Genetic Origin of AHAS2 Genes in Brassica Allotetraploids and Association of Its Orthologs with Agronomic Traits in B. napus

Acetohydroxy acid synthase (AHAS) are key targets for herbicide resistance breeding in Brassica crops, yet the evolutionary origin and functional role of AHAS2 genes in Brassica napus (AACC) and B. carinata (BBCC) remain poorly understood. Here, we investigated the distribution, ancestry, and agronomic trait associations of AHAS2 across 227 accessions representing six Brassica species. Bra.AHAS2 was amplified in 21 of 42 B. rapa (AA) accessions, and Bol.AHAS2 in 10 of 15 B. oleracea (CC) accessions. In B. napus, BnaA.AHAS2 and BnaC.AHAS2 were amplified in 73/131 and 30/131 accessions, respectively, with 19 accessions showing amplification of both homologs. All seven B. carinata accessions amplified BcaC.AHAS2. No AHAS2 homologs were amplified in three B. nigra (BB) or 29 B. juncea (AABB) accessions. Phylogenetic and gene structure analyses revealed that BnaA.AHAS2 (in B. napus) originated from Bra.AHAS2 of B. rapa, whereas BnaC.AHAS2 (in B. napus) and BcaC.AHAS2 (in B. carinata) derived from Bol.AHAS2 of B. oleracea. Association analysis showed the amplification of BnaA.AHAS2 or BnaC.AHAS2 was not associated with tribenuron-methyl resistance. However, amplification of BnaA.AHAS2 was significantly associated with reduced plant height, branching height, silique number on the terminal raceme, seed yield per plant, and thousand-seed weight in B. napus. Furthermore, haplotypes of BnaA.AHAS2 (BnaA05g03070D) were significantly associated with eicosenoic acid content, oleic acid content, flowering time, and cadmium translocation. Collectively, these findings resolve the diploid progenitor origins of AHAS2 in Brassica allotetraploids and reveal previously unrecognized associations of AHAS2 with agronomic and stress-related traits, offering valuable insights for molecular breeding in oilseed Brassica crops.