Skip to main content
. 2020 Jun 12;11:742. doi: 10.3389/fpls.2020.00742

TABLE 2.

SNP and PCR-based markers in rutabaga accessions, their chromosomal location and linkage association with clubroot caused by 17 single-spore and field isolates representing 16 different pathotypes of Plasmodiophora brassicae.

Modelθ Used SNP Markerα Marker physical position Linkage groupβ PathotypeΩ Description of gene functions in Brassica rapa, B. oleracea, B. napus, and Arabidopsis thaliana¥
Start End
PCA + K Bn_A01_p161237 161177 161236 A01 3H and 6M Molecular function unknwon
PCA + K Bn_A01_p3070657a 3070658 3070717 A01 5K Topoisomerase family protein
PCA + K Bn_scaff_16394_1_p847636 23261545 23261593 A01 2F Molecular function unknwon
PCA/Q + K Bn_scaff_16876_1_p908602b 402290 402348 A02 3H Nodulin-related; WAT1-related protein At5g40230-like
PCA/Q + K Bn_A02_p4210188 4209928 4209987 A02 3H Molecular function unknwon
PCA + K Bn_A02_p6615821c 6615522 6615581 A02 3H Molecular function unknwon
PCA/Q + K Bn_A03_p21205471d 19989670 19989721 A02 3H GDSL-motif lipase/hydrolase family protein
PCA + K Bn_scaff_17721_1_p272248 25189709 25189756 A02 8N Molecular function unknwon
PCA + K Bn_A03_p7088375 7088115 7088174 A03 6M EPIDERMAL patterning factor-like protein 6
PCA + K Bn_A03_p7094698 7094346 7094430 A03 6M Molecular function unknwon
PCA + K Bn_A03_p8764481 8764218 8764282 A03 5I Molecular function unknwon
PCA + K Bn_A03_p13610858 13610459 13610518 A03 8P WD-40 repeat family/beige-related; BEACH domain-containing protein
PCA + K Bn_Scaffold000164_p55747e 16537330 16537377 A03 2B Transcription activator; two-component response regulator-like APRR1
PCA + K Bn_A07_p6850383f 19733579 19733672 A03 3O Catalytic/cation binding/hydrolase
PCA/Q + K Bn_A03_p21205471d 21204972 21205062 A03 3H Histone deacetylase
PCA/Q + K Bn_A03_p21377430 21376931 21377030 A03 3H Molecular function unknwon
Q + K Bn_A03_p21487106 21486607 21486666 A03 3H Leucine-rich repeat receptor-like serine/threonine-protein kinase BAM2
PCA + K Bn_scaff_16110_1_p2556157g 28182622 28182702 A03 3H DDB1-CUL4 associated factor 1; nucleotide binding
PCA + K Bn_A01_p3070657a 28201604 28201639 A03 5K DNA topoisomerase family protein
PCA + K Bn_A04_p248884 248621 248685 A04 3H Molecular function unknwon
PCA + K Bn_A04_p251383h 251033 251182 A04 3H OTU-like cysteine protease family protein
PCA + K Bn_A04_p15492182 15488727 15491658 A04 5K Chaperone protein dnaJ 13; DNAJ heat shock N-terminal
PCA + K Bn_scaff_16394_1_p842382 6023280 6023303 A04 2F Condensin complex subunit 3
PCA + K Bn_scaff_16394_1_p920749 6053461 6053519 A04 2F Molecular function unknwon
PCA/Q + K Bn_scaff_16876_1_p908602b 7580663 7580762 A04 3H Transcriptional elongation regulator; WAT1-related protein At5g40230
PCA + K Bn_scaff_15585_1_p978781i 15378727 15381200 A04 3O PLL1 (POLTERGEIST LIKE 1); catalytic/protein serine/threonine phosphatase
PCA/Q + K Bn_A05_p894768 894769 894868 A05 3H DEAD/DEAH box helicase, putative; P-loop containing hydrolases protein
Q + K Bn_A05_p3191390 3191391 3191450 A05 3H Jacalin-related lectin 22-like
PCA + K Bn_scaff_15585_1_p978781i 4971159 4973632 A05 3O PLL1 (POLTERGEIST LIKE 1); catalytic/protein serine/threonine phosphatase
PCA + K Bn_A05_p16738871 16737511 16737570 A05 6M Translocation protein-related; nuclear transcription factor Y subunit A-9
PCA + K Bn_A05_p17894045j 17892395 17892544 A05 6M 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase
PCA + K Bn_A05_p19650278 19648618 19648677 A05 8N Molecular function unknwon
PCA + K Bn_A05_p19650965 19649366 19649425 A05 8N Molecular function unknwon
PCA + K Bn_A05_p17894045j 1871714 1871836 A06 6M Fucosyltransferase, transferring glycosyl groups
PCA/Q + K Bn_A06_p17037739 17036640 17036739 A06 5C ATP binding/endoribonuclease, serine/threonine kinase
PCA/Q + K Bn_A06_p18000461 17999362 17999421 A06 3H Endonuclease, putative, Flap endonuclease
PCA + K Bn_A07_p6850383f 6849583 6849682 A07 3O BGLU9 (BETA GLUCOSIDASE 9); catalytic/cation binding/hydrolase
PCA + K Bn_A07_p6542254k 6541555 6541704 A07 3O Molecular function unknwon
PCA + K Bn_A07_p22005058 22003808 22003957 A07 5I Alpha-1,3/1,6-mannosyltransferase ALG2
PCA + K Bn_A05_p17894045j 2515487 2515609 A08 6M Fucosyltransferase, transferring glycosyl groups
PCA + K Bn_A08_p8869180 8867982 8868079 A08 3H SH3 domain-containing protein 1 (SH3P1)
PCA/Q + K Bn_A08_p10123561 10122198 10122262 A08 5K Molecular function unknwon
PCA + K Bn_scaff_16110_1_p2556157g 13408834 13408889 A08 3H DDB1-CUL4 Associated factor 1; nucleotide binding
PCA + K Bn_A07_p6542254k 16843055 16843176 A08 3O SYP61; syntaxin-61-like; SNAP receptor
PCA + K Bn_A08_p17061248 17059485 17059549 A08 2F Molecular function unknwon
PCA + K Bn_A08_p17393018 17391255 17391319 A08 8N Molecular function unknwon
PCA + K Bn_A08_p18310412 18308549 18308613 A08 5K Molecular function unknwon
PCA/Q + K Bn_A03_p21205471d 2809099 2809170 A09 3H Histone deacetylase
PCA + K Bn_A07_p6542254k 11862168 11862292 A09 3O SYP61 syntaxin-61-like; SNAP receptor
PCA + K Bn_A04_p251383h 30512170 30512309 A09 3H OTU-like cysteine protease family protein
PCA + K Bn_A02_p6615821c 8176867 8176897 A10 3H Molecular function unknwon
PCA/Q + K Bn_scaff_16665_1_p188604 52668601 52668672 C03 3H Molecular function unknwon
PCA/Q + K Bn_scaff_16665_1_p199303 52679244 52679315 C03 3H Molecular function unknown
PCA + K Bn_scaff_17721_1_p273764 49814773 49814837 C02 8N Vegetative storage protein 2
PCA + K Bn_scaff_17721_1_p309137 49779344 49779408 C02 8N Molecular function unknown
PCA/Q + K Bn_scaff_18338_1_p871455 14173597 14173745 C05 2F, 5I and 3A Molecular function unknown
PCA/Q + K Bn_scaff_16876_1_p908602 b 5278 5377 Scaffold000522 3H Molecular function unknwon
PCA + K Bn_Scaffold000247_p28610 28505 28613 Scaffold000247 5K Molecular function unknwon
PCA + K Bn_Scaffold000164_p46170 46171 46230 Scaffold000164 2B ATMRP8; ATPase, coupled to transmembrane movement, ABC transporter C family member 6-like
PCA + K Bn_Scaffold000164_p55747e 55748 55847 Scaffold000164 2B Transcription activator; two-component response regulator-like APRR1
PCA + K KB29N19 (SSR) 24637310 24637562 A03 3H, 6M, 8N, 2B, 3A, 5C, 5G and 5I Molecular function unknown (Overlapping gene Bra019372)
PCA + K B0903 (SSR) 24388788 24389001 A03 5C, 5L and 5K Molecular function unknown (overlapping gene Bra019408)
PCA + K B1005 (InDel) 24376817 24377055 A03 5K Disease resistance protein (TIR-NBS-LRR class) (overlapping gene Bra019410)
PCA + K A08-5021 (SSR) 11614477 11614809 A08 5L Cyclase-associated protein 1-like (overlapping gene Bra034629)

θMixed Linear Model (MLM) designations: PCA, principal component analysis; Q, population structure; K, Kinship. αSNP markers denoted with the same superscript letter mapped to multiple chromosomes on the reference genomes. The type of PCR-based markers showing trait association has been specified. βLinkage groups A1-A10 = Brassica rapa and C1-C9 = Brassica oleracea. ΩPathotype designations are as per the Canadian Clubroot Differential Set (letters) and the system of Williams (numbers). ¥Putative functions are based on matching entries in the GenBank database of NCBI.