Microsatellite and sequence-tagged site markers diagnostic for the rice bacterial leaf blight resistance gene xa-5

• Published in: Theoretical and applied genetics Vol. 95; no. 1/2; pp. 174 - 184
• Main Authors: Blair, M.W, McCouch, S.R
• Format: Journal Article
• Language: English
• Published: Heidelberg Springer 01.07.1997; Berlin Springer Nature B.V
• Subjects: alleles; Biological and medical sciences; blight; chromosome mapping; Classical genetics, quantitative genetics, hybrids; Development and progression; disease resistance; Diseases and pests; DNA sequencing; Fundamental and applied biological sciences. Psychology; Genes; Genetic aspects; genetic markers; genetic resistance; genetic variation; Genetics; Genetics of eukaryotes. Biological and molecular evolution; germplasm; Health aspects; Host-parasite relationships; linkage (genetics); microsatellite repeats; Nucleotide sequencing; Oryza sativa; Physiological aspects; Plant diseases; Plant genetics; Plant immunology; Pteridophyta, spermatophyta; repetitive sequences; restriction fragment length polymorphism; Rice; Vegetals; xa-5 gene; Xanthomonas oryzae oryzae; Xanthomonas oryzae pv. oryzae; United States; Pseudomonadales; Genetic mapping; Monocotyledones; Linkage; Genetic marker; Plant pathogen; Chromosome; Genetic diversity; Cereal crop; Oryza sativa; Germplasm; Microorganism resistance; Gramineae; Microsatellite DNA; Angiospermae; Bacteria; Pseudomonadaceae; Spermatophyta; Xanthomonas oryzae pv. oryzae; Sequence tagged site; Polymorphism
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s001220050545

Microsatellite and sequence-tagged site (STS markers tightly linked to the bacterial leaf blight (BLB) resistance gene xa-5 were identified in this study. A survey was conducted to find molecular markers that detected polymorphisms between the resistant (IRBB5) and susceptible ('IR24') nearly isogenic lines for xa-5, and between Chinsurah Boro II (CBII), an alternative source of xa-5, and a widely planted variety ('IR64') that lacks xa-5. Two F2 populations, from the crosses 'IR24' X IRBB5 and CBII X 'IR64', were used to estimate linkage based on marker genotype and reaction to disease inoculation with Xanthomonas oryzae pv. oryzae. Two RFLP clones, RZ390 and RG556, were found to co-segregate with xa-5 and were converted into STS markers. A microsatellite marker, RM390, was developed based on a simple sequence repeat in the 5' untranslated region of the cDNA probe, RZ390, and found to co-segregate with resistance. Two other microsatellites, RM122 and RM13, were located 0.4 cM and 14.1 cM away from xa-5. A germplasm survey of diverse lines containing BLB resistance genes using automated fluorescent detection indicated the range of allelic diversity for each of the microsatellite loci linked to xa-5 and confirmed their usefulness in following genes through the narrow crosses typical of a breeding program. The limited number of alleles observed at the microsatellite loci linked to the resistance gene in 35 xa-5-containing accessions suggested either a single ancestral origin or a few independent origins of the xa-5 gene. PCR-based markers, like the ones developed in this study, are economical and easy to use, and have applicability in efforts to pyramid the recessive xa-5 gene with other BLB resistance genes.