Table 2.
Summary of the genetic variations detected from the 31 representative indigenous soybean-nodulating bradyrhizobia in the Philippines through the Restriction Fragment Length Polymorphism (RFLP) treatment and sequence analysis of the 16S rRNA gene, 16S-23S rRNA ITS region, and rpoB housekeeping gene.
| Rep. isolate | Isolate (no.) | Cluster (RFLP) |
Cluster (sequence analysis) |
ITS- rpoB type | ||||
|---|---|---|---|---|---|---|---|---|
| 16S rRNA | ITS region | rpoB gene | 16S rRNA | ITS region | rpoB gene | |||
| IS-2 | 40 | Be | Be76 | Be46 | B.elkanii | Be31 | Be46 | Be31-Be46 |
| GI-4 | 30 | Bj | Bj | Bj | B. japonicum | Br | Br | Br-Br |
| GI-8 | 6 | Be | Be76 | Be46 | nd | Be31 | Be46 | Be31-Be46 |
| BA-24 | 31 | Bj | Bj6 | Bj6 | B. japonicum | Bj6’ | Bj6 | Bj6’-Bj6 |
| BA-41 | 1 | Bj | Bj124 | Bj124 | B. japonicum | Bj124’ | Bj124’ | Bj124’-Bj124’ |
| BA-42 | 1 | Be | Be76 | Be76 | B.elkanii | Be31 | Be46 | Be31-Be46 |
| NE1-6 NE1-19 |
49 5 |
Be Br |
Be76 Br |
Be46 Br |
B.elkanii nd | Be76’ Br |
Be46 Br |
Be76’-Be46 Br-Br |
| NE1-34 | 1 | Bj | Bj | Bj | B. japonicum | BrNE | BrNE | BrNE-BrNE |
| NE1-65 | 1 | Bj | Bj | Bj | B. diazoefficiens | Bd110 | Br | Bd110-Br |
| NE2-1 | 3 | Be | Be76 | Be46 | B.elkanii | Be76 | Be46 | Be76-Be46 |
| NE2-3 | 5 | Bj | Br | Br | nd | Br | Br | Br-Br |
| NE2-37 | 26 | Br | Br | Br | B. japonicum | Br | Br | Br-Br |
| NE2-66 | 1 | Bj | Bj | Bj | nd | Br | Bj124’ | Br-Bj124’ |
| SO-1 | 44 | Bj | Bd110 | Bd110 | B. diazoefficiens | Bd110 | Bd110 | Bd110-Bd110 |
| LT-3 | 42 | Bj | Bd110 | Bd110 | B. diazoefficiens | Bd110 | Bd110 | Bd110-Bd110 |
| LT-36 | 1 | Be | Be76 | Be46 | nd | Be76’ | Be46 | Be76’-Be46 |
| NR-1 | 4 | Bj | Bj6 | Bj6 | nd | Bj6 | Bj6 | Bj6-Bj6 |
| NR-2 | 22 | Be | Be76 | Be46 | nd | Be76 | Be46 | Be76-Be46 |
| NR-40 | 3 | Bj | Bj124 | Br | B. japonicum | Bj124’ | Bj | Bj124’-Bj |
| NR-48 | 1 | Bj | Bd110 | Br | B. diazoefficiens | Bd110 | Bd110’ | Bd110-Bd110’ |
| NR-60 | 1 | Br | Be76 | Br | nd | Be76 | Br | Be76-Br |
| BO-4 | 24 | Be | Be76 | Be46 | B.elkanii | Be31 | Be46 | Be31-Be46 |
| BO-15 | 4 | Bj | Bd110 | Bd110 | nd | Bd110 | Bd110 | Bd110-Bd110 |
| BO-52 | 1 | Bj | Bj | Br | nd | Br | Br | Br-Br |
| SK-1 | 4 | Be | Be46 | Be76 | B.elkanii | Be46’ | Be130 | Be46’-Be130 |
| SK-2 | 6 | Be | Be94 | Be94 | B.elkanii | Be94’ | Be94 | Be94’-Be94 |
| SK-5 | 29 | Bj | Bd110 | Bd110 | nd | Bd110 | Bd110 | Bd110-Bd110 |
| SK-12 | 4 | Br | Br | Br | B. yuanmingense | BySK | BySK | BySK-BySK |
| SC-3 | 31 | Bj | Bj6 | Bj6 | B. japonicum | Bj6 | Bj6 | Bj6-Bj6 |
| SC-49 |
3 |
Be |
Be76 |
Be46 |
nd |
Be76 |
Be46 |
Be76-Be46 |
| Total isolates | 424 | |||||||
Note: The prime (’) symbol indicates a variation in the sequence identity of at least 1.00% between the isolates and the Bradyrhizobium USDA reference strains. Be – B. elkanii, Bd – B. diazoefficiens, Bj – B. japonicum, By – B. yuanmingense, Br – Bradyrhizobium sp., nd – not determined due to the similarity with the other isolates that possess an identical ITS-rpoB type.