Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces

Abstract

BackgroundBacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance genes have been mapped on rice chromosomes, while 6 have been cloned, sequenced and characterized. Diversity analysis at the resistance gene level of this disease is scanty, and the landraces from West Bengal and North Eastern states of India have received little attention so far. The objective of this study was to assess the genetic diversity at conserved domains of 6 BLB resistance genes in a set of 22 rice accessions including landraces and check genotypes collected from the states of Assam, Nagaland, Mizoram and West Bengal.ResultsIn this study 34 pairs of primers were designed from conserved domains of 6 BLB resistance genes; Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27. The designed primer pairs were used to generate PCR based polymorphic DNA profiles to detect and elucidate the genetic diversity of the six genes in the 22 diverse rice accessions of known disease phenotype. A total of 140 alleles were identified including 41 rare and 26 null alleles. The average polymorphism information content (PIC) value was 0.56/primer pair. The DNA profiles identified each of the rice landraces unequivocally. The amplified polymorphic DNA bands were used to calculate genetic similarity of the rice landraces in all possible pair combinations. The similarity among the rice accessions ranged from 18% to 89% and the dendrogram produced from the similarity values was divided into 2 major clusters. The conserved domains identified within the sequenced rare alleles include Leucine-Rich Repeat, BED-type zinc finger domain, sugar transferase domain and the domain of the carbohydrate esterase 4 superfamily.ConclusionsThis study revealed high genetic diversity at conserved domains of six BLB resistance genes in a set of 22 rice accessions. The inclusion of more genotypes from remote ecological niches and hotspots holds promise for identification of further genetic diversity at the BLB resistance genes.

Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread

“…In addition to the nine previously reported R proteins with putative decoy domains (Césari et al ., 2014) (Table S1), there are three known R proteins with putative decoy domains: the auto‐immune NLR CHS3, which has a LIM‐type zinc‐finger domain (Bi et al ., 2011), the major splice variant of the rice blast R protein Pi‐ta containing a thioredoxin domain (Costanzo & Jia, 2009), and the rice bacterial blight resistance protein Xa1 which contains a BED‐type zinc‐finger domain that was overlooked when Xa1 was cloned (Yoshimura et al ., 1998) and was also described in several recent studies (Germain & Séguin, 2011; Das et al ., 2014). Moreover, we identified three R proteins with additional domains that had not yet been detected (Fig.…”

“…Integration of decoy domains was first suspected in poplar (Populus trichocarpa) , where 32 NLR proteins were found to carry the same additional domain (Germain & Séguin, 2011). This additional domain, called BED (for BEAF and DREF Drosophila proteins containing this domain; Aravind, 2000), was also found in nine rice ( Oryza sativa ) NLRs, including one that was found to code for the Xa1 functional resistance protein (Das et al ., 2014). The authors of that study speculated about why both rice and poplar have independently acquired this gene architecture and raised the hypothesis that the integrated domain may act as a sensor for pathogen effectors.…”

Effectiveness of selection, parent-offspring correlation and regression in bacterial blight resistance genes introgressed rice segregating population

“…Lesion enlarges in length and width, and may have wavy margins. BB disease of rice, in terms of yield losses across the globe (DAS et al, 2014) and yield losses up to 80% depending on the stage of the crop, cultivar susceptibility, and environmental conditions (SRINIVASAN & GNANAMANICKAM, 2005). For increasing the yield potential, hybrids are considered as an important strategy in any crop.…”

Stability of Four New Sources of Bacterial Leaf Blight Resistance in Thailand Obtained from Indigenous Rice Varieties

“…However, the limited of seasonal confounding could overcome by markerassisted selection (MAS) (Collard & Mackill, 2008). The modes of inheritance of resistance to BLB in rice were differences when evaluated in different sources of resistance (Khan, Naeem, & Iqbal, 2014;Das, Sengupta, Prasad, & Ghose, 2014). This suggests a number of different mechanisms or genes may confer resistance to BLB.…”

“…Mapping several resistance genes or quantitative trait loci (QTLs) shows the same location in a genome region, indicating that some of the resistance genes or QTLs are the same (Das, Sengupta, Prasad, & Ghose, 2014). The use of same resistance gene in large production areas is very often cause resistance breaking by the pathogen.…”