with quantitative characters at both locations. Table 3.

17 represents that SDS

PAGE was positively and significantly correlated to SSR markers. Out of 116

accessions 74 (72%) accessions were grouped in Cluster III based on SDS-PAGE

analysis, while 41 rice accessions were grouped in other six clusters. According

to seed storage protein profile some accessions were put in same cluster because

of complete similarity of protein banding profile which represented different

phenotypes in morphological analysis. However in SSR based cluster analysis

these accessions were grouped in different clusters. In present study seed

storage proteins profile exhibited low genetic diversity as compared with agro-

morphological traits and DNA based SSR primers. Identification of the

accessions on the basis of biochemical analysis alone might not be effective for

diversity assessment in rice crop.

3.4 ASSESMENT OF BACTERIAL BLIGHT RESISTANT GENE (Xa4, xa5,

xa13, Xa21and fgr) THROUGH STS MARKERS

In present study 96 rice accessions from Northern Pakistan were analyzed

for presence and absence of bacterial blight resistant genes (Xa4, xa5, xa13, Xa21

and fgr) through PCR amplification using primers Nbp 181, RG556, RG136, pTA

248 and RG 28 (Table 3.18)

3.4.1 Analysis of rice accessions for Xa4 gene

Ninety six accessions from northern Pakistan were analyzed for the presence and

absence of bacterial blight resistant gene Xa4 by using PCR based technique. For

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primer amplification study a tightly linked STS marker nbp 181 was used. PCR

reaction was carried out in 0.5 ml tube with PCR cycle specific to primer

correspond to Xa4 gene. The PCR product was analyzed on 2% agarose gel

which shows presence or absence of the band. The absence of corresponding

band shows that non polymorphic regions were present in the cultivars and

therefore the products were not amplified. Primer which tightly linked to

dominant bacterial blight resistant Xa4 gene produces 140 bp fragment, while

susceptible accessions produced 120 bp fragment (Fig. 3.25A). Out of 96

accessions 42 accessions were found to have resistant gene, while 54 were lacking

this gene (Table 3.18).

3.4.2 Analysis of rice accessions for xa5 gene

Ninety six accessions from northern areas of Pakistan were analyzed for the

presence and absence of bacterial blight resistant gene xa5 by using PCR based

technique. For primer amplification study a tightly linked STS marker RG 556

was used. Primer which was tightly linked to bacterial blight resistant xa5

produced 500 bp fragment, while susceptible accessions produced 500 and 480

bp double band (Fig. 3.25B). Out of 96 accessions 52 accessions were found to

have resistant gene, while 44 were lacking this gene (Table 3.18).

3.4.3 Analysis of rice accessions for xa13 gene.

Ninety six accessions from northern areas of Pakistan were analyzed for the

presence and absence of bacterial blight resistant gene xa13 by using PCR based

technique. For primer amplification study a tightly linked STS marker RG 136

95
was used. Primer which tightly linked to bacterial blight resistant xa13 produces

1120 bp fragment, while susceptible accessions produced 800 bp band (Fig.

3.25C). Out of 96 accessions 50 accessions were found to have resistant gene,

while 46 accessions were lacking this gene (Table 3.18).

3.4.4 Analysis of rice accessions for Xa21 gene

Ninety six accessions from Northern areas of Pakistan were analyzed for the

presence and absence of bacterial blight resistant gene Xa21 by using PCR based

technique. For primer amplificationstudy a tightly linked STS marker pTA 248

was used. Primer which tightly linked to bacterial blight resistant Xa21 produces

1000 bp fragment, while susceptible accessions produced 700 (Fig. 3.25D). Out of

96 accessions all accessions were found to have susceptible genes (Table 3.18)

3.4.5 Analysis of rice accessions for fgr gene.

Ninety six accessions from northern areas of Pakistan were analyzed for the

presence and absence of aroma gene (fgr) by using PCR based technique. For

primer amplification study a tightly linked STS marker RG 28 was used. Primer

which tightly linked to fgr gene produces 140 bp fragment, while non-aromatic

accessions produced 120 bp band (Fig. 3.25E). Out of 96 accessions only one

check variety Super Basmati had gene for fragrance, while all other accessions

were found non-aromatic (Table 3.18).

96
 A. Xa4

41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 M

B. xa5
M 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62
900
800
700
600
500
400
300

C. xa13
M 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55

D. Xa21

+ - 33 34 35 36 37 38 M 39 40 41 42 43 44 45 M 46 47 48 49 50 51
3000

52 3000 1000
750
1000 500
750 250
500
250

E. fgr
M 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95
1000
500
400
300
200
100

Fig. 3.25(A-E) STS banding pattern of Xa4, xa5, xa13, Xa21 and fgr gene respectively

97