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Meiotic crossovers are tightly restricted in most eukaryotes, despite an excess of initiating DNA double-strand breaks. The majority of plant crossovers are dependent on class I interfering repair, with a minority formed via the class II pathway. Class II repair is limited by anti-recombination pathways; however, similar pathways repressing class I crossovers have not been identified. Here, we performed a forward genetic screen in Arabidopsis using fluorescent crossover reporters to identify mutants with increased or decreased recombination frequency. We identified HIGH CROSSOVER RATE1 (HCR1) as repressing crossovers and encoding PROTEIN PHOSPHATASE X1. Genome-wide analysis showed that hcr1 crossovers are increased in the distal chromosome arms. MLH1 foci significantly increase in hcr1 and crossover interference decreases, demonstrating an effect on class I repair. Consistently, yeast two-hybrid and in planta assays show interaction between HCR1 and class I proteins, including HEI10, PTD, MSH5 and MLH1. We propose that HCR1 plays a major role in opposition to pro-recombination kinases to restrict crossovers in Arabidopsis.

Meiosis recombines genetic variation and influences eukaryote genome evolution. During meiosis, DNA double-strand breaks (DSBs) enter interhomolog repair to yield crossovers and noncrossovers. DSB repair occurs as replicated sister chromatids are connected to a polymerized axis. Cohesin rings containing the REC8 kleisin subunit bind sister chromatids and anchor chromosomes to the axis. Here, we report the genomic landscape of REC8 using chromatin immunoprecipitation sequencing (ChIP-seq) in Arabidopsis (Arabidopsis thaliana). REC8 associates with regions of high nucleosome occupancy in multiple chromatin states, including histone methylation at H3K4 (expressed genes), H3K27 (silent genes), and H3K9 (silent transposons). REC8 enrichment is associated with suppression of meiotic DSBs and crossovers at the chromosome and fine scales. As REC8 enrichment is greatest in transposon-dense heterochromatin, we repeated ChIP-seq in kyp suvh5 suvh6 H3K9me2 mutants. Surprisingly, REC8 enrichment is maintained in kyp suvh5 suvh6 heterochromatin and no defects in centromeric cohesion were observed. REC8 occupancy within genes anti-correlates with transcription and is reduced in COPIA transposons that reactivate expression in kyp suvh5 suvh6. Abnormal axis structures form in rec8 that recruit DSB-associated protein foci and undergo synapsis, which is followed by chromosome fragmentation. Therefore, REC8 occupancy correlates with multiple chromatin states and is required to organize meiotic chromosome architecture and interhomolog recombination.

Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).

This research establishes molecular breeding capability for adapting common bean (Phaseolus vulgaris L.) to UK growing conditions. A high-resolution linkage map was constructed for a bi-parental recombinant inbred population (large brown x small white haricot) using genotyping-by-sequencing data. Pre-breeding material was exploited to enable genetic mapping and marker-assisted selection of essential adaptive traits, including (1) resistance to halo blight, caused by Pseudomonas syringae pathovar phaseolicola (Psph), (2) root architecture related to abiotic stress tolerance and nutrient acquisition, (3) earliness of maturity, (4) plant architecture amenable to mechanical harvest, and (5) seed coat colour of consumer interest.\ud \ud A 500-kb mapping interval was defined for quantitative resistance to the broadly virulent Psph race 6, a devastating bacterial pathogen that threatens global bean production with losses from halo blight. Complementary research generating high-quality draft genomes for 32 pathogenically and geographically diverse isolates of Psph identified five high-probability candidate determinants of the broad virulence of Psph race 6, including avirulence protein AvrD. Pathogenicity effectors that are highly conserved within the pathovar were identified as candidate targets for potential race-nonspecific resistance to halo blight.\ud \ud Putative QTL for root architecture traits associated with water and nutrient acquisition were detected on chromosome Pv07. A useful breeding strategy may be to select for larger taproot diameter in view of the comparatively high heritability of this trait. Potentially desirable alleles on Pv07 are linked in coupling phase with the dominant allele of seed coat pigmentation factor P. Identification of lines recombinant for these alleles may prove useful for the introgression of genes governing physiological resilience into white-seeded varieties adapted to UK growing conditions. Provisional QTL for morphological and reproductive traits of agronomic importance, including plant architecture, growth stage and yield, were identified using phenotypic data obtained from pilot field and polytunnel evaluations of the recombinant inbred population.

Significance Meiosis is fundamental to eukaryotic reproduction and shapes patterns of genetic variation. Meiotic recombination is also a vital tool during crop improvement, which allows introgression of wild variation into agricultural strains. Despite this, the levels and distributions of crossovers along chromosomes can limit breeding. For example, many crops show highly skewed crossover distributions toward the telomeres. This can lead to the problem of linkage drag when variation within nonrecombining regions is selected. Our findings demonstrate how gene dosage of key components of the meiotic chromosome axis can be used to remodel the recombination landscape. Therefore, modifying ASY1 and ASY3 gene dosage in crop species may provide a strategy to change recombination patterns or levels in order to accelerate strain improvement., During meiosis, interhomolog recombination produces crossovers and noncrossovers to create genetic diversity. Meiotic recombination frequency varies at multiple scales, with high subtelomeric recombination and suppressed centromeric recombination typical in many eukaryotes. During recombination, sister chromatids are tethered as loops to a polymerized chromosome axis, which, in plants, includes the ASY1 HORMA domain protein and REC8–cohesin complexes. Using chromatin immunoprecipitation, we show an ascending telomere-to-centromere gradient of ASY1 enrichment, which correlates strongly with REC8–cohesin ChIP-seq data. We mapped crossovers genome-wide in the absence of ASY1 and observe that telomere-led recombination becomes dominant. Surprisingly, asy1/+ heterozygotes also remodel crossovers toward subtelomeric regions at the expense of the pericentromeres. Telomeric recombination increases in asy1/+ occur in distal regions where ASY1 and REC8 ChIP enrichment are lowest in wild type. In wild type, the majority of crossovers show interference, meaning that they are more widely spaced along the chromosomes than expected by chance. To measure interference, we analyzed double crossover distances, MLH1 foci, and fluorescent pollen tetrads. Interestingly, while crossover interference is normal in asy1/+, it is undetectable in asy1 mutants, indicating that ASY1 is required to mediate crossover interference. Together, this is consistent with ASY1 antagonizing telomere-led recombination and promoting spaced crossover formation along the chromosomes via interference. These findings provide insight into the role of the meiotic axis in patterning recombination frequency within plant genomes.