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Table 3 Numbers of Oryza sativa accessions with SNPs and deletions associated with virus resistance among the 3,000 sequenced accessions

From: Allele mining and enhanced genetic recombination for rice breeding

Gene name

Locus namea

SNP/deletion associated with phenotypeb

Expected phenotypec

Number of corresponding accessions among 3,000 accessions (%)

Reference

 

LOC_Os07g36940

3167

   

tsv1

T

A

T

G

T

T

S to RTSV

2,821 (94)

Lee et al. (2010)

T

G

T

G

T

T

R to RTSV

78 (2.6)

T

A

T

G

C

T

R to RTSV

21 (0.7)

T

A

T

−

−

−

R to RTSV

52 (1.7)

  

Othersd

Uncertain

28 (0.9)

  

727

 

STV11

LOC_Os11g30910

G

C

G

G

C

G

S to RSV

2,798 (93.3)

Wang et al. (2014)

−

−

−

−

−

−

R to RSV

10 (0.3)

  

Othersd

Uncertain

192 (6.4)

  

925

RYMV1

LOC_Os04g42140

G

A

A

A

T

A

S to RYMV

3,000 (100)

Albar et al. (2006)

A

A

A

A

T

A

R to RYMV

0(0)

  1. aFrom Michigan State University’s Rice Genome Annotation Project Release 7 (Os-Nipponbare-Reference-IRGSP-1.0 (Kawahara et al. 2013)
  2. bNumbers above the first nucleotides indicate the positions in the coding sequences of the corresponding genes. Nucleotides (underlined bold) and deletions (−) are those reported to be associated with resistance to the corresponding viruses
  3. cS: susceptible, R: resistant, RTSV: Rice tungro spherical virus, RSV: Rice stripe virus, RYMV: Rice yellow mottle virus
  4. dSequences with other SNPs or deletions, and uncertain sequences