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As in other rice growing locales around the world, bacterial blight (BB) caused by
Xanthomonas oryzae pv. oryzae (Xoo) assumes a huge role in deciding rice profitability in
Kerala. The elite rice varieties of Kerala, both PTB 39 (Jyothi) and Mo 16 (Uma), are found
to be extremely susceptible to bacterial blight. Since both the major rice cropping seasons
(virippu and mundakan) in the state coincide with monsoons, the control of the disease
through chemicals or biological agents proves inadequate owing to the washing-off of the
applied materials. Host-plant resistance is advocated as the most effective breeding strategy
to combat the bacterial blight (BB) pathogen.
Considering the impact of the disease on food security and sustainability, efforts were
taken to introgress three R-genes (xa5, xa13 and Xa21) into the variety Uma from donor
parent Improved Samba Mahsuri (ISM) through Marker Assisted Selection (MAS). Further,
backcrossing to Uma (recurrent parent) and advancing the resultant BC1F1s have resulted in
production of BC2F1 generation (21 Nos.). The present study aimed to identify BC2F1 plants
pyramided with genes (xa5, xa13 and Xa21) conferring resistance to bacterial blight using
functional markers. In addition, advancing the R-gene introgressed BC2F1s to BC3F1 and
BC2F2 generation was envisaged. Pathotyping of BC1F2s (850 Nos.) and generating BC1F3s
from the plants exhibiting resistance to BB pathogen was also aimed at.
Foreground selection of the BC2F1 individuals using the xa5 gene linked STS marker
RG 556 and functional marker xa5 SR confirmed the presence of the R-gene in the parents as
well as the 21 BC2F1 individuals. Screening of BC2F1 individuals with STS marker RG 136
linked to R-gene xa13 and functional marker xa13 promoter revealed that the BC2F1 Plant
No. 8.3.9.10 was heterozygous at xa13 locus while, all other BC2F1 individuals possessed
alleles similar to that of the recurrent parent (RP) Uma. The result also pointed out that BC2F1
Plant No. 8.3.9.10 was a 2-R-gene pyramid (xa5xa5 + Xa13xa13). Foreground selection with
STS marker pTA 248 to detect the presence of Xa21 gene revealed that none of the BC2F1
plants analysed except BC2F1 Plant No. 8.3.9.10, possessed the resistant allele of R-gene
Xa21. However, presence of alleles of both the parents in Plant No. 8.3.9.10 indicated that it
was heterozygous at Xa21 locus. Results obtained thus revealed that, of the 21 BC2F1s
subjected to foreground selection, BC2F1 Plant No. 8.3.9.10 was the only 3-R-gene
introgressed pyramid (xa5xa5 + Xa13xa13 + Xa21xa21).
In addition, the 3-R-gene introgressed BC2F1 Plant No. 8.3.9.10 was subjected to
background screening using 22 rice microsatellite (RM) markers. Background profiling
revealed that the banding pattern in Plant No. 8.3.9.10 was similar to recurrent parent in case
of thirteen RM markers. The plant was found to be heterozygous at five other marker loci.
Considering the segregation of the 22 markers, the magnitude of recovery of recurrent
parent genome in 3-R-gene introgressed BC2F1 Plant No. 8.3.9.10 was found to be 81.82 per
cent. The dendrogram based on molecular data grouped the individuals into two major
clusters. Cluster 1 was monogenic with only the donor parent ISM and cluster 2 comprised of
the recurrent parent Uma and Plant No.8.3.9.10, further suggesting that the 3-R-gene
introgressed BC2F1 Plant No. 8.3.9.10 was more similar to the recurrent parent Uma.
Wide variability was observed among the BC2F1 individuals for various
morphological traits. The 3-R-gene introgressed BC2F1 Plant No. 8.3.9.10 was shorter in
duration than both the parents and also possessed red kernels similar to the recurrent parent
Uma. The dendrogram generated based on the morphological characters also indicated
greater similarity between the 3-R-gene pyramid and recurrent parent Uma.
The identified 3-R-gene pyramid (BC2F1 Plant No. 8.3.9.10) was backcrossed to both
recurrent parent Uma as well as selfed resulting in production of BC3F1s (15 Nos.) and
BC2F2s (28 Nos.) respectively.
Bioassay of BC1F2 population (106 Nos.) through leaf clipping method of pathotyping
suggested by IRRI (1991) revealed that more than half the BC1F2 individuals screened
exhibited resistance to BB pathogen. The plants that exhibited moderate reaction to BB
infection ranged between 16.87 per cent and 34.78 per cent in progeny of BC1F2 Plant No.
8.3.2 and BC1F2 Plant No. 8.3.9 respectively. Selfing of the BC1F2 individuals exhibiting
resistance and moderate resistance to BB pathogen resulted in production of 725 BC1F3
seeds.
Modern molecular techniques make it possible to use markers and probes to track the
simultaneous introgression of several R-genes into a single cultivar during a crossing
programme. Foreground and background profiling of backcross generations can ensure
precise identification of R-gene introgressed genotypes that resemble the recurrent parent
Uma.