Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance.

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

[1]  C. Bastien,et al.  Presence of defeated qualitative resistance genes frequently has major impact on quantitative resistance to Melampsora larici-populina leaf rust in P. × interamericana hybrid poplars , 2007, Tree Genetics & Genomes.

[2]  E. Lagudah,et al.  Resistance gene analogues of wheat: molecular genetic analysis of ESTs , 2006, Theoretical and Applied Genetics.

[3]  R. Henry,et al.  Characterisation of single nucleotide polymorphisms in sugarcane ESTs , 2006, Theoretical and Applied Genetics.

[4]  P. Jackson,et al.  A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar , 2005, Theoretical and Applied Genetics.

[5]  J. Drenth,et al.  Homologues of the maize rust resistance gene Rp1-D are genetically associated with a major rust resistance QTL in sorghum , 2004, Theoretical and Applied Genetics.

[6]  S. Chapman,et al.  Identification of Differentially Expressed Transcripts from Maturing Stem of Sugarcane by in silico Analysis of Stem Expressed Sequence Tags and Gene Expression Profiling , 2004, Plant Molecular Biology.

[7]  P. Arruda,et al.  Collection for Tropical Crop Sugarcane Analysis and Functional Annotation of an Expressed Sequence Tag , 2006 .

[8]  A. D'Hont,et al.  Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane , 2003, Molecular Genetics and Genomics.

[9]  J. Bennetzen,et al.  Comparative Sequence Analysis of the Sorghum RphRegion and the Maize Rp1 Resistance Gene Complex , 2002, Plant Physiology.

[10]  D. Kudrna,et al.  A barley gene family homologous to the maize rust resistance gene Rp1-D , 2002, Theoretical and Applied Genetics.

[11]  J. Glaszmann,et al.  Genetic dissection of a modern sugarcane cultivar (Saccharum spp.).II. Detection of QTLs for yield components , 2002, Theoretical and Applied Genetics.

[12]  G. Kahl,et al.  Resistance gene analogues of chickpea (Cicer arietinum L.): isolation, genetic mapping and association with a Fusarium resistance gene cluster , 2002, Theoretical and Applied Genetics.

[13]  G. Wenzel,et al.  A resistance gene analog useful for targeting disease resistance genes against different pathogens on group 1S chromosomes of barley, wheat and rye , 2002, Theoretical and Applied Genetics.

[14]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[15]  A. Paterson,et al.  Construction of a Saccharum Consensus Genetic Map from Two Interspecific Crosses , 2002 .

[16]  A. Adam-Blondon,et al.  Identification of resistance gene analogs linked to a powdery mildew resistance locus in grapevine , 2002, Theoretical and Applied Genetics.

[17]  M. Foolad,et al.  A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on a Lycopersicon esculentum x Lycopersicon hirsutum cross. , 2002, Genome.

[18]  D. Brunel,et al.  Expression, mapping, and genetic variability of Brassica napus disease resistance gene analogues. , 2001, Genome.

[19]  S. C. Liu,et al.  QTL analysis in a complex autopolyploid: genetic control of sugar content in sugarcane. , 2001, Genome research.

[20]  A. Risterucci,et al.  Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers , 2001, Theoretical and Applied Genetics.

[21]  M. Combes,et al.  Origin, diversity and evolution of NBS-type disease-resistance gene homologues in coffee trees (Coffea L.) , 2001, Molecular Genetics and Genomics.

[22]  S. Tingey,et al.  Rice ESTs with disease-resistance gene- or defense-response gene-like sequences mapped to regions containing major resistance genes or QTLs , 2001, Molecular Genetics and Genomics.

[23]  B. Keller,et al.  Molecular evolution of receptor-like kinase genes in hexaploid wheat. Independent evolution of orthologs after polyploidization and mechanisms of local rearrangements at paralogous loci. , 2001, Plant physiology.

[24]  R. Wing,et al.  Chromosome landing at the bacterial blight resistance gene Xa4 locus using a deep coverage rice BAC library , 2001, Molecular Genetics and Genomics.

[25]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[26]  J. Glaszmann,et al.  Application of synteny across Poaceae to determine the map location of a sugarcane rust resistance gene , 2000, Theoretical and Applied Genetics.

[27]  Taylor,et al.  Characterisation of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species. , 2000, Plant science : an international journal of experimental plant biology.

[28]  D. Butler,et al.  Identification of genomic regions associated with stay green in sorghum by testing RILs in multiple environments , 2000, Theoretical and Applied Genetics.

[29]  J. Ellis,et al.  The maize rp1 rust resistance gene identifies homologues in barley that have been subjected to diversifying selection , 2000, Theoretical and Applied Genetics.

[30]  D. Zamir,et al.  Comparative genetics of nucleotide binding site-leucine rich repeat resistance gene homologues in the genomes of two dicotyledons: tomato and arabidopsis. , 2000, Genetics.

[31]  B. Sobral,et al.  Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide‐binding superfamily , 1999 .

[32]  M. Yano,et al.  RFLP- and physical mapping of resistance gene homologues in rice (O. sativa) and Barley (H. vulgare) , 1999, Theoretical and Applied Genetics.

[33]  P. Schulze-Lefert,et al.  A SUPERFAMILY OF DISEASE RESISTANCE GENE ANALOGS IS LOCATED ON ALL HOMOEOLOGOUS CHROMOSOME GROUPS OF WHEAT (TRITICUM AESTIVUM) , 1998 .

[34]  B C Meyers,et al.  Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. , 1998, Genome research.

[35]  S. Seah,et al.  Cloning and characterisation of a family of disease resistance gene analogs from wheat and barley , 1998, Theoretical and Applied Genetics.

[36]  S. Seah,et al.  The isolation and mapping of disease resistance gene analogs in maize. , 1998, Molecular plant-microbe interactions : MPMI.

[37]  R. Michelmore,et al.  Resistance gene candidates identified by PCR with degenerate oligonucleotide primers map to clusters of resistance genes in lettuce. , 1998, Molecular plant-microbe interactions : MPMI.

[38]  J. Beynon,et al.  Identification of R-gene homologous DNA fragments genetically linked to disease resistance loci in Arabidopsis thaliana. , 1998, Molecular plant-microbe interactions : MPMI.

[39]  B. Sobral,et al.  Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[40]  P. Dufour,et al.  Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid , 1997, Theoretical and Applied Genetics.

[41]  R. Shoemaker,et al.  Resistance gene analogs are conserved and clustered in soybean. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[42]  J. Mudge,et al.  A RAPD Genetic Map of Saccharum officinarum , 1996 .

[43]  J. Glaszmann,et al.  A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar ‘R570’ , 1996, Theoretical and Applied Genetics.

[44]  J. Glaszmann,et al.  RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid. , 1996, Genetics.

[45]  P. Dufour,et al.  Comparative genome mapping of sugar cane with other species within the Andropogoneae tribe , 1994, Heredity.

[46]  David J. States,et al.  Identification of protein coding regions by database similarity search , 1993, Nature Genetics.

[47]  E. D. Earle,et al.  Nuclear DNA content of some important plant species , 1991, Plant Molecular Biology Reporter.

[48]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[49]  J. Bennetzen,et al.  Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[50]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[51]  S. Price.  Cytological Studies in Saccharum and Allied Genera. III. Chromosome Numbers in Interspecific Hybrids , 1957, Botanical Gazette.

[52]  M. Warburton.  Laboratory Protocols CIMMYT Applied Molecular Genetics Laboratory , 2005 .

[53]  B. Sobral,et al.  Saccharum spontaneum L. ‘SES 208’ genetic linkage map combining RFLP- and PCR-based markers , 2005, Molecular Breeding.

[54]  D. Jordan,et al.  Identification of genomic regions for rust resistance in sorghum , 2004, Euphytica.

[55]  D. Hogarth,et al.  Chromosome composition analysis of various Saccharum interspecific hybrids by genomic in situ hybridisation (GISH). , 2001 .