Molecular and phenotypic diversity of bacterial leaf blight resistance in green super rice germplasm

Bacterial leaf blight (BLB), resulting from Xanthomonas oryzae pv. oryzae, poses a significant threat to rice production worldwide, highlighting the urgent need for the development of resistant cultivars through the strategic deployment of resistance genes. This study combined phenotypic and molecular characterization of 110 Green Super Rice (GSR) accessions to clarify the architecture of BLB resistance and pinpoint elite breeding materials. Phenotypic evaluation showed significant variation in lesion length (LL, 2.00–16.00 cm; mean: 9.28 ± 2.96 cm), with genotypes categorized as resistant (5.5%), moderately resistant (13.6%), moderately susceptible (34.5%), and susceptible (46.4%). K-means clustering identified three phenotypic groups, with Cluster 1 (36.4%) representing elite germplasm that combines high paddy yield (PY, 2520 kg/ha) with superior resistance (6.51 ± 1.83 cm LL). Molecular screening utilizing eight markers identified five significant resistance genes: three dominant (Xa4, Xa10 and Xa21) and two recessive alleles (xa5 and xa13), with frequencies varying from 44.5% to 91.8%. The xa5 gene showed the highest prevalence at 91.8%, followed closely by Xa21 at 90.9%, Xa4 at 78.2%, Xa10 at 76.4%, and xa13 at 44.5%. The analysis of genetic diversity categorized the germplasm into ten separate clusters, with genotypes exhibiting 1–8 resistance markers (mean: 5.6 ± 1.3). Marker-trait association indicated that xa13_1 is strongly correlated with improved resistance (r = -0.344, p < 0.001). Integrated clustering identified Cluster 3 (20.0%) with optimal breeding value, featuring comprehensive resistance gene profiles (Xa4, xa5, Xa10, xa13 and Xa21), high PY (2470 kg/ha), and robust field resistance (7.70 ± 3.00 cm). Genotype–phenotype discordance in various clusters notably underscored the complexity of resistance gene interactions. The findings offer a thorough framework for marker-assisted selection and strategic gene pyramiding aimed at developing durable BLB-resistant cultivars that exhibit improved yield potential.