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Rice

Table 1 Sampled O. sativa loci under positive selection during the early domestication period

From: Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies

Trait category

Locusd

5′ mutationsa

Coding mutationsa,b

References

Grain shattering/awn length

SH4

6(1 idl)

1(nons)c

Li et al. (2006b)

 

An-1(Awn-1)

 

2(1non, 1 idl:1 aa)

Luo et al. (2013)

 

An-2(Awn-2)

4

 

Gu et al. (2015)

 

RAE2

3(1 idl)

1(idl:stop codon)

Wang et al. (1995)

Grain taste/color

C1

2(1 idl)

 

Reddy et al. (1998)

 

DFR

2(1 idl)

 

Furukawa et al. (2007)

 

Rc

3(1 idl)

2(1 nons, 1 idl:stop codon)

Sweeney et al. (2006)

 

MYB3

 

2(1 nons, 1 idl:3 aa)

This study

Grain productivity

GIF1

2(idl)

2(2 nons)

Wang et al. (2008)

 

GL3.2

7(3 idl)

3(1 nons)

Xu et al. (2015)

 

AGO2

3(3 idl)

1(1 nons)

Yin et al. (2020)

Flowering time

Hd1

1

3(2 nons,1 idl:2 aa)

Yano et al. (2000)

 

Hd6

2(1 idl)

 

Takahashi et al. (2001)

 

Hd3a

4(1 idl)

 

Kojima et al. (2002)

Tolerance/resistance

EPSPS

3(1 idl)

 

Xu et al. (2002)

 

MYB15

3(1 idl)

3(2 idl:5 aa)

This study

 

AGO2

3(3 idl)

1(1 nons)

Yin et al. (2020)

 

DAHPS2

3

1

This study

Growth

PROG1

2(1 idl)

1

Jin et al. (2008)

 

TCP19

2(1 idl)

 

Liu et al. (2021b)

Unknown

ME

3

1(idl:2 aa)

This study

 

Os04g47040

 

1(idl:5 aa)

This study

 

Os12g34860.1

 

2(1 nons, 1 idl:stop codon)

This study

  1. aNumber of mutations includes those of substitutions (synonymous or nonsynonymous (nons) for coding regions) and indels (idl). Only nons and idl are listed for simplicity. Amino acid (aa) changes introduced by each indel was listed after comma
  2. bAll mutations are listed but only those underlined were considered under positive selection
  3. cThis mutation was experimentally confirmed by Li et al. (2006b)
  4. dLoci in bold have selected mutation(s) tested functional in at least one experiment
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