Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize

Ying Hu, Jie Ren, Zhao Peng, Arnoldo A. Umana, Ha Le, Tatiana Danilova, Junjie Fu, Haiyan Wang, Alison Robertson, Scot H. Hulbert, Frank F. White, Sanzhen Liu

Goss's wilt (GW) of maize is caused by the Gram-positive bacteriumClavibacter michiganensissubsp.nebraskensis(Cmn) and has spread in recent years throughout the Great Plains, posing a threat to production. The genetic basis of plant resistance is unknown. Here, a simple method for quantifying disease symptoms was developed and used to select cohorts of highly resistant and highly susceptible lines known as extreme phenotypes (XP). Copy number variation (CNV) analyses using whole genome sequences of bulked XP revealed 141 genes containing CNV between the two XP groups. The CNV genes include the previously identified common rust resistant locusrp1. MultipleRp1accessions with distinctrp1haplotypes in an otherwise susceptible accession exhibited hypersensitive responses upon inoculation. GW provides an excellent system for the genetic dissection of diseases caused by closely related subspecies ofC. michiganesis. Further work will facilitate breeding strategies to control GW and provide needed insight into the resistance mechanism of important related diseases such as bacterial canker of tomato and bacterial ring rot of potato.