposons are DSB coldspots (Fig. 1C) (Choi et al., 2017). The specific DSB hotspot transposons are enriched in pericentromeres and gene regulatory regions of proximal promoters and introns, whereas DSB coldspot transposons are often found within centromeres. Each transposon family also displays a distinct distribution pattern across chromosomes (Choi et al., 2017; Underwood et al., 2017a). The DSB hotspot DNA transposons are significantly associated with plant immunity genes such as defensin and the NBS-LRR gene family. This association suggests that the DNA transposons may play a role in enhancing the recombination frequency of these genes during adaptation. Hence, the detection of meiotic DSB hotspot inside transposons upon sequencing Arabidopsis SPO11-1 oligonucleotides expands the concept of McClintock’s Controlling Elements from modifying transcription to meiotic recombination that contributes to genome diversity and evolution (Chuong et al., 2016; McClintock, 1956; Slotkin and Martienssen, 2007). Compared with current meiotic DSB maps in other species, the SPO11-1-oligonucletide maps in Arabidopsis show the strongest quantitative correlations between levels of meiotic DSBs, nucleosome occupancy, and AT sequence richness that excludes nucleosomes in both gene regulatory regions and DNA transposon hotspots (Choi et al., 2017). In addition, the meiotic DSB coldspots in transposons, pericentromeres, and centromeres are associated with heterochromatin marks of DNA methylation and H3K9 dimethylation (me2) (Choi et al., 2017; Underwood et al., 2017b). The inhibition of DSB formation in centromeres is required to limit meiotic, non-allelic, homologous recombination-induced genome instability (Sasaki et al., 2010). Decreased levels of DNA cytosine methylation or H3K9me2 lead to an increase in the number of meiotic DSBs in the heterochromatic regions including centromeres with reduced nucleosome occupancy. This finding demonstrates a crucial role for these epigenetic marks in suppressing meiotic DSB formation on a genomic scale (Choi et al., 2017; Underwood et al., 2017b).
Following the dissociation of SPO11-oligonucletide complexes and 5′ to 3′ single-strand resection, DMC1 recombinase and its cofactor RAD51 lead the invasion of the homologous duplex with the 3′ end of single-stranded DNA (ssDNA), producing a recombination intermediate molecule (Fig. 1A) (Cloud et al., 2012; Da Ines et al., 2013; Gray and Cohen, 2016; Mercier et al., 2015). Two main DNA repair pathways - class I and class II - process these recombination intermediates to generate the limited number of crossovers (Fig. 2A). In the class I interfering pathway, ZMM (ZIP1, MSH4, MSH5 and MER3) proteins stabilize the recombination intermediate molecules and contribute to most crossovers (85–90%) via MLH1/MLH3. In the class II non-interfering pathway, 10–15% of crossovers rely on MUS81 (Fig. 2A) (Lambing et al., 2017; Mercier et al., 2015). In Arabidopsis,
Firstly, FANCONI ANEMIA COMPLEMENTATION GROUP M (FANCM) helicase and its cofactors limit crossover formation (Crismani et al., 2012; Girard et al., 2014). The
Secondly, the RECQ4A and RECQ4B proteins in Arabidopsis are two redundant orthologs of BLM/Sgs1 helicase that form a complex with TOP3α and RMI1 that has the strongest anti-crossover activity observed so far (Séguéla-Arnaud et al., 2015; 2017). Arabidopsis
Besides the genetic disruptions of anti-crossover genes for enhancing crossovers, the natural variations in meiotic crossover-promoting factor genes such as RNF212, PRDM9 and HEI10, also contribute to regulating crossover frequency and distribution (Kong et al., 2008; Sandor et al., 2012; Ziolkowski et al., 2017). In Arabidopsis, recombination quantitative trait loci (rQTL) mapping between Col-0 and Ler-0 accessions shows that one of two genetic variations of transacting modifiers maps to the
Although genetic disruption of the anti-crossover genes and adding extra copies of the HEI10 gene result in the formation of more crossovers in gene-rich chromosome arms, crossovers in the pericentromeres and centromeres remain suppressed in Arabidopsis (Fig. 1B) (Fernandes et al., 2017b; Serra et al., 2017). The heterochromatic features DNA cytosine methylation, H3K9me2, H2A.W, and transposons are highly enriched in the pericentromeres and centromeres (Lippman et al., 2004; Lister et al., 2008; Stroud et al., 2013; Yelagandula et al., 2014). DNA demethylation was expected to increase crossovers in the heterochromatic regions; however, the loss of DNA CG methylation maintenance by mutation of
The dependence of plant crop breeding on meiotic crossover frequency and crossover distribution can delay breeding time and restrict both combination and genetic mapping of desirable traits. To accelerate crop breeding and unlock genetic diversity, we can use the CRISPR system as a precise genome editing tool to manipulate the genomes of higher eukaryotes and control of meiotic recombination (Doudna and Charpentier, 2014; Hsu et al., 2014; Kim, 2016; Puchta, 2017). CRISPR approaches represent DNA-free gene editing tools that can be applied directly to the genomes of elite crop cultivars to implement genetic variations that are known to contribute to desirable traits, such as productivity and herbicide resistance (Kim, 2016; Puchta, 2017; Soyk et al., 2017; Wolter and Puchta, 2017; Yin et al., 2017). In addition, CRISPR or RNAi systems can be used to mutate or knock-down the genes encoding anti-crossover and epigenetic factors simultaneously, which may lead to an increase in crossover frequency in both euchromatin and heterochromatin (Tables 1 and 2; Fig. 2B). The DNA mismatch repair protein MSH2 represents an additional target for disruption using these systems, as mutation of the
Meiotic recombination has a profound effect on genetic diversity, which is crucial for both the adaption of plants to their environment and the improvement of crop traits of agricultural value. CRISPR tools can now be used to precisely edit the genomes of elite cultivars. However, the natural variation in the wild relatives of crop plants, landraces, and diverse cultivars also provide a valuable resource for crop improvement, as does genetic variation by chemical and radiation-driven mutagenesis. The discovery of anti-crossover and epigenetic factor genes that affect meiotic crossover in Arabidopsis will add new branches to crop breeding programs that aim to create new combinations of favorable traits and unlock unexplored genetic diversity. To further understand the mechanism of crossover formation in plants, the meiotic factors that control DSB formation and act in the ZMM pathway that limits crossovers must be elucidated. In addition to the first plant SPO11-1 oligonucleotide maps, genomic profiling of meiotic proteins will provide insights into how meiotic recombination is controlled, and how it can be induced at specific sites in plant genomes.
Arabidopsis genes involved in meiotic crossover frequency and location
Complex/Pathway | Gene | AT number | Increased fold CO rate in mutant or transgene | Reference | ||
---|---|---|---|---|---|---|
Inbred context | Hybrid context | |||||
FANCM helicase | AT1G35530 | yes | 3 | 1 | Crismani et al., 2012; Fernandes et al., 2017b | |
AT5G50930 | yes | 1.5–2 | n.d | Girard et al., 2014 | ||
AT1G78790 | yes | 1.5–2 | n.d | Girard et al., 2014 | ||
RTR complex | AT1G10930 | yes | 6 | 5 | Fernandes et al., 2017b | |
AT1G60930 | ||||||
AT5G63920 | yes | 3 | n.d | Séguéla-Arnaud et al., 2015 | ||
AT5G63540 | yes | 3 | n.d | Séguéla-Arnaud et al., 2017 | ||
FIGL1 helicase | AT3G27120 | yes | 2 | 2 | Girard et al., 2015 | |
AT1G04650 | yes | 1.2 | n.d | Fernandes et al., 2017a | ||
Class I CO pathway | AT1G53490 | no | 2 | 2 | Serra et al., 2017; Ziolkowski et al., 2017 | |
non-CG methylation | AT1G69770 | no | * | * | Underwood et al., 2017b | |
H3K9me2 | AT5G13960 | no | * | n.d. | Underwood et al., 2017b | |
AT2G35160 | no | |||||
AT2G22740 | no | |||||
Anti-crossover | AT3G18524 | no | n.d | 1.4 | Emmanuel et al., 2006 |
n.d. indicates that crossover rate is not determined.
Star (*) indicates that crossover frequency is increased in pericentromeric regions.
Crop plant orthologous genes to
Arabidopsis gene | Plant species | Locus |
---|---|---|
Rice | LOC9271031 | |
Wheat | AK331006 | |
Maize | LOC100193153 | |
Tomato | LOC101262887 | |
Soybean | LOC100789161, LOC100776024 | |
Rice | LOC_Os11g48090(A), LOC_Os04g35420(B) | |
Wheat | AK334643 | |
Maize | LOC100274706 | |
Tomato | LOC101260976 | |
Soybean | LOC100800006, LOC100817867 | |
Rice | OsCMT3a(LOC_Os10g01570), OsCMT3b(LOC_Os03g12570) | |
Wheat | AK332918 | |
Maize | Zmet2(GQ923937) | |
Tomato | LOC101265056, LOC101267211 | |
Soybean | LOC100799480 |
Mol. Cells 2017; 40(11): 814-822
Published online November 30, 2017 https://doi.org/10.14348/molcells.2017.0171
Copyright © The Korean Society for Molecular and Cellular Biology.
Kyuha Choi*
Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
Correspondence to:*Correspondence: kyuha@postech.ac.kr
Meiotic homologous recombination generates new combinations of preexisting genetic variation and is a crucial process in plant breeding. Within the last decade, our understanding of plant meiotic recombination and genome diversity has advanced considerably. Innovation in DNA sequencing technology has led to the exploration of high-resolution genetic and epigenetic information in plant genomes, which has helped to accelerate plant breeding practices via high-throughput genotyping, and linkage and association mapping. In addition, great advances toward understanding the genetic and epigenetic control mechanisms of meiotic recombination have enabled the expansion of breeding programs and the unlocking of genetic diversity that can be used for crop improvement. This review highlights the recent literature on plant meiotic recombination and discusses the translation of this knowledge to the manipulation of meiotic recombination frequency and location with regards to crop plant breeding.
Keywords: breeding, crossover, epigenetics, meiotic DSBs, meiotic recombination
Meiosis is a specialized cell division process that occurs in sexually-reproducing organisms in which a single round of DNA replication is followed by two successive rounds of chromosome segregation, resulting in gametes that have half the chromosome number (n) of their parental cells (2n). During fertilization, two gametes fuse together to restore the number of chromosomes in the resulting zygote to the same number that the parent cells had prior to meiosis (2n). During meiosis, programmed double-stranded breaks (DSBs) are formed by an evolutionally conserved SPO11 topoisomerase-like complex and are then repaired resulting in either reciprocal crossover, or non-crossovers by using a homologous template. By these processes, gametes are produced with recombined chromosomes (Hunter, 2015; Mercier et al., 2015; Villeneuve et al., 2001). Therefore, meiosis profoundly affects the genetic diversity of populations, and consequently adaptation potential, through meiotic recombination, independent chromosome segregation, and random fertilization (Barton and Charlesworth, 1998). This population genetic diversity also represents an important resource for selection of desirable traits in crop breeding (Bevan et al., 2017; Chaney et al., 2016).
Extensive genomic diversity has been revealed in plants by next-generation sequencing (NGS) technologies and computational analyses. Innovations in DNA sequencing and bioinformatics allow for the detection of genetic variations within plant populations that are used to recombine or map genomic locations of favorable traits by linkage and association mapping (Bevan et al., 2017; Chaney et al., 2016; Soyk et al., 2017). Genomics and computational approaches such as genotyping-by-sequencing and LDhat that is a package of estimating historical recombination by analyzing patterns of linkage disequilibrium (LD) in population have also contributed to the map of fine-scale meiotic crossovers in plant genomes (Choi et al., 2013; Hellsten et al., 2013; Wijnker et al., 2013). Like other eukaryotes, plant meiotic crossover frequency is not uniform along a chromosome, but instead occurs frequently within narrow regions of approximately 1–2 kb called recombination hotspots (Baudat et al., 2013; Choi and Henderson, 2015; Lichten and Goldman, 1995; Mercier et al., 2015). Fine-scale maps show that plant meiotic crossover hotspots occur near gene promoters and terminators in euchromatin while crossovers are suppressed in heterochromatic regions (Choi and Henderson, 2015; Lambing et al., 2017). Importantly, the suppression of crossover formation within heterochromatin is one of main bottlenecks in attempts to recombine favorable traits in the place of unfavorable traits in crop plants such as wheat and barley (Bevan et al., 2017; Choulet et al., 2014; Mayer et al., 2012; Tomato Genome Consortium, 2012). Notably, the heterochromatin of crop genomes is large, covering hundreds of mega base-pairs, and also contains functional genes (Bevan et al., 2017; Choulet et al., 2014; Mayer et al., 2012).
Despite the excessive DSBs that are made during the initiation of meiotic recombination, only one to three DSBs result in crossovers along chromosome after repair. The rest of the DSBs result in either repair by a sister chromatid, or non-crossovers through repair by a different repair pathway, such as synthesis-dependent strand annealing (SDSA) (Gray and Cohen, 2016; Hunter, 2015; Mercier et al., 2015). The limited number of crossovers per chromosome is relatively conserved among species with the exception of a few fungal species that generate more crossovers, although at least one crossover is required to ensure proper chromosomal segregation (Mercier et al., 2015). Enhancing the crossover frequency in both euchromatin and heterochromatin should help breeders acquire desirable traits or remove undesirable traits along chromosomes in crop plant genomes, as both the resolution of genetic mapping and the recombination of desirable trait variations are dependent on meiotic crossover rates and locations (Bevan et al., 2017).
This review describes the recent advances in understanding and control of plant meiotic recombination in Arabidopsis, including meiotic DSBs as well as the genetic and epigenetic factors that contribute to crossovers. This is followed by a discussion of the application of these advances to crop breeding using the CRISPR (clustered regularly interspace palindromic repeats) system.
In Arabidopsis, SPO11-1 and SPO11-2 are homologs of the archaeal DNA topoisomerase TOPOVI subunit A (TOPOVIA) that interact with MEIOTIC TOPOISOMERASE VIB-LIKE (MTOPVIB) to form a DNA topoisomerase VI-like heterotetrameric complex that catalyzes DSBs to initiate meiotic recombination (Fig. 1A) (Grelon et al., 2001; Hartung et al., 2007; Vrielynck et al., 2016). During DSB formation, the catalytically active tyrosine residue of SPO11 is covalently attached to 5′ end of the DNA by a phosphodiester bond. Subsequent endo- and exonuclease activities of the MRNS (MRE11, RAD50, NBS1/XRS2, SAE2/COM1) complex with EXOI process the 3′ region near the SPO11 attachment site, which releases SPO11 protein-oligonucleotide as a complex from the DNA (Fig. 1A) (Cannavo and Cejka, 2014; Choi et al., 2017; Garcia et al., 2011; Lam and Keeney, 2014; Neale et al., 2005; Pan et al., 2011). Accordingly, purified SPO11-associated oligonucleotides (~20–40 nucleotide) have been sequenced and used to generate high resolution genome-wide maps of meiotic recombination initiation sites in fungi and mice (Fowler et al., 2014; Lam and Keeney, 2014, 2015; Lange et al., 2016; Pan et al., 2011). The first plant meiotic DSB map was developed by sequencing Arabidopsis SPO11-1 oligonucleotides (30–50 nt) and revealed both conserved and plant-specific features compared with fungal and mammalian maps (Choi et al., 2017).
As in yeasts, meiotic DSB location and frequency in plants are mainly determined by nucleosome occupancy (Fig. 1B–1C) (Choi et al., 2017; Fowler et al., 2014; Pan et al., 2011). In mammals, the PRDM9 protein directs meiotic DSBs to specific DNA sequences (Baudat et al., 2013; Clément and de Massy, 2017; Lange et al., 2016). Since plants and yeasts do not have PRDM9, the nucleosome-depleted gene promoters are the highest DSB hotspots (Choi et al., 2017). Notably, plant gene terminators and introns are also DSB hotspots with low nucleosome occupancy (Fig. 1C), yet gene terminators are not DSB hotspots in yeast, even though they also have lower nucleosome occupancy (Choi et al., 2017; Pan et al., 2011). The DSB hotspots that were identified in Arabidopsis gene terminators are consistent with the occurrence of crossover hotspots in Arabidopsis and monkey flower plants (Choi et al., 2013; 2016; Hellsten et al., 2013; Wijnker et al., 2013). Bird genomes also display crossover hotspots in both gene promoters and terminators, implying that a similar pattern of recombination hotspots is present in plants and birds (Singhal et al., 2015).
Strikingly, Arabidopsis DSB hotspots occur within specific DNA transposon families (such as Helitron, Tc1/mariner, and pogo) that are nucleosome-depleted, while retrotransposons and nucleosome-occupied DNA transposons are DSB coldspots (Fig. 1C) (Choi et al., 2017). The specific DSB hotspot transposons are enriched in pericentromeres and gene regulatory regions of proximal promoters and introns, whereas DSB coldspot transposons are often found within centromeres. Each transposon family also displays a distinct distribution pattern across chromosomes (Choi et al., 2017; Underwood et al., 2017a). The DSB hotspot DNA transposons are significantly associated with plant immunity genes such as defensin and the NBS-LRR gene family. This association suggests that the DNA transposons may play a role in enhancing the recombination frequency of these genes during adaptation. Hence, the detection of meiotic DSB hotspot inside transposons upon sequencing Arabidopsis SPO11-1 oligonucleotides expands the concept of McClintock’s Controlling Elements from modifying transcription to meiotic recombination that contributes to genome diversity and evolution (Chuong et al., 2016; McClintock, 1956; Slotkin and Martienssen, 2007). Compared with current meiotic DSB maps in other species, the SPO11-1-oligonucletide maps in Arabidopsis show the strongest quantitative correlations between levels of meiotic DSBs, nucleosome occupancy, and AT sequence richness that excludes nucleosomes in both gene regulatory regions and DNA transposon hotspots (Choi et al., 2017). In addition, the meiotic DSB coldspots in transposons, pericentromeres, and centromeres are associated with heterochromatin marks of DNA methylation and H3K9 dimethylation (me2) (Choi et al., 2017; Underwood et al., 2017b). The inhibition of DSB formation in centromeres is required to limit meiotic, non-allelic, homologous recombination-induced genome instability (Sasaki et al., 2010). Decreased levels of DNA cytosine methylation or H3K9me2 lead to an increase in the number of meiotic DSBs in the heterochromatic regions including centromeres with reduced nucleosome occupancy. This finding demonstrates a crucial role for these epigenetic marks in suppressing meiotic DSB formation on a genomic scale (Choi et al., 2017; Underwood et al., 2017b).
Following the dissociation of SPO11-oligonucletide complexes and 5′ to 3′ single-strand resection, DMC1 recombinase and its cofactor RAD51 lead the invasion of the homologous duplex with the 3′ end of single-stranded DNA (ssDNA), producing a recombination intermediate molecule (Fig. 1A) (Cloud et al., 2012; Da Ines et al., 2013; Gray and Cohen, 2016; Mercier et al., 2015). Two main DNA repair pathways - class I and class II - process these recombination intermediates to generate the limited number of crossovers (Fig. 2A). In the class I interfering pathway, ZMM (ZIP1, MSH4, MSH5 and MER3) proteins stabilize the recombination intermediate molecules and contribute to most crossovers (85–90%) via MLH1/MLH3. In the class II non-interfering pathway, 10–15% of crossovers rely on MUS81 (Fig. 2A) (Lambing et al., 2017; Mercier et al., 2015). In Arabidopsis,
Firstly, FANCONI ANEMIA COMPLEMENTATION GROUP M (FANCM) helicase and its cofactors limit crossover formation (Crismani et al., 2012; Girard et al., 2014). The
Secondly, the RECQ4A and RECQ4B proteins in Arabidopsis are two redundant orthologs of BLM/Sgs1 helicase that form a complex with TOP3α and RMI1 that has the strongest anti-crossover activity observed so far (Séguéla-Arnaud et al., 2015; 2017). Arabidopsis
Besides the genetic disruptions of anti-crossover genes for enhancing crossovers, the natural variations in meiotic crossover-promoting factor genes such as RNF212, PRDM9 and HEI10, also contribute to regulating crossover frequency and distribution (Kong et al., 2008; Sandor et al., 2012; Ziolkowski et al., 2017). In Arabidopsis, recombination quantitative trait loci (rQTL) mapping between Col-0 and Ler-0 accessions shows that one of two genetic variations of transacting modifiers maps to the
Although genetic disruption of the anti-crossover genes and adding extra copies of the HEI10 gene result in the formation of more crossovers in gene-rich chromosome arms, crossovers in the pericentromeres and centromeres remain suppressed in Arabidopsis (Fig. 1B) (Fernandes et al., 2017b; Serra et al., 2017). The heterochromatic features DNA cytosine methylation, H3K9me2, H2A.W, and transposons are highly enriched in the pericentromeres and centromeres (Lippman et al., 2004; Lister et al., 2008; Stroud et al., 2013; Yelagandula et al., 2014). DNA demethylation was expected to increase crossovers in the heterochromatic regions; however, the loss of DNA CG methylation maintenance by mutation of
The dependence of plant crop breeding on meiotic crossover frequency and crossover distribution can delay breeding time and restrict both combination and genetic mapping of desirable traits. To accelerate crop breeding and unlock genetic diversity, we can use the CRISPR system as a precise genome editing tool to manipulate the genomes of higher eukaryotes and control of meiotic recombination (Doudna and Charpentier, 2014; Hsu et al., 2014; Kim, 2016; Puchta, 2017). CRISPR approaches represent DNA-free gene editing tools that can be applied directly to the genomes of elite crop cultivars to implement genetic variations that are known to contribute to desirable traits, such as productivity and herbicide resistance (Kim, 2016; Puchta, 2017; Soyk et al., 2017; Wolter and Puchta, 2017; Yin et al., 2017). In addition, CRISPR or RNAi systems can be used to mutate or knock-down the genes encoding anti-crossover and epigenetic factors simultaneously, which may lead to an increase in crossover frequency in both euchromatin and heterochromatin (Tables 1 and 2; Fig. 2B). The DNA mismatch repair protein MSH2 represents an additional target for disruption using these systems, as mutation of the
Meiotic recombination has a profound effect on genetic diversity, which is crucial for both the adaption of plants to their environment and the improvement of crop traits of agricultural value. CRISPR tools can now be used to precisely edit the genomes of elite cultivars. However, the natural variation in the wild relatives of crop plants, landraces, and diverse cultivars also provide a valuable resource for crop improvement, as does genetic variation by chemical and radiation-driven mutagenesis. The discovery of anti-crossover and epigenetic factor genes that affect meiotic crossover in Arabidopsis will add new branches to crop breeding programs that aim to create new combinations of favorable traits and unlock unexplored genetic diversity. To further understand the mechanism of crossover formation in plants, the meiotic factors that control DSB formation and act in the ZMM pathway that limits crossovers must be elucidated. In addition to the first plant SPO11-1 oligonucleotide maps, genomic profiling of meiotic proteins will provide insights into how meiotic recombination is controlled, and how it can be induced at specific sites in plant genomes.
. Arabidopsis genes involved in meiotic crossover frequency and location.
Complex/Pathway | Gene | AT number | Increased fold CO rate in mutant or transgene | Reference | ||
---|---|---|---|---|---|---|
Inbred context | Hybrid context | |||||
FANCM helicase | AT1G35530 | yes | 3 | 1 | Crismani et al., 2012; Fernandes et al., 2017b | |
AT5G50930 | yes | 1.5–2 | n.d | Girard et al., 2014 | ||
AT1G78790 | yes | 1.5–2 | n.d | Girard et al., 2014 | ||
RTR complex | AT1G10930 | yes | 6 | 5 | Fernandes et al., 2017b | |
AT1G60930 | ||||||
AT5G63920 | yes | 3 | n.d | Séguéla-Arnaud et al., 2015 | ||
AT5G63540 | yes | 3 | n.d | Séguéla-Arnaud et al., 2017 | ||
FIGL1 helicase | AT3G27120 | yes | 2 | 2 | Girard et al., 2015 | |
AT1G04650 | yes | 1.2 | n.d | Fernandes et al., 2017a | ||
Class I CO pathway | AT1G53490 | no | 2 | 2 | Serra et al., 2017; Ziolkowski et al., 2017 | |
non-CG methylation | AT1G69770 | no | * | * | Underwood et al., 2017b | |
H3K9me2 | AT5G13960 | no | * | n.d. | Underwood et al., 2017b | |
AT2G35160 | no | |||||
AT2G22740 | no | |||||
Anti-crossover | AT3G18524 | no | n.d | 1.4 | Emmanuel et al., 2006 |
n.d. indicates that crossover rate is not determined..
Star (*) indicates that crossover frequency is increased in pericentromeric regions..
. Crop plant orthologous genes to
Arabidopsis gene | Plant species | Locus |
---|---|---|
Rice | LOC9271031 | |
Wheat | AK331006 | |
Maize | LOC100193153 | |
Tomato | LOC101262887 | |
Soybean | LOC100789161, LOC100776024 | |
Rice | LOC_Os11g48090(A), LOC_Os04g35420(B) | |
Wheat | AK334643 | |
Maize | LOC100274706 | |
Tomato | LOC101260976 | |
Soybean | LOC100800006, LOC100817867 | |
Rice | OsCMT3a(LOC_Os10g01570), OsCMT3b(LOC_Os03g12570) | |
Wheat | AK332918 | |
Maize | Zmet2(GQ923937) | |
Tomato | LOC101265056, LOC101267211 | |
Soybean | LOC100799480 |
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