Appendix 6. Figures

Coefficient0.29 0.46 0.63 0.80 0.98

ShaheenBasmati

Azucena Jasmati KDML105 MahiSugandha IR64 KalingaIII Sugandha-1 Sherbati1 Sherbati2 PusaSugandha1 PusaSugandha2 PusaSugandha3 Pak386 Supra Basmati198 Basmati370 Ranbir Taraori SuperBasmati Basmati2000 ShaheenBasmati Basmati385F Pusa1121 PusaBasmati

Figure 1A. 24 rice varieties with 41 InDel markers.

Coefficient0.27 0.45 0.64 0.82 1.00

HaryanaBasmati

Basmati370 DehraDun Basmati217 Ranbir Taraori Kernel Basmati198 Yamini SuperBasmati PunjabBasmati Basmati2000 ShaheenBasmati Basmati385 Azucena Jasmati PusaBasmati Pusa1121 PusaSugandha2 PusaSugandha3 MahiSugandha KDML105 MugadSugandha Sugandha-1 Superfine PusaSugandha1 Sherbati1 Sherbati(awns) IR64 KalingaIII Sherbati2 Supra Pak386 Kasturi HaryanaBasmati

Figure 1B. 34 rice varieties with a sub-set of nine InDel markers

Figure 2. Example of ISSR fragments separated on the Bioanalyser. The problem of variable band intensity meant that this marker system was not considered further.

Pusasugandha

II

Pusasugandha

I

Supra

Pak 386

SherbatiA

SherbatiII

SherbatiI

ShaheenB

as

Basm

ati 2000

Super

PusaB

asmati 1

Taraori

Figure 3.. INDEL Multiplex panel 1 (IMPX1).

Figure 4a. Four INDEL variety test

Figure 4b. Four INDEL variety test

Figure 4a. Four INDEL variety test

Figure 5. Agilent fingerprint profiles for 12 different samples tested with 4-INDEL test. (Note ignore the band between 400 and 500 bp in lane 4; this is an artifact of the software).

Figure 6. Manual Height Threshold (FU) indicated by a green line is reduced from 20 to 2 which allows the area for the 168 non-basmati peak to be given.

Figure 7a. INDEL B8 Quantitative test showing replicate test samples

Figure 7. b. INDEL B8 quantitative test showing standards

Quantitative SOP Validation

0.07.0

14.021.028.035.042.049.056.063.070.077.084.0

CEQ Agilent Agilent Agilent Agilent

RM201 SOP1(RM201)

SOP1(RM201)

SOP2(INDEL)

SOP2(INDEL)

FDNAS FDNAS WSS FDNAS WSS

Estim

ated

% n

on-b

asm

ati

2861

3021

3028

3101

Figure 8 Validation of Quantitative SOPs in two laboratories (WSS and FDNAS). The results for four different commercial “unknown”samples are shown relative to Quantification with RM201 on the CEQ 8000 (CEQ). Note the permitted level of non-basmati is 7%.