Analyses of genetic diversity of bacterial blight pathogen, Xanthomonas oryzae pv. oryzae using IS1112 in Bangladesh

Abstract

Bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae (Xoo), a most destructive disease of rice, mostly in Asia, including Bangladesh. Altogether 96 isolates of Xoo were collected from 19 rice-growing districts of Bangladesh in both the rain-fed and irrigated seasons of 2014 to assess their pathotypic and genetic variation. Pathotypic analyses were carried out on a set of 12 Near Isogenic Lines (NILs) of rice containing a single resistance gene and two check varieties IR24 and TN1 by the leaf clipping inoculation method. A total of 24 pathotypes were identified based on their virulence patterns on the NILs tested. Among these, pathotypes VII, XII and XIV, considered as major, containing a maximum number of isolates (9.38% each), are frequently distributed in seven northern to mid-eastern districts of Bangladesh. The most virulent pathotype I was recorded in the Habiganj and Brahmanbaria districts. The molecular analysis of variability among the isolates was carried out through PCR analysis using multi-locus primers Jel1 and Jel2 (based on the repetitive element IS1112 in the Xoo genome). Using the genotypic data, a dendrogram was constructed with 17 clusters along with 17 molecular haplotypes at the 65% similarity index. Cluster I was composed of 46 isolates considered as major, whereas clusters X, XI, XII and XVII were represented by a single isolate. A phenogram was constructed based on virulence to interpret the relationship between the pathotypes and the molecular haplotypes. At the 50% similarity level, among 10 clusters, cluster I, considered as major, consisted of a maximum of 10 pathotypes out of 24. In case of haplotypes, a maximum of 7 haplotypes were obtained from pathotype XII, whereas pathotypes IX, X, XV, XXII and XXIV were represented by a single haplotype. However, the present study revealed that different isolates belonging to the same pathotypes belonged to different haplotypes. Conversely, genetically similar haplotypes were also detected from different pathotypes collected from separate districts. This relationship appeared due to a high degree of DNA polymorphism among strains within many pathotypes existing in Bangladesh.

Pathotype profiling, distribution and virulence analysis of Xanthomonas oryzae pv. oryzae causing bacterial blight disease of rice in Bangladesh

“…The variability of Xoo isolates has been reported from many countries including Bangladesh (Alam et al, 2016;Islam et al, 2016;Noer et al, 2018;Tekete et al, 2020). But no one yet uses the Xa23 gene for the identification of pathotypic variations in Xoo.…”

“…A total of 165 isolates of Xoo were successfully isolated on peptone sucrose agar (PSA) medium by following the method described by Islam et al., 2016. Isolated bacteria were purified and identified according to the description of Jalaluddin & Kashem, 1999 and stored temporarily in a 4°C refrigerator.…”

Participatory Varietal Selection for Promising Rice Lines

“…The control strategy for brown planthopper and Xoo disease is by the breeding plants' genetic resistance and developing environmentally-friendly rice cultivation [55][56][57]. The sources of resistance Pyricularia oryzae which were identified from genetic resources can be explored in future multiple resistance rice breeding programs [58,59].…”

Potential Role of Rice Plant Growth Promoting Phylloplane and Rhizospheric Bacteria in Controlling Xanthomonas oryzae pv. oryzae

“…Excess amount of nitrogenous fertilizer in rice varieties (HYV) facilitates the emergence of this disease and its severity in the field [8][9][10][11][12]. In Bangladesh different pathogenic [13,14] and genetic variability [15] have been detected and those were excessively perilous for rice [16].…”