Allelic variation in the wheat homolog of topoisomerase II is associated with crossover rate

Meiotic recombination is a fundamental biological process that impacts genetic diversity and response of variants to selection. The increase in crossover (CO) frequency by modulating the activity of meiotic genes has been suggested as potential means to improve the efficiency of selection and mitigate the negative impact of linkage drag in crop improvement programs. In this study, we used the wheat nested association mapping (NAM) population to map QTL associated with CO rate and harboring TaTOPII-A1, a gene encoding topoisomerase II that is involved in the regulation of meiosis. An amino acid changing SNP (T/C) located in exon 19 of TaTOPII-A1 with a predicted functional effect showed an association with CO rate. The T-allele of TaTOPII-A1 was associated with a statistically significant 5.9 % increase in COs across several NAM families. The involvement of TaTOPII-A1 in processes affecting CO rate in wheat was confirmed using a TaTOPII-A1 mutant. A strong-effect missense mutation in the TaTOPII-A1 coding region resulted in 1.4-fold increase in the genetic map length and 53% increase in CO rate compared to the wild-type allele. These results demonstrate that functional mutations in TaTOPII-A1 can lead to increased CO frequency. The mutant and natural alleles of TaTOPII-A1 identified in our study could serve as new sources of recombination-promoting genes to manipulate CO rate in wheat and possibly other crops.