Identification of RFLP and NBS/PK profiling markers for disease resistance loci in genetic maps of oats

Abstract

Two of the domains most widely shared among R genes are the nucleotide binding site (NBS) and protein kinase (PK) domains. The present study describes and maps a number of new oat resistance gene analogues (RGAs) with two purposes in mind: (1) to identify genetic regions that contain R genes and (2) to determine whether RGAs can be used as molecular markers for qualitative loci and for QTLs affording resistance to Puccinia coronata. Such genes have been mapped in the diploid A. strigosa × A. wiestii (Asw map) and the hexaploid MN841801-1 × Noble-2 (MN map). Genomic and cDNA NBS-RGA probes from oat, barley and wheat were used to produce RFLPs and to obtain markers by motif-directed profiling based on the NBS (NBS profiling) and PK (PK profiling) domains. The efficiency of primers used in NBS/PK profiling to amplify RGA fragments was assessed by sequencing individual marker bands derived from genomic and cDNA fragments. The positions of 184 markers were identified in the Asw map, while those for 99 were identified in the MN map. Large numbers of NBS and PK profiling markers were found in clusters across different linkage groups, with the PK profiling markers more evenly distributed. The location of markers throughout the genetic maps and the composition of marker clusters indicate that NBS- and PK-based markers cover partly complementary regions of oat genomes. Markers of the different classes obtained were found associated with the two resistance loci, PcA and R-284B-2, mapped on Asw, and with five out of eight QTLs for partial resistance in the MN map. 53 RGA-RFLPs and 187 NBS/PK profiling markers were also mapped on the hexaploid map A. byzantina cv. Kanota × A. sativa cv. Ogle. Significant co-localization was seen between the RGA markers in the KO map and other markers closely linked to resistance loci, such as those for P. coronata and barley yellow dwarf virus (Bydv) that were previously mapped in other segregating populations.

Cloning and characterization of gene-resistant analogs (RGAs) involved in rust (Puccinia psidii) resistance in Eucalyptus grandis

“…Unlike the pathosystem of E. grandis and P. psidii, the high number of resistant genes in maize and Arabidopsis may make it easier to identify large amount of RGAs. The effectiveness of this technique for mapping resistance genes were developed in several crops, including melons, chickpeas, soybeans, and oats have been well documented (Garcia-Mas et al 2001;Huettel et al 2002;Wang et al 2004;Satheeskumar et al 2011;Sanz et al 2013 Studies involving a larger number of RGAs can increase the chances of identifying loci linked to the Ppr1 gene, as well as allow for inferences about the presence or absence of an NBS domain in this gene. However, as NBS domains are found in many protein families, including atpases, elongation factors, and G proteins (Saraste et al 1990), it may be difficult to identify RGAs contributing to disease resistance as mentioned above.…”

Oat Fungal Diseases and the Application of Molecular Marker Technology for Their Control

“…There are currently more than 100 described Pc genes (Sanz et al 2013 ;Gnanesh et al 2014 ), but because their chromosomal locations have not been determined, many could be the same or allelic. Most Pc genes are inherited dominantly, but some are either partially dominant or recessive (Simons et al 1978 ).…”

“…Cloning and study of members of defi ned resistant gene families, such as wheat Lrk10 -type genes in oats (Cheng et al 2003 ). Sanz et al ( 2013 ) found that nucleotide binding site (NBS) and protein kinase (PK) based markers cover partly complementary regions of oat genomes. Markers of the different classes obtained were found to be associated with the two resistance loci, PcA and R-284B-2, mapped on A. strigosa × A. wiestii (Asw map), and with fi ve out of eight QTLs for partial resistance in the MN841801-1 × Noble-2 (MN) map.…”

PK-profiling method for identifying the expression of resistance-associated genes in partially resistant oats to crown rust

“…However, efforts have been made to characterize oat RGAs that might be useful in the development of genetic markers of resistance. Using individual RGA amplicons and motif-directed-profiling, a number of markers have been located in several oat genetic reference maps [14, 21]. Some of these markers lie close to previously mapped Mendelian genes for resistance.…”