Novel QTL for Lateral Root Density and Length Improve Phosphorus Uptake in Rice (Oryza sativa L.)

Rice

Table 3 Putative QTL for lateral root traits detected in BC1F5 population (n = 98) grown in a field experiment on phosphorus-deficient soil in Tsukuba, 2021

Trait	QTL	Chromo some	Nearest marker^a	Physical position (bp)	Position (cM)	Support interval	LOD	LOD threshold	R²	Additive effect	Allelic effect (%)	Positive allele
L-type density on crown root (LDC)	qLDC5	5	S05_27313585	26,276,202	60	51–75	11.4	3.6	0.46	0.43	33.8	DJ123
S-type density on crown root (SDC)	qSDC1	1	S01_29957378	29,269,714	180	176–188	6.3	4.0	0.17	0.79	22.9	DJ123
S-type density on L-type (SDL)	qSDL9	9	S09_8741627	8,182,160^b	17	8–25	4.0	3.6	0.17	0.81	16.8	DJ123
Single S-type length on L-type (SLL)	qSLL1	1	S01_41579214	40,879,329	258	242–260	5.5	4.5	0.24	0.10	4.21	DJ123
Root Number (RNO)	qRNO9	9	S09_13090502	12,924,104	43	40–44	3.6	3.6	0.17	0.69	10.1	DJ123

LOD thresholds were determined through 1000-time permutations at α = 0.05
^aMarker names indicate chromosomal location followed by their physical position based on the alignement with the Azucena genome (S09_8965532 indicates a SNP position at 8.965 Mb on chromosome 9). Physical position: correscponding position based on the Nipponbare referennce genome. Additive effects were estimated as the phenotypic effect of substituting one A (DJ123) allele with a B (Nerica4) allele with positive values indicating DJ123 alleles having a positive effect on phenotypic values. Allelic effects were calculated based on additive effects for the difference between homozygous individuals (AA vs. BB) and are given in % based on the overall mean of each trait
^bA BLAST search identified a second hit in the Nipponbare genome at 7,069,632 bp on chromosome 9