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Table 6 Associations between KASP markers and phenotypes

From: Development of a core SNP arrays based on the KASP method for molecular breeding of rice

KASP marker Traits P value R 2 Chr. Physical Position Gene located or gene closely linked Gene locus Encoded protein Known associated trait
SK05_27,742,506 # ML 0.0067 0.1959 5 27,742,506 LTN1* LOC_Os05g48390 ubiquitin conjugating enzyme protein yield
LWR 0.006 0.1928
MT 0.0096 0.0797
MRW 0.0053 0.2028
SK02_1,968,779 ML 0.0067 0.1959 2 1,968,779 * LOC_Os02g04450 plant-specific domain TIGR01589 family protein  
LWR 0.006 0.1928
MT 0.0096 0.0797
SK02_8,978,321 ML 0.0067 0.1959 2 8,978,321 * LOC_Os02g15870 molybdenum cofactor biosynthesis protein 1  
LWR 0.006 0.1928
ML 0.0096 0.0797
SK03_15,001,183 ML 0.0067 0.1959 3 15,001,183 IRO3* LOC_Os03g26210 helix-loop-helix DNA-binding domain containing protein Green leafhopper resistance
LWR 0.006 0.1928
MT 0.0096 0.0797
SK03_16,075,626 # ML 0.0067 0.1959 3 16,075,626 * LOC_Os03g27990 STRUBBELIG-RECEPTOR FAMILY 7 precursor Brown rice surface area
LWR 0.006 0.1928
MT 0.0096 0.0797
SK03_28,852,757 ML 0.0068 0.1961 3 28,852,757 * LOC_Os03g50530 expressed protein Alkali digestion value
LWR 0.0061 0.1928
MT 0.0097 0.0804
SK04_20,396,474 ML 0.0069 0.1965 4 20,396,474 Intergenic  
LWR 0.0061 0.1926
MT 0.0094 0.0809
SK04_25,898,378 ML 0.0053 0.2347 4 25,898,378 * LOC_Os04g43750 kinase, pfkB family  
LWR 0.0046 0.2383
MT 0.0078 0.0887
SK06_26,266,828 ML 0.0069 0.1965 6 26,266,828 * LOC_Os06g43650 secreted salivary protein, putative, expressed  
LWR 0.0061 0.1926
MT 0.0094 0.0809
SK09_3,717,701 ML 0.0067 0.1959 9 3,717,701 Intergenic  
LWR 0.006 0.1928
MT 0.0096 0.0797
SK03_15,397,382 MW 0.0081 0.1784 3 15,397,382 * LOC_Os03g26920 OsSCP12  
LWR 0.0077 0.1824
SK04_22,435,296 ML 0.0036 0.2392 4 22,435,296 * LOC_Os04g37730 RING-H2 finger protein ATL3B precursor  
LWR 0.0092 0.1749
SK05_5,396,755# ML 0.0074 0.1985 5 5,396,755 * LOC_Os05g09550 Der1-like family domain containing protein grain width
LWR 0.0066 0.1939
SK05_5,537,852# ML 0.0027 0.2493 5 5,537,852 GW5 LOC_Os05g09520 Calmodulin-binding motif family protein grain width
LWR 0.0046 0.2085
SK06_7,670,859 ML 0.0074 0.1956 6 7,670,859 Intergenic Alkali digestion value
MRW 0.0067 0.1872
SK09_15,765,355 ML 0.0075 0.1979 9 15,765,355 Intergenic  
LWR 0.0073 0.1881
SK06_2,781,588 MW 0.0067 0.1871 6 2,781,588 OsSSI Intergenic quality
LWR 0.0066 0.191
SK06_873,670 MW 0.0076 0.1908 6 873,670 * LOC_Os06g02520 interacting protein of DMI3, putative, expressed amylose content
LWR 0.0025 0.26
SK03_16,733,441# ML 0.0038 0.2296 3 16,733,441 GS3 * Os03g0407400 Transmembrane protein grain shape
SK03_872,082# ML 0.0091 0.1816 3 872,082 * LOC_Os03g02440 WD repeat-containing protein 44, putative, expressed number of spikelets per panicle
SK04_4,599,886 MT 0.0073 0.0958 4 4,599,886   LOC_Os04g08510 OsFBX117 - F-box domain containing protein, expressed Green leafhopper resistance
SK05_5,339,085# MW 0.0077 0.1796 5 5,339,085 GW5* LOC_Os05g09500 Calmodulin-binding motif family protein grain width
SK06_27,438,624# LWR 0.0049 0.2072 6 27,438,624 APO1 * LOC_Os06g45460 OsFBX202 - F-box domain containing protein yield
SK06_27,481,339# LWR 0.0048 0.2056 6 27,481,339 APO1 * LOC_Os06g45460 OsFBX202 - F-box domain containing protein, expressed yield
SK06_27,498,819# LWR 0.0048 0.2056 6 27,498,819 APO1 LOC_Os06g45460 OsFBX202 - F-box domain containing protein yield
SK06_27,526,542# LWR 0.0048 0.2056 6 27,526,542 APO1 LOC_Os06g45460 OsFBX202 - F-box domain containing protein yield
SK06_647,869 LWR 0.0073 0.1893 6 647,869 * LOC_Os06g02160 AMP-binding enzyme family protein, expressed Brown planthopper resistance
SK06_701,439 LWR 0.0088 0.194 6 701,439 * LOC_Os06g02240 RNA recognition motif containing protein Brown planthopper resistance
SK07_472,805# ML 0.0021 0.2688 7 472,805 DEP * LOC_Os07g01820 OsMADS15 yield
SK08_21,582,840# ML 0.0094 0.184 8 21,582,840 COE1* LOC_Os08g34380 Receptor-like kinase, putative, expressed yield
SK11_23,607,373 LWR 0.0084 0.1769 11 23,607,373 Intergenic Green leafhopper resistance
  1. # means the KASP marker was developed based on cloned genes or on identified loci responsible for yield; * means the KASP marker site is within the genomic sequence; − means the KASP marker is located within an intergenic region