Table 2.

Most promising SNPs for marker development

Resistance Gene	SNP	Chromosome	Position	Resistant Allelea	Breeding Line and Variety having R Allele (%)b
xa5	S5_440644	5	440644	A	10
xa5	S5_453169	5	453169	A	10
Xa7	S6_28100960	6	28100960	A	1
Xa7	S6_28158893	6	28158893	G	2
Xa7	S6_28160615	6	28160615	G	2
Xa7	S6_28171883	6	28171883	C	2
Xa7	S6_28173425	6	28173425	A	2
xa13	S8_26013849	8	26013849	A	2
xa13	S8_26044514	8	26044514	A	2
xa13	S8_26044528	8	26044528	C	2
xa13	S8_27319974	8	27319974	C	2
xa13	S8_27520607	8	27520607	G	2
xa13	S8_27536844	8	27536844	C	2
xa13	S8_27641374	8	27641374	A	2
xa13	S8_27663433	8	27663433	C	2
Xa21	S11_21190115	11	21190115	T	4
Xa21	S11_21246561	11	21246561	G	3
Xa4	S11_27603791	11	27603791	T	60
Xa4	S11_27603799	11	27603799	A	59
xa25	S12_17305618	12	17305618	A	15
xa25	S12_17305619	12	17305619	T	72

^a Allele corresponding to resistant phenotype based on 198 indica genotypes

^b Percentage of indica breeding lines and varieties having the putative resistant allele