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

Yang, Guili; Chen, Siping; Chen, Likai; Sun, Kai; Huang, Cuihong; Zhou, Danhua; Huang, Yuting; Wang, Jiafeng; Liu, Yongzhu; Wang, Hui; Chen, Zhiqiang; Guo, Tao

doi:10.1186/s12284-019-0272-3

Rice

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
SK03_15,397,382	LWR	0.0077	0.1824	3	15,397,382	*	LOC_Os03g26920	OsSCP12
SK04_22,435,296	ML	0.0036	0.2392	4	22,435,296	*	LOC_Os04g37730	RING-H2 finger protein ATL3B precursor
SK04_22,435,296	LWR	0.0092	0.1749	4	22,435,296	*	LOC_Os04g37730	RING-H2 finger protein ATL3B precursor
SK05_5,396,755#	ML	0.0074	0.1985	5	5,396,755	*	LOC_Os05g09550	Der1-like family domain containing protein	grain width
SK05_5,396,755#	LWR	0.0066	0.1939	5	5,396,755	*	LOC_Os05g09550	Der1-like family domain containing protein	grain width
SK05_5,537,852#	ML	0.0027	0.2493	5	5,537,852	GW5	LOC_Os05g09520	Calmodulin-binding motif family protein	grain width
SK05_5,537,852#	LWR	0.0046	0.2085	5	5,537,852	GW5	LOC_Os05g09520	Calmodulin-binding motif family protein	grain width
SK06_7,670,859	ML	0.0074	0.1956	6	7,670,859	–	–	Intergenic	Alkali digestion value
SK06_7,670,859	MRW	0.0067	0.1872	6	7,670,859	–	–	Intergenic	Alkali digestion value
SK09_15,765,355	ML	0.0075	0.1979	9	15,765,355	–	–	Intergenic
SK09_15,765,355	LWR	0.0073	0.1881	9	15,765,355	–	–	Intergenic
SK06_2,781,588	MW	0.0067	0.1871	6	2,781,588	OsSSI	–	Intergenic	quality
SK06_2,781,588	LWR	0.0066	0.191	6	2,781,588	OsSSI	–	Intergenic	quality
SK06_873,670	MW	0.0076	0.1908	6	873,670	*	LOC_Os06g02520	interacting protein of DMI3, putative, expressed	amylose content
SK06_873,670	LWR	0.0025	0.26	6	873,670	*	LOC_Os06g02520	interacting protein of DMI3, putative, expressed	amylose content
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

# 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

Back to article page