Genome-wide association study identifies elite alleles of FLA2 and FLA9 controlling flag leaf angle in rice

BMC Genomics

Table 2 Genome-wide significant association of rice FLA traits

QTLs	Chromosome	Position	Allele	Log₁₀(P)^a	Environment	MAF^b	Known Genes/QTLs
qFLA1.1	1	12,713,277	G/C	7.43	2022, DY	0.35
	1	12,908,893	T/C	7.04	2023, LJ	0.34
qFLA1.2	1	13,332,762	G/A	6.31	2022, DY	0.38
	1	13,158,926	T/G	8.24	2023, LJ	0.34
qFLA1.3	1	16,203,835	A/C	6.67	2022, DY	0.40
	1	16,418,160	A/G	6.37	2023, LJ	0.38
qFLA1.4	1	24,305,157	T/C	6.29	2022, DY	0.38
	1	24,514,119	T/C	8.61	2023, LJ	0.37
qFLA2	2	32,057,055	C/T	6.57	2022, DY	0.36
	2	32,035,468	G/A	7.15	2023, LJ	0.37
qFLA7.1	7	19,733,783	A/T	6.65	2022, DY	0.34
	7	19,528,068	A/T	6.38	2023, LJ	0.05
qFLA7.2	7	29,419,260	C/T	6.36	2022, DY	0.06	qFLA7e [7]
	7	29,641,042	A/G	6.29	2023, LJ	0.26	qFLA7e [7]
qFLA8.1	8	15,708,371	A/G	7.75	2022, DY	0.11
	8	15,704,229	C/T	6.04	2023, LJ	0.67
qFLA8.2	8	21,508,180	A/G	8.89	2022, DY	0.32	qFLA8f [7]
	8	21,599,529	C/T	6.37	2023, LJ	0.32	qFLA8f [7]
qFLA9.1	9	1,568,461	C/T	6.54	2022, DY	0.32
	9	1,403,199	G/A	6.57	2023, LJ	0.06
qFLA9.2	9	4,404,631	C/T	6.42	2022, DY	0.06
	9	4,217,431	A/G	6.36	2023, LJ	0.06

^aThe -log₁₀ (P) value obtained by GWAS in different environments are described [58]
^bMinimum allele frequency

ISSN: 1471-2164