Marker-assisted pyramiding of bacterial leaf blight resistance genes (Xa21, xa13 and xa5) in a short-duration rice cultivar Luit

Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae, remains a major constraint to rice production in the humid and flood-prone rice-growing regions of northeastern India. In this study, BLB resistance was improved in the elite short-duration rice cultivar Luit through marker-assisted backcross breeding by pyramiding three widely used resistance genes, Xa21, xa13 and xa5, with IRBB60 serving as the donor parent. Gene-specific functional markers were used for foreground selection, while genome-wide SSR markers supported background selection and accelerated recovery of the recurrent parent genome. Screening of the BC₂F₂ population identified 57 lines homozygous for all three resistance genes. These pyramided lines showed high recurrent parent genome recovery (81.25–93.84%) and largely retained the agronomic characteristics of Luit, including grain yield, spikelet fertility and flowering duration. When evaluated under artificial inoculation with three virulent X. oryzae pv. oryzae isolates prevalent in Assam, the three-gene pyramided lines consistently exhibited significantly shorter lesion lengths than lines carrying one or two resistance genes, indicating enhanced and stable resistance. The results demonstrate that pyramiding Xa21, xa13 and xa5 through marker-assisted backcrossing is an effective approach for developing agronomically competitive rice breeding lines with durable BLB resistance. The identified lines constitute valuable genetic resources for further multi-location evaluation and for use in rice improvement programmes targeting BLB-prone environments.