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GrainGenes Reference Report: TAG-126-203

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Reference	TAG-126-203
Title	Identification of RFLP and NBS/PK profiling markers for disease resistance loci in genetic maps of oats
Journal	Theoretical and Applied Genetics
Year	2013
Volume	126
Pages	203-218
Author	Sanz MJ Loarce Y Fominaya A Vossen JH Ferrer E
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 x A. wiestii (Asw map) and the hexaploid MN841801-1 x 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 x 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.
External Databases	https://doi.org/10.1007/s00122-012-1974-8
Locus	[ Hide all but 1 of 456 ] 113c 113d 113e 11a 11b 11c 11d 21c 72a 72b 72c 81e 97a 97b 9a 9b 9c 9d 9e 9f 9h AluI/NBS1_10 AluI/NBS1_3 AluI/NBS1_4 AluI/NBS1_5 AluI/NBS1_7 AluI/NBS1_8 AluI/NBS1_9 AluI/NBS2_1 AluI/NBS2_2 AluI/NBS2_4 AluI/NBS2_A AluI/NBS2_B AluI/NBS2_C AluI/NBS2_D AluI/NBS2_E AluI/NBS2_F AluI/NBS2_G AluI/NBS2_H AluI/NBS3_A AluI/NBS3_B AluI/NBS3_C AluI/NBS5A_1 AluI/NBS5A_2 AluI/NBS5A_4 AluI/NBS6_1 AluI/NBS6_6 AluI/PK1Fa_1 AluI/PK1Fa_2 AluI/PK1Fa_3 AluI/PK1Fb_1 AluI/PK1Fb_3 AluI/PK1Fb_4 AluI/PK3Fa_1 AluI/PK3Fa_10 AluI/PK3Fa_11 AluI/PK3Fa_12 AluI/Pk3Fa_5 AluI/PK3Fa_6 AluI/PK3Fa_7 AluI/PK3Fa_8 AluI/PK3Fa_9 AluI/PK3Fa_A AluI/PK3Fa_B AluI/PK3Fa_C AluI/PK3Fa_D AluI/PK3Fa_E AluI/PK3Fa_F AluI/PK3Fa_G AluI/PK3Fa_H AluI/PK3Fa_I AluI/PK3Fa_J AluI/PK3Fa_K AluI/PK3Fb_1 AluI/PK3Fb_2 AluI/PK3Fb_5 AluI/PK3Fb_A AluI/PK3Fb_B AluI/PK3Fb_C AluI/PK3Fb_D AluI/PK3Fb_E AluI/PK3Fb_F AluI/PK3Fb_G AluI/PK3Fb_H AluI/PK3Fb_I AluI/PK3Fb_J AluI/PK3Fb_K AluI/PK3Fb_L AluI/PK3Fb_M AluI/PK3Fb_N AluI/Pk4R1a_1 AluI/PK4R1a_10 AluI/PK4R1a_11 AluI/PK4R1a_12 AluI/PK4R1a_13 AluI/PK4R1a_14 AluI/PK4R1a_15 AluI/PK4R1a_17 AluI/PK4R1a_18 AluI/PK4R1a_2 AluI/PK4R1a_3 AluI/PK4R1a_4 AluI/PK4R1a_5 AluI/PK4R1a_6 AluI/PK4R1a_8 AluI/PK4R1a_9 AluI/PK4R1a_B AluI/PK4R1a_C AluI/PK4R1a_D AluI/PK4R1a_E AluI/PK4R1a_F AluI/PK4R1a_G AluI/PK4R1b_1 AluI/PK4R1b_13 AluI/PK4R1b_15 AluI/PK4R1b_16 AluI/PK4R1b_2 AluI/PK4R1b_3 AluI/PK4R1b_4 AluI/PK4R1b_5 AluI/PK4R1b_6 AluI/PK4R1b_7 AluI/PK4R1b_8 AluI/PK4R1b_9 AluI/PK4R1b_A AluI/PK4R1b_B AluI/PK4R1b_C AluI/PK4R1b_D AluI/PK4R1b_E AluI/PK4R1b_F AluI/PK4R1b_G AluI/PK4R1b_H AluI/PK4R1b_I AluI/PK4R1b_J AP4a73 AP4a73a AP4b14 AP4b14a AP4b14b b2 b4 b5 b6x b6y b9a b9b b9c DAMII6 HaeIII/NBS1_1 HaeIII/NBS1_10 HaeIII/NBS1_2 HaeIII/NBS1_6 HaeIII/NBS1_8 HaeIII/NBS1_9 HaeIII/NBS1_A HaeIII/NBS1_B HaeIII/NBS1_C HaeIII/NBS1_D HaeIII/NBS1_E HaeIII/NBS1_F HaeIII/NBS1_G HaeIII/NBS1_H HaeIII/NBS1_I HaeIII/NBS2_1 HaeIII/NBS2_10 HaeIII/NBS2_11 HaeIII/NBS2_2 HaeIII/NBS2_3 HaeIII/NBS2_4 HaeIII/NBS2_8 HaeIII/NBS2_A HaeIII/NBS2_B HaeIII/NBS2_C HaeIII/NBS2_D HaeIII/NBS2_E HaeIII/NBS2_F HaeIII/NBS2_G HaeIII/NBS3_2 HaeIII/NBS3_4 HaeIII/NBS3_5 HaeIII/NBS5A_1 HaeIII/NBS5A_2 HaeIII/NBS5A_4 HaeIII/NBS5A_5 HaeIII/NBS5A_7 HaeIII/NBS6_1 HaeIII/NBS6_3 HaeIII/NBS6_4 HaeIII/NBS6_5 HaeIII/NBS6_6 HaeIII/PK1Fa_2 HaeIII/PK1Fa_3 HaeIII/PK1Fa_4 HaeIII/PK1Fa_5 HaeIII/PK1Fb_3 HaeIII/PK3Fa_4 HaeIII/PK3Fa_A HaeIII/PK3Fa_B HaeIII/PK3Fa_C HaeIII/PK3Fa_D HaeIII/PK3Fa_E HaeIII/PK3Fa_F HaeIII/PK3Fa_G HaeIII/PK3Fa_H HaeIII/PK3Fa_I HaeIII/PK3Fb_1 HaeIII/PK3Fb_13 HaeIII/PK3Fb_2 HaeIII/PK3Fb_5 HaeIII/PK3Fb_A HaeIII/PK3Fb_B HaeIII/PK3Fb_C HaeIII/PK3Fb_D HaeIII/PK3Fb_E HaeIII/PK3Fb_F HaeIII/PK3Fb_G HaeIII/PK3Fb_H HaeIII/PK3Fb_I HaeIII/PK3Fb_J HaeIII/PK3Fb_K HaeIII/PK3Fb_L HaeIII/PK3Fb_M HaeIII/PK3Fb_N HaeIII/PK3Fb_O HaeIII/PK3Fb_P HaeIII/PK3Fb_Q HaeIII/PK4R1a_1 HaeIII/PK4R1a_2 HaeIII/PK4R1a_4 HaeIII/PK4R1a_5 HaeIII/PK4R1a_6 HaeIII/PK4R1a_7 HaeIII/PK4R1a_8 HaeIII/PK4R1a_9 HaeIII/PK4R1b_1 HaeIII/PK4R1b_2 HaeIII/PK4R1b_3 HaeIII/PK4R1b_4 HaeIII/PK4R1b_5 HaeIII/PK4R1b_6 HaeIII/PK4R1b_7 HaeIII/PK4R1b_8 II2.17 II2.3 II2.3a II2.3b III2.18a III2.18b III2.18c III2.18d L7M2.3 L7M2.3a L7M2.3b L7M2.3c L7M4.9 L7M4.9a L7M4.9b L8 L8M3.8 MseI/NBS6_1 MseI/NBS6_2 MseI/NBS6_3 MseI/NBS6_4 MseI/NBS6_5 MseI/NBS6_6 MseI/NBS6_7 MseI/PK4R1b_A MseI/PK4R1b_B MseI/PK4R1b_C MseI/PK4R1b_D MseI/PK4R1b_E MseI/PK4R1b_F MseI/PK4R1b_G MseI/PK4R1b_H RN182 RN182a RN182b RN182c RN182e RN182f RN182g RP4a81a RP4a81b RP4a81c RP4a81e RP4a81f RsaI/NBS1_1 RsaI/NBS1_10 RsaI/NBS1_11 RsaI/NBS1_12 RsaI/NBS1_13 RsaI/NBS1_2 RsaI/NBS1_3 RsaI/NBS1_4 RsaI/NBS1_5 RsaI/NBS1_6 RsaI/NBS1_7 RsaI/NBS1_8 RsaI/NBS1_9 RsaI/NBS1_A RsaI/NBS1_B RsaI/NBS1_C RsaI/NBS1_D RsaI/NBS2_1 RsaI/NBS2_11 RsaI/NBS2_2 RsaI/NBS2_3 RsaI/NBS2_4 RsaI/NBS2_6 RsaI/NBS2_8 RsaI/NBS3_1 RsaI/NBS3_2 RsaI/NBS3_3 RsaI/NBS3_5 RsaI/NBS3_A RsaI/NBS3_B RsaI/NBS3_C RsaI/NBS3_D RsaI/NBS3_E RsaI/NBS3_F RsaI/NBS3_G RsaI/NBS3_H RsaI/NBS3_I RsaI/NBS5A_1 RsaI/NBS5A_2 RsaI/NBS5A_3 RsaI/NBS5A_4 RsaI/NBS5A_5 RsaI/NBS5A_6 RsaI/NBS5A_8 RsaI/NBS6_2 RsaI/NBS6_3 RsaI/NBS6_4 RsaI/PK1Fa_1 RsaI/PK1Fa_10 RsaI/PK1Fa_11 RsaI/PK1Fa_2 RsaI/PK1Fa_3 RsaI/PK1Fa_4 RsaI/PK1Fa_5 RsaI/PK1Fa_6 RsaI/PK1Fa_8 RsaI/PK1Fa_9 RsaI/PK1Fb_1 RsaI/PK1Fb_2 RsaI/PK1Fb_3 RsaI/PK1Fb_5 RsaI/PK3Fa_1 RsaI/PK3Fa_2 RsaI/PK3Fa_3 RsaI/PK3Fa_4 RsaI/PK3Fa_5 RsaI/PK3Fa_6 RsaI/PK3Fa_7 RsaI/PK3Fa_8 RsaI/PK3Fa_9 RsaI/PK3Fa_A RsaI/PK3Fa_B RsaI/PK3Fa_C RsaI/PK3Fa_D RsaI/PK3Fa_E RsaI/PK3Fa_F RsaI/PK3Fa_G RsaI/PK3Fa_H RsaI/PK3Fa_I RsaI/PK3Fa_J RsaI/PK3Fa_K RsaI/PK3Fa_L RsaI/PK3Fa_M RsaI/PK3Fb_1 RsaI/PK3Fb_3 RsaI/PK3Fb_4 RsaI/PK3Fb_5 RsaI/PK3Fb_7 RsaI/PK3Fb_8 RsaI/PK3Fb_9 RsaI/PK4R1a_1 RsaI/PK4R1a_10 RsaI/PK4R1a_11 RsaI/PK4R1a_12 RsaI/PK4R1a_13 RsaI/PK4R1a_14 RsaI/PK4R1a_16 RsaI/PK4R1a_17 RsaI/PK4R1a_18 RsaI/PK4R1a_19 RsaI/PK4R1a_2 RsaI/PK4R1a_20 RsaI/PK4R1a_21 RsaI/PK4R1a_3 RsaI/PK4R1a_4 RsaI/PK4R1a_6 RsaI/PK4R1a_7 RsaI/PK4R1a_8 RsaI/PK4R1a_9 RsaI/PK4R1a_A RsaI/PK4R1a_B RsaI/PK4R1a_C RsaI/PK4R1a_D RsaI/PK4R1a_E RsaI/PK4R1a_F RsaI/PK4R1a_G RsaI/PK4R1a_H RsaI/PK4R1a_I RsaI/PK4R1a_J RsaI/PK4R1a_K RsaI/PK4R1b_1 RsaI/PK4R1b_12 RsaI/PK4R1b_13 RsaI/PK4R1b_2 RsaI/PK4R1b_3 RsaI/PK4R1b_4 RsaI/PK4R1b_5 RsaI/PK4R1b_6 RsaI/PK4R1b_7 RsaI/PK4R1b_8 RsaI/PK4R1b_9 RsaI/PK4R1b_A RsaI/PK4R1b_B RsaI/PK4R1b_C RsaI/PK4R1b_D RsaI/PK4R1b_E RsaI/PK4R1b_F RsaI/PK4R1b_G RsaI/PK4R1b_H RsaI/PK4R1b_I RsaI/PK4R1b_J RsaI/PK4R1b_K RsaI/PK4R1b_L S-114 S-120a S-120b S3S1.24a S5S1.1.6 S5S2.2.11 S-9202 S-9202a S-9202b S-9202c S-9202d S-9204 S-9204a S-9204b S-9204c SgSATII3 SgSATII3b SgSATII3d VAVIII8 VAVIII8a VAVIII8b VAVIII8c VAVIII8d b6 III2.18 RP4a81 S3S1.24
Map Data	Oat-2013-MxN-RGA Oat-2013-SxW-RGA Oat-2013-KxO-RGA
Probe	AluI/NBS1 [ Show all 36 ]

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