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Table 8 List of haplotype variation identified in genomic regions with sequence information on selected rice landraces

From: Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces

Chr. (Physical position in Mba)

Marker located

Reference Allele

Alt Allele

Position (Mb)

SNP type

Traits associated in MLM approach

CHR1 (9318264–9318812)

RM1032

T

C

C

A

9318278

9318295

Up-stream gene variant

Intergenic region variant

PH, RL (Panel II)

CHR4 (13083892–13084502)

RM5633

T

A

A

C

T

C

13083944

13083963

13084032

Intergenic region variant

Intergenic region variant

Intergenic region variant

DSI, RYR (Panel I)

SPAD, Chl, SLA (Panel II)

CHR6 (31082906–31089743)

RM1031

G

A

31089179

Down-stream gene variant

SF (Panel I)

CHR11 (19926456–19926984)

RM5961

T

A

G

G

19926506

19926513

Down-stream gene variant

Down-stream gene variant

1000GW (Panel I)

PH, CID, SLA (Panel II)

  1. Abbreviations: Chl Chlorophyll content, CID Carbon Isotope Discrimination, DSI Drought susceptibility index, PH Plant Height, RL Root length, RYR Relative Yield Ratio, SPAD Chlorophyll content (%), SLA Specific Leaf Area, SF Spikelet Fertility, 1000GW Thousand grain weight
  2. a The physical position of SSR markers and genes underlying were obtained from www.ricebase.org