Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Rice

Table 1 21 QTLs identified for plant description traits in the full panel, and Indica and Japonica subpanels. Detailing for the QTL analysis; significance threshold -log₁₀ (p value) ≥ 8.0; panel in which significant associations were detected, highest level of significance for all panels and overlaps with publish QTLs for Vietnamese rice populations or for the 3 K RGP

QTL Name	Trait	Chrom	Panel	Segment position (bp)	Sig SNPs nb	min P.value	Number of genes	Overlap with QTLs
1_DI	Diameter_Internode	2	FP	6,805,273 - 6,923,410	3	3.12E-08	18
2_GL	Grain_Length	2	FP & Jap	15,480,976 - 16,798,043	27	2.69E-12	197	panicle morphology [Ta 2018]
3_GL_jap	Grain_Length	2	Jap	35,638,527 - 35,927,940	4	3.16E-11	58
4_GW_jap	Grain_Width	3	Jap	3,334,516–3,532,506	3	5.26E-09	34	Leaf Length [Phung 2016]
5_GS	Grain_Length	3	FP & Ind & Jap	16,520,656 - 16,908,475	30	9.26E-17	53	grain width and grain length [Mansueto 2017, Li 2018]
6_GS	Grain_Width	3	FP & Jap	17,686,248 - 20,833,777	355	2.02E-13	471	panicle morphology [Ta 2018]
7_GL	Grain_Length	4	FP	12,043,539 - 13,108,767	14	5.51E-11	167
8_HD	Heading_Date	4	FP	16,165,354 - 16,384,087	4	1.72E-08	37
9_PL	Panicle_Length	5	FP	667,557 - 767,557	2	6.17E-08	20
10_GS	Grain_Width	5	FP & Ind	4,802,345 - 5,383,914	57	2.40E-11	75	grain width and grain length [Mansueto 2017, Li 2018]
11_GL	Grain_Length	6	FP & Ind	1,561,006 - 1,664,716	16	2.68E-10	17
12_GL	Grain_Length	6	FP & Ind	6,680,831 - 7,190,137	51	1.81E-14	78
13_GL	Grain_Length	6	FP	7,453,914 - 7,553,914	2	5.90E-08	13
14_PL	Panicle_Length	6	FP	20,400,110 - 20,500,110	2	2.72E-08	13
15_GL_jap	Grain_Length	7	Jap	11,519,294–12,296,525	3	5.76E-08	99
16_FP	Floret_Pubescence	8	FP	18,004,654 - 18,104,654	2	1.64E-08	17
17_FP	Floret_Pubescence	8	FP	26,175,268 - 26,275,268	2	6.06E-08	15
18_FP	Floret_Pubescence	9	FP	6,656,837 - 7,940,621	51	7.23E-12	168
19_HD	Heading_Date	9	FP	14,067,272 - 14,807,406	7	6.86E-09	115
20_GW_jap	Grain_Width	10	Jap	1,098,998 - 1,404,807	6	3.61E-12	52
21_LW	Leaf_width	12	FP	17,445,137 - 17,561,823	2	2.14E-09	13

FP Full panel, Ind Indica subpanel, Jap Japonica subpanel, Chrom Chromosome, Sig SNPs nb Number of significant SNPs. References: Ta 2018 (Ta et al. 2018), Phung 2016 (Phung et al. 2016), Mansueto 2017 (Mansueto et al. 2017), Li 2018 (Li et al. 2018)