DNA Fingerprinting and Genotyping of Four BlackSeed hybrids

JKAU: Met., Env. & Arid Land Agric. Sci., Vol. 21, No.1, pp: 93-108 (2010 A.D./1431 A.H.)


DOI: 10.4197/Met. 21-1.7

93

DNA Fingerprinting and Genotyping of Four Black

Seed (Nigella sativa L.) Taxa

Asma Al-Huqail and Faisal Al-Saad

Faculty of Botany and Microbiology Dept., College of Science,

King Saud University, Riyadh, Saudi Arabia

Abstract. DNA fingerprints of four Taxa of black seeds (Nigella sativa

L.) from Qassim (Saudi Arabia), Ethiopia, Egypt, and Syria were

studied. The results showed that there are several genetic differences

between these different black seeds Taxa, which could be considered

as genotypic characteristics and lead to classifying them as varieties

under the sativa species. To study the DNA fingerprinting of these

Taxa, the Inter Simple Sequence Repeat (ISSR) method was employed

in the PCR technique to determine the levels of polymorphism

between their genetic makeups. The ISSR-PCR investigated the intermicrosatellites

sequences in their three types (Di, Tri, and Tetra) of

the Short Tandem Repeats. Seventeen proper primers representing

these three primers' types were used. The obtained banding pattern

indicated a high level of polymorphism. The scored bands of the DNA

fingerprints in these Taxa were 108, 106, 100 and 81 in Qassim,

Ethiopia, Syria, and Egypt, respectively. When the percentages of

dissimilarity between them were computed, the range was between

21.5-36.3%. Such a relatively high level of polymorphism

substantiated the objectives of the present study which supposed that

black seeds grown in the different localities in the world over time

have undergone genetic changes to the level that could make them

different varieties. Twenty four genes representing 24 different

enzymes and isozymes were selected and scanned via PCR technique

using suitable SSR primers. The obtained results, showed some

changes in the genetic structure of some of these genes. The

differences in the DNA fingerprints and the number of comparable

genes should be reflected on the gene expression manifested in the

protein homology and hence on the metabolism.

Asma Al-Huqail and Faisal Al-Saad

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Introduction

Nigella sativa L. (Ranunculaceae family), commonly known as black

seed has been employed for thousands of years as spice and food

preservative, as well as a protective and curative remedy for numerous

disorders. In Islamic culture, it is regarded as one of the greatest forms of

healing medicine available. Prophet Muhammad once stated that the

black seed can heal every disease except death. N. sativa L. has been

used traditionally for centuries in the Middle East, Northern Africa and

India for the treatment of various diseases (Worthen, 1998, Burits and

Bucar, 2000, Al-Ghamdi, 2001, and Gilani et al., 2004). Research from

around the globe is giving increasing support for black seed's widespread

healing powers. Extracts of the black seeds have many therapeutic effects

such as antidiabetes, antibacteria, and antitumor (Khan et al., 2003,

Kanter et al., 2004, and Hussein et al., 2005).

Despite the voluminous research published about the great medicinal

benefits of the black seed consumed around the world, there is no

published research, to our knowledge, on the application of molecular

markers to study the genetic structure of Nigella sativa L. Moreover, the

questions of whether the black seeds grown in different localities are

different varieties of one species or not, have not been addressed. Hence,

this imposes a second important question: Are all the black seed grown

around the world having the same genetic/metabolic components in

quality and quantity for medicinal effects?

The objective of the present study was to evaluate the genetic

makeup by using the genetic markers in PCR technique to characterize

and compare DNA Fingerprints in four Black Seed (Nigella sativa L.)

Taxa that are widely consumed for food and medicine.

Materials and Methods

DNA Extraction

The black seeds Nigella sativa L. were collected from Qassim (Saudi

Arabia), Ethiopia, Egypt, and Syria. After complete germination of seeds,

seedlings were shock-frozen in liquid nitrogen and stored at -20°C until

DNA isolation was performed. Plant genomic DNA was extracted using

the DNA Extraction Kit from Roche Company (Roche, Germany). This

DNA Fingerprinting and Genotyping…

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method has given a large amount of DNA with high degree of purity.

DNA purity and concentration were checked by measuring absorbency

ratio OD260/OD280, using a Gene-Quant spectrophotometer (Amersham

Company, USA). Then samples’ DNAs were diluted to the working

concentration of 100 ng/ μL (Al- Huqail, 2006).

Primers

Anchored and nonanchored (di, tri and tetra) oligonucleotide primers

were used for amplifications with specific and optimal annealing

temperatures (Table 1). All Primers were supplied by Amersham

Pharmacia Biotech, Sweden.

ISSR Amplifications

Each reaction contained 1.5 mM MgCl2; 10 mM Tris-HCl (pH 8.3);

50 mM KCl; 0.4 mM of each deoxyribonucleotide phosphate dNTPs; 0.5

μM primer; 100 ng DNA template/reaction and 1.25 units of Taq DNA

Polymerase in a final reaction volume of 25 μl. Many factors of PCR

amplification influence pattern quality. MgCl2 used at final concentration

of 1.5 mM was generally found to generate bands of high intensity.

Template DNA concentration was found to influence band intensity.

Thus, from different concentrations tested, 100 ng DNA per reaction

gave the best amplification products, while the Primer concentration of

0.5 μM resulted in a higher number of bands. Reactions without DNA

were used as negative controls (Al-Huqail, 2006).

PCR Program

Amplifications were carried out in a thermal cycler (AMPLITRON

II Thermolyne. USA). ISSR-PCR amplifications and analyses were as

described by Nagaraju et al. (2002), but with some modifications. The

apparatus was programmed to execute the following conditions: Initial

denaturation step of 4 min at 95°C, followed by 35 cycles each of

which composed of 30 s. at 95°C, 45 s. at the primer’s specific

annealing temperature at 42-64°C and 2 min for extension at 72°C. A

final extension step of 10 min at 72°C was run at the end of the last

PCR cycle. Different



annealing temperatures were tried for each primer


and the temperatures ranged from 40 to 65°C (Table 1).

Asma Al-Huqail and Faisal Al-Saad

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Table 1. Anchored and nonanchored oligonucleotide primers.

Primer Type Sequence Ta

45

45

45

45

45

45

45

42

42

42

5-CACACACACACAAC-3

CACACACACACAGT

CACACACACACAAG

CACACACACACAGG

CACACACACACAGA

CACACACACACACT

CTCTCTCTCTCTCTCTTG

AGAGAGAGAGAGAGAGCC

AGAGAGAGAGAGAGAGCA

AGAGAGAGAGAGAGAGCT

Anchored

Anchored

Anchored

Anchored

Anchored

Anchored

Anchored

Anchored

Anchored

Anchored

Di:

(CA)6AC

(CA)6GT

(CA)6AG

(CA)6GG

(CA)6GA

(CA)6CT

(CT)8TG

(AG)8CC

(AG)8CA

(AG)8CT

54

64

42

45

CAACAACAACAACAA

CAGCAGCAGCAGCAG

AGTAGTAGTAGTAGTAGT

GTGGTGGTGGC

Non anchored

Non anchored

Non anchored

Anchored

Tri:

(CAA)5

(CAG)5

(AGT)6

(GTG)3GC

52

42

42

GACAGACAGACAGACA

GATAGATAGATAGATA

GATAGATAGACAGACA

Non anchored

Non anchored

Non anchored

Tetra:

(GACA)4

(GATA)4

(GATA)2(GACA)2

Electrophoresis of PCR Amplicons

The PCR amplification products (amplicons) were analyzed by

electrophoresis using a 2.25% agarose gel in 1x Tris Acetic cid EDTA

(TAE). DNA was stained by soaking the gel in a0.5 mg/mL ethidium

bromide solution and run at 60 v for 3 h. Stained gel was visualized

and photographed on UV Transilluminator (Al-Huqail, 2006).

Index of Similarity

Similarity coefficient (index of similarity) was calculated to compare

the results of the genetic fingerprints for the determination of the

percentage of similarities between the Taxa. The following formula was

used:

Bab = 2 Nab / (Na + Nb)

Where Nab is the number of bands that appear common in all types a, b.

While each of the Na, and Nb are the total number of bands that appear in

both a and b, respectively (Lynch, 1990).

DNA Fingerprinting and Genotyping…

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Genes Scan via PCR Technique

Twenty four genes representing 24 different enzymes and isozymes

were selected and scanned via PCR technique using suitable SSR primers.

These genes were selected from the list of Arabidopsis thaliana, grains, and

legumes cited in the gene bank (NCBI.org). The genes codes and numbers

were checked in the web site http://www.Entrez PubMed to find their base

pair sequence to select proper lengths of bases for the SSR primers design in

both directions (Forward and Reverse). The Melting-Temperatures of the

selected SSR primers were computed in the appropriate program on the

website: http://www.promega.com/biomath/default.htm. (Al-Huqail, 2006).

Results and Discussion

DNA Fingerprinting

Results clearly indicate that the four Black Seed (Nigella sativa)

Taxa (Qassim, Ethiopia, Egypt and Syria) differ in their DNA structures,

as their DNA fingerprints show a high degree of polymorphism. Hence,

the results mean that these four Taxa of Nigella sativa do have different

relative frequencies of microsatellite motifs of their respective DNAs, as

can be seen from the scored banding patterns. Furthermore, these

banding patterns represent the ISSR-PCR markers obtained by the use of

the selected 17 ISSR primers. The figures presented in this paper (Fig. 1

& 2) show the amplified fingerprints of 8 primers (the remainder ISSR

primers results can be seen in Al-Huqail, 2006).

The total number of bands and their total base pairs yielded by the 17

ISSR primers are presented in Table 2 .The Qassim’s taxon yielded a

total of 108 bands with total bands lengths of 63795 base pair. While, the

total bands of the Ethiopia’s taxon was 106 with a total of 59240 base

pair. Moreover, the total number of bands in the Egypt’s taxon was 81

bands totalling 47995 base pair, whereas the total number of bands in the

Syria’s taxon was 100 bands with 60820 base pair of total lengths.

The index of similarity between bands of DNA fingerprinting of

black seeds Nigella sativa Taxa for Qassim and Ethiopia (Table 3) was

0.78, between Qassim and Egypt 0.62, between Qassim and Syria 0.69,

between Ethiopia and Egypt 0.71, between Ethiopia and Syria 0.68, and

between Egypt and Syria 0.72.

Asma Al-Huqail and Faisal Al-Saad

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Fig. 1. Gel electrophoresis of ISSR bands obtained with primers: (a)- (CA)6GT, (b) -

(CA)6AC, (c)- (AG)8 CC, (d)- (AGT)6. In the X-axis, numbers from (1-4 ) represent

four black seeds (Nigella sativa L.) Taxa from Qassim, Ethiopia, Egypt, and Syria

respectively.

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On the other hand, when the percentages of dissimilarity between

these Taxa were computed, they ranged between 21.5-36.3 %.

Fig. 2. Gel electrophoresis of ISSR bands obtained with primers : (e) - (CAA)5, (f) -(GTG)3

GC, (g)- (CAG)5, (h)- (GATA)2(GACA)2.. In the X-axis, numbers from (1-4)

represent four black seeds (Nigella sativa L.) Taxa from Qassim, Ethiopia, Egypt,

and Syria, respectively.

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Table 2. Total number of bands and total bands’ base pair from DNA fingerprinting of

black seeds (Nigella sativa L.) Taxa from Qassim, Ethiopia, Egypt, and Syria.

Primer Qassim Ethiopia Egypt Syria

(CA)6CT 2 0 3 7

(CA)6AG 11 6 2 6

(CA)6GT 7 8 7 9

(CA)6GA 8 6 4 8

(CA)6GG 7 8 7 5

(CA)6AC 8 9 9 7

(CT)8 TG 6 7 7 6

(AG)8CA 9 9 6 7

(AG)8CC 9 9 9 9

(AG)8CT 6 9 2 9

(AGT)6 2 4 3 2

(CAA)5 5 5 3 2

(GTG)3 GC 8 6 4 7

(CAG)5 6 5 5 5

(GATA)4 4 4 4 5

(GACA)4 4 4 4 4

(GATA)2(GACA)2 6 7 2 2

Total no. of bands 108 106 81 100

Total bands base pair 63795 59240 47995 60820

Such a relatively high level of polymorphism has substantiated the

objectives of the present study which supposed that black seeds grown in

different localities over time have undergone genetic changes to the level

that could make them different varieties. The ISSR marker technique

involves polymerase chain reaction (PCR) amplification of DNA using a

single primer composed of a microsatellite sequence such as (GACA)4,

anchored at the 3' or 5' end by two to four arbitrary, often degenerate,

nucleotides (Zietkiewicz et al. 1994).

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Table 3. Index of similarity between bands of DNA fingerprinting of black seeds (Nigella

sativa L.) Taxa from Qassim, Ethiopia, Egypt, and Syria.

Nigella sativa L. Taxa Qassim Ethiopia Egypt Syria

Qassim - 0.78 0.62 0.69

Ethiopia 0.78 - 0.71 0.68

Egypt 0.62 0.71 - 0.72

Syria 0.69 0.68 0.72 -

The ISSRs have proven to be a reliable, rapid, simple, cost

effective, easy to generate, and versatile set of markers that do not require

previous knowledge of the genome sequence to generate DNA markers,

unlike SSRs (Zietkiewicz et al., 1994, Gupta et al., 1994, Bornet and

Branchard, 2001, & Bornet et al. 2002).

The flexibility to design primers containing a di-, tri-, or tetranucleotide

repetitive motifs anchored by one or more nucleotides at the 3'

or 5' end make them ideal to explore the genome of any species,

including those without previous knowledge of DNA sequence

(Zietkiewicz et al., 1994).

Furthermore, previous investigators have demonstrated that ISSR

analysis usually detects a higher level of polymorphism than that

detected with Restriction Fragment Length Polymorphism (RFLP) or

Random Amplified Polymorphic DNA (RAPD) analyses (Kantety et al.,

1995 and Nagaoka and Ogihara, 1997). Thus, ISSR markers are useful in

studies on genetic diversity, phylogeny, genetagging, genome mapping

and evolutionary biology and are widely applied in plant genetic analyses

(McClean et al., 2002, Reddy et al., 2002, Gonzalez et al., 2005, Hou et

al., 2005, Manimekali et al., 2006, Martinez, 2006, Thomas et al., 2006,

and Li et al., 2006). ISSR has also been used in barley for detecting

genetic diversity, genotype identification and genetic mapping (Matus

and Hayes, 2002, and Hou et al., 2005). Furthermore, ISSRs have been

used for cultivar identification in maize (Kantety et al., 1995), wheat

(Nagaoka and Ogihara, 1997). In addition, ISSR-PCR markers are scored

as dominant, highly reproducible and consistent because the anchors

serve to fix the annealing of the primer to a single position of the target

site, thus, resulting in a low level of slippage during amplification

(Zietkiewicz et al., 1994). ISSR method has been considered an efficient

molecular marker to reveal genetic relationships in traditional and

evolved Basmati and semidwarf non-Basmati rice varieties (Nagaraju et

Asma Al-Huqail and Faisal Al-Saad

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al., 2002). SSR and ISSR were compared and evaluated for the

determination of the similarity degree between 41 commercial cultivars

of apple (Malus domestica Borkh). The scored similarity coefficient

between cultivars ranged from 0.20 to 0.87 for SSR analysis and from

0.71 to 0.92 for the ISSR methodology (Goulao and Oliveira, 2001).

Genotyping of Four Black Seed (Nigella sativa L.) Taxa

Results in Fig. 3 and 4 show some of the scanned twenty four genes

representing 24 different enzymes and isozymes via PCR technique using

the selected SSR primers (the results of the remainder scanned genes can

be seen in Al-Huqail, 2006). The obtained results revealed some changes

in the genetic structure of some of these genes. The Qassim taxon

contained all 24 genes as indicated by the presence of their bands, while

the Ethiopian and Egyptian Taxa gave 23 bands representing 23 genes.

On the other hand, only 17 bands appeared in the Syrian taxon. These

results indicate that there are several genotypic differences between these

different Taxa of black seeds, which can be considered as genotypic

characteristics. These genotyping results do add further evidence to the

supposition put forth in this research that these four Taxa may be

different varieties of the Nigella sativa species.

Although the traditional taxonomic classification of varieties has

been based on analysis of the morphological traits, the development of

molecular genetic markers has made it possible and more accurate to

differentiate between Taxa even if they have the same morphological

traits. The cited literature for genotyping is enormously voluminous and,

thus, only some examples will be reported here. In previous studies, the

genetic diversity of denitrifying bacteria was investigated by using two

distinct PCR methods for the nitrite reductase genes to differentiate

between the sampled Taxa (Braker et al., 1998). Moreover the

polymorphic β -amylase gene loci in various barley varieties in Ukraine

were studied by Stratula and Sivolap, (2007) and their results showed

that the genotypes of the different barley varieties included different

alleles of the β-amylase genes. Furthermore, in another study, alcohol

dehydrogenase (Adh) genes were scanned in two distantly related

legumes, and their sequences were used to examine the molecular

evolutionary history of the basic nuclear gene (Fukuda et al., 2005).

Hence, it can be concluded that genes can undergo evolutionary changes

over time by generating different base pair sequences when compared

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with the original base pair sequence present in the original gene. Such

evolutionary changes will lead to different genetic makeup to the level

that could classify the Taxa as different varieties of the pertaining

species.

Fig. 3. Gel electrophoresis of genes scan using PCR technique with SSR primers (a)

represent gene band of Alcohol dehydrogenase enzyme, (b)- Catalases, (c)-

Glutamine synthetases, (d) Lipase. In the X-axis; numbers from (1-4) represent

four black seeds (Nigella sativa L.) Taxa from Qassim, Ethiopia, Egypt, and Syria

respectively.

Asma Al-Huqail and Faisal Al-Saad

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Fig. 4. Gel electrophoresis of genes scan using PCR technique with SSR primers (e)

represent gene band of Amylases enzyme, (f) - Nitrate reductase and Nitrite

reductase , (g)- GOT, (h) Cellulase and Kinases. In the X-axis; numbers from (1-4 )

represent four black seeds (Nigella sativa L.) Taxa from Qassim, Ethiopia, Egypt,

and Syria respectively.

DNA Fingerprinting and Genotyping…

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