Linkage analysis of rice bacterial blight resistance gene <i>xa20</i> in XM6, a mutant line from IR24

Abstract

Bacterial blight caused by Xanthomonas oryzae pv. oryzae ( Xoo ) is an important disease constraining rice ( Oryza sativa L.) production worldwide. The XM6 line was induced by N-methyl-N-nitrosourea from IR24, an Indica cultivar that is susceptible to Philippine and Japanese Xoo races. XM6 was confirmed to carry a recessive gene named xa20 , resistant to six Philippine and five Japanese Xoo races. The chromosomal gene location was found using 10 plants with the shortest lesion length in an F 2 population consisting of 298 plants from a susceptible Japonica variety Koshihikari × XM6. Analysis using PCR-based DNA markers covering the whole rice genome indicated the gene as located on the distal region of the long arm of chromosome 3. The IKC3 line carries IR24 genetic background with Koshihikari fragment on chromosome 3 where a resistance gene was thought to be located. The F 2 population from IKC3 × XM6 clearly showed a bimodal distribution separating resistant and susceptible plants. Further linkage analysis conducted using this F 2 population revealed that xa20 is located within the 0.8 cM region flanked by DNA markers KIC3-33.88 (33.0 Mb) and KIC3-34.06 (33.2 Mb). This study yields important findings for resistance breeding and for the genetic mechanism of Xoo resistance.

QTL Analysis Revealed One Major Genetic Factor Inhibiting Lesion Elongation by Bacterial Blight (Xanthomonas oryzae pv. oryzae) from a japonica Cultivar Koshihikari in Rice

“…To dissect the quantitative difference in the reaction to Xoo genetically, the population from the cross between KO and AR was subjected to inoculation to Race II strain ( Figure 1 ), which was frequently used in our earlier studies [ 19 , 30 , 31 ] as a tester Xoo in genetic analysis of Xoo resistance in rice. The F 2 population derived from the cross between the two cultivars represented continuous distribution of 5.5–60 cm ( Figure 2 ).…”

“…Bacterial leaf blight (BB) caused by the Xoo pathogen is regarded as a devastating and widespread disease affecting rice in parts of the world where rice is mostly cultivated. The approximately 42 resistance genes to BB which have been identified are increasingly being used in breeding programs [ 31 , 36 , 37 ]. Because these resistant genes have been used in elite cultivars for decades, they make the cultivars highly vulnerable to evolving Xoo pathotypes, thereby necessitating the reservoir of rice germplasm against them.…”

“…The DNA concentration was quantified using a spectrophotometer (Nanodrop 8000; Thermo Fisher Scientific Inc. Wilmington, DE, USA). For this study, 107 simple sequence repeat (SSR) and insertion/deletion (InDel) markers were acquired from earlier publications [ 31 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 ] ( Supplementary Materials: Table S1 ). The polymerase chain reaction (PCR) cocktail mixture (4.5 µL) comprised genomic DNA 10 ng, dNTPs 200 µM, 10 × buffer containing MgCl 2 , individual DNA markers 0.2 µM, distilled H 2 O 1.6 µL, and Taq polymerase 0.25 U.…”

Chromosomal Location of xa19, a Broad-Spectrum Rice Bacterial Blight Resistant Gene from XM5, a Mutant Line from IR24

“…Furthermore, according to our survey, xa-45(t) [ 13 ], and Xa46(t) [ 14 ] were recently reported. We induced mutation to IR24 using a chemical mutagen N-methyl-N-nitrosourea (MNU), and developed three Xoo resistant mutant lines, XM5, XM6 and XM14 [ 15 , 16 , 17 , 18 , 19 , 20 ]. Although IR24 is susceptible to almost all Xoo strains, the three XM lines are resistant to all Xoo races tested [ 16 , 17 , 18 , 20 ].…”

“…We induced mutation to IR24 using a chemical mutagen N-methyl-N-nitrosourea (MNU), and developed three Xoo resistant mutant lines, XM5, XM6 and XM14 [ 15 , 16 , 17 , 18 , 19 , 20 ]. Although IR24 is susceptible to almost all Xoo strains, the three XM lines are resistant to all Xoo races tested [ 16 , 17 , 18 , 20 ]. XM6 carries one recessive mutant Xoo resistant gene xa20 located on the long arm of chromosome 3 [ 17 , 20 ].…”