Pathotyping and genetic screening of type III effectors in Indian strains of Xanthomonas oryzae pv. oryzae causing bacterial leaf blight of rice

•The 780 Xanthomonas oryzae pv. oryzae (Xoo) isolates from 13 Indian states were pathotyped into six races.•Races 4 and 6 were predominant in north-western India; while races 2 and 3 were in north-eastern India.•Xoo population consisted of both less and more virulent races from a particular location.•Rice R-genes, Xa1, Xa2 were less effective compared to Xa4, Xa11, xa13, and Xa21.•We demonstrated 21 Xop and 18 TAL effectors in the most virulent and predominant Indian Xoo race 4.

Bacterial leaf blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the important biotic threat in rice production worldwide. Xoo populations vary greatly across the geographical locations. In this study, 780 Xoo isolates collected from 13 different states of north-west and -eastern India were grouped into six races based on disease reaction to 12 near isogenic lines (NILs). Race 4 and 6 were predominant in north-western part of India; while races 2 and 3 were in the north-eastern hills and plains. The detailed analysis of disease reaction, revealed that race 1, and race 2 are less virulent compared to the other races. It is interesting to note the co-existence of both less virulent (like race 1) and more virulent races (like race 5) in the Xoo population in a particular location. Among the R-genes the most vulnerable are Xa1 and Xa2 showing susceptible reaction to all the races while Xa4, Xa11, xa13, and Xa21 were found to be stable showing resistant to moderately resistant type BB reaction. This suggests that genes like Xa4, Xa11, xa13, and Xa21 could be used as promising candidates for resistance breeding programme. Xoo like most of the phytopathogenic bacteria secrets type three effectors (T3Es) directly into the rice cell to induce blight. Thus T3Es effectors, both Xop and TAL, function as major virulence determinants in Xoo. We demonstrated the presence of 21 Xop-T3Es and 18 TAL-T3Es in the most predominant and virulent Indian Xoo race 4. Altogether, the present study brings an updated picture of race status along with T3E profiles of north-west and -eastern Indian Xoo strains, and this insight would be of enormous importance in understanding rice–Xoo interaction through subsequent functional analysis of these T3Es in BB induction.