Molecular insights into the origin of the brown rust resistance gene Bru1 among Saccharum species

Abstract

Analysis of 387 sugarcane clones using Bru 1 diagnostic markers revealed two possible sources of Bru 1 in Chinese cultivars: one from Saccharum spontaneum and another from Saccharum robustum of New Guinea. Sugarcane brown rust (SBR) is an important fungal disease in many sugarcane production areas around the world, and can cause considerable yield losses in susceptible sugarcane cultivars. One major SBR resistance gene, named Bru1, initially identified from cultivar R570, was shown to be a major SBR resistance source in most of the sugarcane producing areas of the world. In this study, by using the two Bru1-associated markers, R12H16 and 9O20-F4, we surveyed the presence of Bru1 in a Chinese sugarcane germplasm collection of 387 clones, consisting of 228 hybrid cultivars bred by different Chinese sugarcane breeding establishments, 54 exotic hybrid cultivars introduced from other countries and 105 clones of sugarcane ancestral species. The Bru1-bearing haplotype was detected in 43.4% of Chinese sugarcane cultivars, 20.4% of exotic hybrid cultivars, and only 3.8% of ancestral species. Among the 33 Chinese cultivars for which phenotypes of resistance to SBR were available, Bru1 was present in 69.2% (18/26) of the resistant clones. Analyses of the allelic sequence variations of R12H16 and 9O20-F4 suggested two possible sources of Bru1 in Chinese cultivars: one from S. spontaneum and another from S. robustum of New Guinea. In addition, we developed an improved Bru1 diagnostic marker, 9O20-F4-HaeIII, which can eliminate all the false results of 9O20-F4-RsaI observed among S. spontaneum, as well as a new dominant Bru1 diagnostic marker, R12E03-2, from the BAC ShCIR12E03. Our results provide valuable information for further efforts of breeding SBR-resistant varieties, searching new SBR resistance sources and cloning of Bru1 in sugarcane.

Identifying Quantitative Trait Loci (QTLs) and Developing Diagnostic Markers Linked to Orange Rust Resistance in Sugarcane (Saccharum spp.)

“…For example, since the discovery of Bru 1 and the identification of its co-segregating markers (R12H16 and 9O20-F4) ( Costet et al, 2012a ), the diagnostic markers have widely been used in sugarcane breeding programs. In Florida sugarcane breeding program, the markers for Bru 1 are being utilized to evaluate brown rust resistance in sugarcane germplasm and hybrid clones ( Glynn et al, 2013 ). It was estimated that 27% of the clones used for crossing (a total of 1027) contained Bru 1, and the frequency of Bru 1 in sugarcane clones increased from 15% (1975–1985) to 47% (2002–2012) after brown rust was introduced to Florida.…”

Sugarcane Ratooning Ability: Research Status, Shortcomings, and Prospects

“…The first marker to be identified was 10 cM from the Bru1 gene [78]. Furthermore, markers that were 1.9 cM and 2.2 cM from the gene were observed [79], but only the markers that were 0.28 cM and 0.14 cM from the Bru1 gene were identified [80] and used to assist the selection in breeding [81][82][83]. Nevertheless, these markers still have the problem of false positive [81], that is, the markers can be detected in a line without the actual disease resistance.…”

Development and application of SSR loci in monoploid reference genome of sugarcane cultivar

“…1887 , , , , [5][6] (simple sequence repeats, SSR) [5][6] , [7] , [8] SSR DNA , DNA [9] , [10] , SSR , [11] [ [12][13][14] [15 -17] ( ) [18] , , SSR , Singh [13] 4085 EST 351 EST-SSRs, 134 Shamshad [19] NCBI 10,000 EST , 406 SSRs, 63 42 Oliveira [14] EST [20] , , R570…”