Distribution of Xanthomonas oryzae pv. oryzae Pathotypes in Basmati-Rice-Growing Areas of Jammu and Kashmir, India
Abstract
:1. Introduction
2. Materials and Methods
2.1. Collection of Samples
2.2. Isolation of Xanthomonas oryzae pv. oryzae
2.3. Identification of Xanthomonas oryzae pv. oryzae
2.3.1. Colony and Biochemical Characterization
2.3.2. Molecular Identification
2.3.3. Pathogenicity Assay
2.4. Virulence Profiling of Xanthomonas oryzae pv. oryzae Isolates
2.5. Virulence Frequencies of Xanthomonas oryzae pv. oryzae
2.6. Statistical Analysis
3. Results
3.1. Isolation of Xanthomonas oryzae pv. oryzae Collected from Basmati-Rice-Growing Areas
3.2. Identification of Xanthomonas oryzae pv. oryzae Collected from Basmati-Rice-Growing Areas
3.3. Pathogenicity Assay Xanthomonas oryzae pv. oryzae Isolates on Rice Cultivars
3.4. Virulence Profiling of Xanthomonas oryzae pv. oryzae Isolates
3.5. Pathotyping of Xanthomonas oryzae pv. oryzae Isolates
3.6. Pathotype Abundance
3.7. Frequency Virulence of Xanthomonas oryzae pv. oryzae Isolates
4. Discussion
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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S. No. | Differential Host | Gene | S. No. | Differential | Gene(s) |
---|---|---|---|---|---|
1 | IRBB1 | Xa1 | 9 | IRBB13 | Xa13 |
2 | IRBB 3 | Xa3 | 10 | IRBB14 | Xa14 |
3 | IRBB4 | Xa4 | 11 | IRBB21 | Xa21 |
4 | IRBB5 | Xa5 | 12 | IRBB50 | Xa4 + Xa5 |
5 | IRBB7 | Xa 7 | 13 | IRBB51 | Xa4 + Xa13 |
6 | IRBB8 | Xa8 | 14 | IRBB 52 | Xa4 + Xa21 |
7 | IRBB10 | Xa10 | 15 | IRBB 53 | Xa5 + Xa13 |
8 | IRBB11 | Xa11 | 16 | TN1 | Susceptible check |
District | Location | No. of Isolates Collected | Variety(ies) | Isolate(s) |
---|---|---|---|---|
Jammu | Chatha | 2 | Pusa Basmati 1121 and Pusa Basmati 1637 | Xoo-1, Xoo-2 |
R S Pura | 2 | Basmati 370 and Ranbir Basmati | Xoo-3, Xoo-4 | |
Marh | 2 | Pusa Basmati 1728 and Basmati 564 | Xoo-5, Xoo-6 | |
Bishnah | 3 | Pusa Basmati 1637, Basmati 564 and Basmati 370 | Xoo-7, Xoo-8, Xoo-9 | |
Samba | Vijaypur | 3 | Pusa Basmati 1728, Pusa Basmati 1121 and Pusa Basmati 1637 | Xoo-10, Xoo-11, Xoo-12 |
Samba | 2 | Basmati 370 and Basmati 564 | Xoo-13, Xoo-14 | |
Ghagwal | 1 | Pusa Basmati 1121 | Xoo-15 | |
Kathua | Hiranagar | 2 | Jammu Basmati 138 and Jammu Basmati 123 | Xoo-16, Xoo-17 |
Nagri | 1 | Basmati 370 | Xoo-18 | |
Kathua | 2 | Pusa Basmati 1121 and Basmati 370 | Xoo-19, Xoo-20 |
Isolate | Cultural Characteristics | Morphological Characteristics | Biochemical Tests | |||
---|---|---|---|---|---|---|
Gram Reaction | KOH Test | Catalyst Test | Esterase Test | |||
Xoo1 | Light yellow, circular | Short rods with rounded ends single or in pairs | +ve | +ve | +ve | +ve |
Xoo2 | Light yellow, circular | |||||
Xoo3 | Yellow, circular | |||||
Xoo4 | Yellow, circular | |||||
Xoo5 | Whitish yellow to straw-colored, convex | |||||
Xoo6 | Whitish yellow to straw-colored, convex | |||||
Xoo7 | Whitish yellow to straw-colored, convex | |||||
Xoo8 | Yellow, slightly raised | |||||
Xoo9 | Yellow, slightly raised | |||||
Xoo10 | Yellow, slightly raised | |||||
Xoo11 | Yellow, slightly raised | |||||
Xoo12 | Yellow, slightly raised | |||||
Xoo13 | Yellow, slightly raised | |||||
Xoo14 | Light yellow, convex | |||||
Xoo15 | Light yellow, convex | |||||
Xoo16 | Light yellow, circular | |||||
Xoo17 | Yellow, circular | |||||
Xoo18 | Yellow, circular | |||||
Xoo19 | Whitish yellow | |||||
Xoo20 | Yellow |
Isolate | Lesion Length (cm) of Bacterial Leaf Blight on Selected Rice Varieties | ||||
---|---|---|---|---|---|
Basmati 370 | Pusa 1121 | TN 1 | SJR 5 | Jaya | |
Xoo1 | 15.90 ± 0.17 | 15.90 ± 0.34 | 18.60 ± 0.43 | 12.20 ± 1.11 | 13.73 ± 0.46 |
Xoo2 | 17.60 ± 0.43 | 16.53 ± 0.52 | 18.43 ± 0.55 | 13.70 ± 0.26 | 13.96 ± 0.56 |
Xoo3 | 16.66 ± 0.68 | 15.96 ± 0.76 | 17.80 ± 0.36 | 12.96 ± 0.61 | 13.73 ± 0.55 |
Xoo4 | 17.73 ± 0.93 | 16.83 ± 0.52 | 18.40 ± 0.45 | 11.53 ± 1.08 | 13.86 ± 0.38 |
Xoo5 | 17.16 ± 0.20 | 16.63 ± 0.31 | 18.16 ± 0.37 | 14.30 ± 0.23 | 13.16 ± 0.56 |
Xoo6 | 16.50 ± 0.72 | 17.03 ± 0.86 | 18.96 ± 0.68 | 12.40 ± 1.24 | 13.63 ± 0.61 |
Xoo7 | 18.33 ± 0.60 | 16.06 ± 0.39 | 18.83 ± 0.73 | 11.70 ± 1.05 | 14.10 ± 0.17 |
Xoo8 | 16.03 ± 0.68 | 16.53 ± 0.54 | 18.83 ± 0.34 | 13.23 ± 1.21 | 14.36 ± 0.06 |
Xoo9 | 18.10 ± 0.79 | 16.66 ± 0.18 | 17.73 ± 0.33 | 11.76 ± 0.24 | 13.10 ± 0.50 |
Xoo10 | 18.56 ± 0.69 | 15.66 ± 0.12 | 17.93 ± 0.38 | 13.26 ± 0.51 | 14.30 ± 0.23 |
Xoo11 | 17.00 ± 0.86 | 16.93 ± 0.29 | 18.13 ± 0.67 | 11.36 ± 0.60 | 14.13 ± 0.31 |
Xoo12 | 16.56 ± 0.54 | 16.36 ± 0.60 | 18.63 ± 0.70 | 11.73 ± 0.47 | 13.83 ± 0.20 |
Xoo13 | 16.30 ± 0.60 | 16.56 ± 0.61 | 18.93 ± 0.36 | 12.00 ± 0.15 | 14.33 ± 1.00 |
Xoo14 | 16.53 ± 0.63 | 15.96 ± 0.43 | 18.73 ± 0.56 | 13.40 ± 0.75 | 13.60 ± 0.58 |
Xoo15 | 16.36 ± 0.67 | 16.13 ± 0.33 | 17.96 ± 0.23 | 12.13 ± 0.69 | 13.46 ± 0.52 |
Xoo16 | 16.30 ± 0.30 | 16.13 ± 0.26 | 17.33 ± 0.27 | 12.03 ± 1.19 | 13.56 ± 0.57 |
Xoo17 | 16.53 ± 0.69 | 16.56 ± 0.67 | 19.46 ± 0.20 | 13.36 ± 0.75 | 13.46 ± 0.29 |
Xoo18 | 17.46 ± 0.98 | 16.60 ± 0.46 | 19.00 ± 0.20 | 13.40 ± 0.66 | 14.06 ± 0.13 |
Xoo19 | 16.13 ± 0.43 | 16.60 ± 0.60 | 18.20 ± 0.85 | 12.83 ± 0.73 | 14.13 ± 0.27 |
Xoo20 | 16.36 ± 1.02 | 15.56 ± 0.17 | 18.43 ± 0.60 | 12.93 ± 1.12 | 13.33 ± 0.37 |
p-value | ≤0.195 | ≤0.795 | ≤0.405 | ≤0.466 | ≤0.695 |
Xoo Isolate | Differential (IRBB) Lines | Pathotype | |||||||||||||||
IRBB 1 | IRBB 3 | IRBB 4 | IRBB 5 | IRBB 7 | IRBB 8 | IRBB 10 | IRBB 11 | IRBB 13 | IRBB 14 | IRBB 21 | IRBB 50 | IRBB 51 | IRBB 52 | IRBB 53 | TN1 | ||
Xoo1 | 7 (S) | 5 (MS) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7(S) | 1 (R) | 7 (S) | 3 (MR) | 5 (MS) | 1 (R) | 3 (MR) | 1 (R) | 7 (S) | Pathotype 5 |
Xoo2 | 7 (S) | 5 (MS) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7(S) | 1 (R) | 7 (S) | 3 (MR) | 5 (MS) | 1 (R) | 3 (MR) | 1 (R) | 7 (S) | |
Xoo3 | 7 (S) | 5 (MS) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7(S) | 1 (R) | 7 (S) | 3 (MR) | 5 (MS) | 1 (R) | 3 (MR) | 1 (R) | 7 (S) | |
Xoo4 | 7 (S) | 5 (MS) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7(S) | 1 (R) | 7 (S) | 3 (MR) | 5 (MS) | 1 (R) | 3 (MR) | 1 (R) | 7 (S) | |
Xoo5 | 7 (S) | 7 (S) | 3 (MR) | 3 (MR) | 3 (MR) | 1 (R) | 7 (S) | 7 (S) | 1(R) | 7 (S) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | Pathotype 3 |
Xoo6 | 7 (S) | 7 (S) | 3 (MR) | 3 (MR) | 3 (MR) | 1 (R) | 7 (S) | 7 (S) | 1(R) | 7 (S) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | |
Xoo7 | 7 (S) | 7 (S) | 5 (MS) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 1(R) | 7 (S) | 3 (MR) | 3 (MR) | 1 (R) | 3 (MR) | 1 (R) | 7 (S) | Pathotype 7 |
Xoo8 | 7 (S) | 7 (S) | 5 (MS) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 1(R) | 7 (S) | 3 (MR) | 3 (MR) | 1 (R) | 3 (MR) | 1 (R) | 7 (S) | |
Xoo9 | 7 (S) | 7 (S) | 5 (MS) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 1(R) | 7 (S) | 3 (MR) | 3 (MR) | 1 (R) | 3 (MR) | 1 (R) | 7 (S) | |
Xoo10 | 7 (S) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | Pathotype 2 |
Xoo11 | 7 (S) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | |
Xoo12 | 7 (S) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | |
Xoo13 | 7 (S) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | |
Xoo14 | 7 (S) | 5 (MS) | 1(R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | |
Xoo15 | 7 (S) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 5 (MS) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | |
Xoo16 | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 7 (S) | 3 (MR) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | Pathotype 6 |
Xoo17 | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 7 (S) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 7 (S) | 3 (MR) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | |
Xoo18 | 7 (S) | 7 (S) | 5 (MS) | 5 (MS) | 7 (S) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 7 (S) | 3 (MR) | 1 (R) | 1 (R) | 1 (R) | 1 (R) | 7 (S) | Pathotype 6 |
Xoo19 | 7 (S) | 7 (S) | 5 (MS) | 5 (MS) | 5 (MS) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 1 (R) | 5 (MS) | 1 (R) | 7 (S) | Pathotype 6 |
Xoo20 | 7 (S) | 7 (S) | 5 (MS) | 5 (MS) | 5 (MS) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 7 (S) | 7 (S) | 1 (R) | 1 (R) | 5 (MS) | 1 (R) | 7 (S) |
Pathotype | Collected from District | Xoo Isolate | Virulent against (Differential Lines) | Lesion Length (cm) | Moderately Susceptible against (Differential Lines) | Lesion Length (cm) | Moderately Resistant against (Differential Lines) | Lesion Length (cm) | Avirulent against (Differential Lines) | Lesion Length (cm) |
---|---|---|---|---|---|---|---|---|---|---|
Pathotype 1 | Kathua | Xoo-18 | Xa1 (IRBB1) Xa3 (IRBB3) Xa7 (IRBB7) Xa10 (IRBB10) Xa11 (IRBB11) Xa14 (IRBB14) TN-1 | 16.2 15.8 15.9 16.4 18.6 15.6 18.7 | Xa4 (IRBB4) Xa5 (IRBB5) | 14.3 11.9 | Xa21 (IRBB21) | 7.8 | Xa8 (IRBB8) Xa13 (IRBB13) Xa4 + Xa5 (IRBB50) Xa4 + Xa13 (IRBB51) Xa4 + Xa21 (IRBB52) Xa5 + Xa13 (IRBB53) | 2.3 4.3 3.7 1.9 2.9 3.8 |
Pathotype 2 | Samba | Xoo-10 Xoo-11 Xoo-13 Xoo-14 Xoo-15 | Xa1 (IRBB1) Xa10 (IRBB10) Xa11 (IRBB11) TN-1 | 15.6 16.7 17.2 19.4 | Xa3 (IRBB3) Xa14 (IRBB14) | 12.3 12.8 | - | - | Xa4 (IRBB4) Xa5 (IRBB5) Xa7 (IRBB7) Xa8 (IRBB8) Xa13 (IRBB13) Xa21 (IRBB21) Xa4 + Xa5 (IRBB50) Xa4 + Xa13 (IRBB51) Xa4 + Xa21 (IRBB52) Xa5 + Xa13 (IRBB53) | 2.9 1.8 2.7 4.4 4.3 3.3 4.4 2.9 3.4 3.7 |
Pathotype 3 | Jammu | Xoo-5 Xoo-6 | Xa1 (IRBB1) Xa3 (IRBB3) Xa10 (IRBB10) Xa11 (IRBB11) Xa14 (IRBB14) TN-1 | 15.7 16.4 17.1 15.6 15.3 17.8 | Xa21 (IRBB21) | 11.8 | Xa4 (IRBB4) Xa5 (IRBB5) Xa7 (IRBB7) | 9.3 6.5 6.3 | Xa8 (IRBB8) Xa13 (IRBB13) Xa4 + Xa5 (IRBB50) Xa4 + Xa13 (IRBB51) Xa4 + Xa21 (IRBB52) Xa5 + Xa13 (IRBB53) | 1.8 4.6 4.2 3.9 3.6 1.9 |
Pathotype 4 | Kathua | Xoo-19 Xoo-20 | Xa1 (IRBB1) Xa3 (IRBB3) Xa10 (IRBB10) Xa11 (IRBB11) Xa14 (IRBB14) Xa21 (IRBB21) TN-1 | 16.7 15.6 17.3 17.5 16.7 16.9 17.8 | Xa4 (IRBB4) Xa5 (IRBB5) Xa7 (IRBB7) Xa4 + Xa21 (IRBB52) | 13.8 14.8 11.6 11.8 | Xa8 (IRBB8) Xa13 (IRBB13) Xa4 + Xa5 (IRBB50) Xa4 + Xa13 (IRBB51) Xa5 + Xa13 (IRBB53) | 2.6 4.3 3.4 2.9 4.6 | ||
Pathotype 5 | Jammu | Xoo-1 Xoo-2 Xoo-3 Xoo-4 | Xa1 (IRBB1) Xa4 (IRBB4) Xa5 (IRBB5) Xa7 (IRBB7) Xa8 (IRBB8) Xa10 (IRBB10) Xa11 (IRBB11) Xa14 (IRBB14) TN-1 | 15.4 15.6 16.4 16.6 17.6 17.8 15.4 16.7 18.7 | Xa3 (IRBB3) Xa4 + Xa5 (IRBB50) | 12.5 11.9 | Xa21 (IRBB21) Xa4 + Xa21 (IRBB52) | 7.3 7.1 | Xa13 (IRBB13) Xa4 + Xa13 (IRBB51) Xa5 + Xa13 (IRBB53) | 3.8 4.1 4.9 |
Pathotype 6 | Kathua | Xoo-16 Xoo-17 | Xa1(IRBB1) Xa3 (IRBB3) Xa4 (IRBB4) Xa5 (IRBB5) Xa7 (IRBB7) Xa10 (IRBB10) Xa11 (IRBB11) Xa14 (IRBB14) TN-1 | 17.8 16.8 17.5 16.3 15.3 15.6 16.5 16.7 19.2 | - | - | Xa21 (IRBB21) | 7.8 | Xa8 (IRBB8) Xa13 (IRBB13) Xa4 + Xa5 (IRBB50) Xa4 + Xa13 (IRBB51) Xa4 + Xa21 (IRBB52) Xa5 + Xa13 (IRBB53) | 3.6 4.6 3.2 2.9 4.8 3.8 |
Pathotype 7 | Jammu | Xoo-7 Xoo-8 Xoo-9 | Xa1 (IRBB1) Xa3 (IRBB3) Xa5 (IRBB5) Xa7 (IRBB7) Xa8 (IRBB8) Xa10 (IRBB10) Xa11 (IRBB11) Xa14 (IRBB14) TN-1 | 16.4 17.3 16.4 17.9 18.3 16.7 16.4 17.2 18.7 | Xa4 (IRBB4) | 11.2 | Xa21 (IRBB21) Xa4 + Xa5 (IRBB50) Xa4 + Xa21 (IRBB52) | 5.8 7.4 7.3 | Xa13 (IRBB13) Xa4 + Xa13 (IRBB51) Xa5 + Xa13 (IRBB53) | 4.2 1.9 4.3 |
Pathotype | Jammu | Samba | Kathua | Total | Percent Distribution |
---|---|---|---|---|---|
Pathotype 1 | - | - | 1/5 (20) | 1 | 5 |
Pathotype 2 | - | 6/6 (100) | - | 6 | 30 |
Pathotype 3 | 2/9 (22.22) | - | - | 2 | 10 |
Pathotype 4 | - | - | 2/5 (40) | 2 | 10 |
Pathotype 5 | 4/9 (44.44) | - | - | 4 | 20 |
Pathotype 6 | - | - | 2/5 (40) | 2 | 10 |
Pathotype 7 | 3/9 (33.333) | - | - | 3 | 15 |
(Isolates) | 3/9 * | 1/6 * | 3/5 * | 7/20 * | 100 |
Differential Line | BB Resistance Gene (s) | Virulent Isolate | Virulence Frequency (%) |
---|---|---|---|
IRBB1 | Xa1 | 20 | 100 |
IRBB3 | Xa3 | 20 | 100 |
IRBB4 | Xa4 | 12 | 60 |
IRBB5 | Xa5 | 12 | 60 |
IRBB7 | Xa7 | 12 | 60 |
IRBB8 | Xa8 | 7 | 35 |
IRBB10 | Xa10 | 20 | 100 |
IRBB11 | Xa11 | 20 | 100 |
IRBB13 | Xa13 | 0 | 0 |
IRBB14 | Xa14 | 20 | 100 |
IRBB21 | Xa21 | 4 | 20 |
IRBB50 | Xa4 + Xa5 | 4 | 20 |
IRBB51 | Xa4 + Xa13 | 0 | 0 |
IRBB52 | Xa4 + Xa21 | 2 | 10 |
IRBB53 | Xa5 + Xa13 | 0 | 0 |
TN1 | 0 | 20 | 100 |
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Amin, T.; Gupta, V.; Sharma, A.; Rai, P.K.; Razdan, V.K.; Sharma, S.K.; Singh, S.K.; Lone, J.A.; Yaqoob, M.; Singh, B.; et al. Distribution of Xanthomonas oryzae pv. oryzae Pathotypes in Basmati-Rice-Growing Areas of Jammu and Kashmir, India. Agronomy 2023, 13, 713. https://doi.org/10.3390/agronomy13030713
Amin T, Gupta V, Sharma A, Rai PK, Razdan VK, Sharma SK, Singh SK, Lone JA, Yaqoob M, Singh B, et al. Distribution of Xanthomonas oryzae pv. oryzae Pathotypes in Basmati-Rice-Growing Areas of Jammu and Kashmir, India. Agronomy. 2023; 13(3):713. https://doi.org/10.3390/agronomy13030713
Chicago/Turabian StyleAmin, Tabasia, Vishal Gupta, Akash Sharma, Pardeep Kumar Rai, Vijay Kumar Razdan, Satish Kumar Sharma, Santosh Kumar Singh, Javeed Ahmad Lone, Munazah Yaqoob, Brajeshwar Singh, and et al. 2023. "Distribution of Xanthomonas oryzae pv. oryzae Pathotypes in Basmati-Rice-Growing Areas of Jammu and Kashmir, India" Agronomy 13, no. 3: 713. https://doi.org/10.3390/agronomy13030713