Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution

Botanical Studies

Table 2 Pi54 alleles of blast susceptible and resistant cultivars at the same SNP position

Cultivar	Resistant or susceptible	# mismatch	Alleles at chromosome 11 SNP position
Cultivar	Resistant or susceptible	# mismatch	25,263,636	25,264,119	25,264,164
Nipponbare	Susceptible (Thakur et al. 2015)	0	C	G	T
CO-39	Susceptible (Thakur et al. 2015)	12	C	A	C
Parijat	Susceptible (Thakur et al. 2015)	0.5	C/T	G	T
Pusa basmati 1	Susceptible (Thakur et al. 2015)	24	C	A	C
Budda	Resistant (Thakur et al. 2015)	30	C	A	C
IRAT-144	Resistant (Thakur et al. 2015)	4.5	C/T	G/A	T/C
Salumpikit	Resistant (Thakur et al. 2015)	2	T	G	T
Tetep	Resistant (Wang et al. 2019b)	–	C	A	C
TN1	Susceptible	1.5	C/T	G	T
Haplotype
Haplotype 1	–		T	G	T
Haplotype 2	–		C	A	C
Major/minor allele and MAF
Major allele	–		C	G	T
Minor allele	–		T	A	C
Minor allele frequency (MAF)	–		38.80%	35.86%	35.84%

Haplotype numbers are based on the kgroup numbers in Additional file 5: Dataset S4. SNP information and allele frequency were obtained from SNP-Seek (Mansueto et al. 2017)
The reference genome is the Nipponbare cultivar, which was included in the study of Thakur et al. (Thakur et al. 2015) and also part of the 3 K RGP
Alleles of Tetep were obtained through show-snps of the MUMmer version 4 package (Marçais et al. 2018), after nucmer alignment of Tetep chromosome 11 (which has the Pi54 gene) against Nipponbare chromosome 11