Table 1 Association between OsTb2 polymorphic sites and tiller numbers.

From: Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice

Polymorphic sites

Position on chr09

Segregating genotypes

P-valuea (40 DAG)

P-value (50 DAG)

SNP1

15272303

C/T

0.08713

0.5717

SNP2

15272752

G/A

0.07238

0.8106

indel1

15273436~15273438

3bp+/3bp−b

0.01099

1.30E-11

SNP3

15274099

T/C

3.80E-05

2.55E-12

SNP4

15274295

T/C

0.4748

0.0003731

indel2

15274601~15274603

3bp+/3bp-

0.3998

5.88E-08

SNP5

15274707

G/A

0.2722

1.38E-08

SNP6

15274798

C/T

rare SNPs

rare SNPs

SNP7

15274921

G/A

0.2306

9.45E-07

  1. Source data are provided as a Source Data file.
  2. aFor each polymorphic site, we divided the accessions into two homozygous groups. Students’ t-test was then used to assess the differences in tiller numbers and determine significant P values between two groups. Indel I and SNP3 are significantly associated with tiller numbers at both 40 DAG and 50 DAG. The effect sizes are shown in Supplementary Table 1.
  3. b3bp+ refers to the three base pair insertion; 3bp− refers to the three base pair deletion. The positions on Chr09 are in reference to genome version IRGSP 5.0.
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