MutS homologue 4 and MutS homologue 5 maintain the obligate crossover in wheat despite stepwise gene loss following polyploidization

Crossovers (COs) ensure accurate chromosome segregation during meiosis whilst creating novel allelic combinations. Here we show that allotetraploid (AABB) durum wheat (Triticum turgidum subsp. durum), utilises two pathways of meiotic recombination. The class I pathway requires MSH4 and MSH5 (MutSγ) to maintain the obligate CO/chiasma and accounts for ~85% of meiotic COs, whereas the residual ~15% are consistent with the class II CO pathway. Class I and class II chiasmata are skewed towards the chromosome ends, but class II chiasmata are significantly more distal than class I chiasmata. Chiasma distribution does not reflect the abundance of double strand breaks, detected by proxy as RAD51 foci at leptotene, but only ~2.3% of these sites mature into chiasmata. MutSγ maintains the obligate chiasma despite a 5.4-kb deletion in MSH5B rendering it non-functional that occurred early in the evolution of tetraploid wheat and was then domesticated into hexaploid (AABBDD) common wheat (Triticum aestivum), as well as an 8-kb deletion in MSH4D in hexaploid wheat, predicted to create a non-functional pseudogene. Stepwise loss of MSH5B and MSH4D following hybridization and whole-genome duplication may have occurred due to gene redundancy (as functional copies of MSH5A, MSH4A, and MSH4B are still present in the tetraploid and MSH5A, MSH5D, MSH4A, and MSH4B are present in the hexaploid), or as an adaptation to modulate recombination in allopolyploid wheat.