{"id":1184,"date":"2015-03-25T08:55:45","date_gmt":"2015-03-25T08:55:45","guid":{"rendered":"http:\/\/biomedpharmajournal.org\/?p=1184"},"modified":"2017-01-09T09:36:22","modified_gmt":"2017-01-09T09:36:22","slug":"human-specific-alu-insertiondeletion-polymorphisms-in-gujjar-population-of-jammu-region-of-j-and-k-state","status":"publish","type":"post","link":"https:\/\/biomedpharmajournal.org\/staging\/vol3no1\/human-specific-alu-insertiondeletion-polymorphisms-in-gujjar-population-of-jammu-region-of-j-and-k-state\/","title":{"rendered":"Human-Specific Alu Insertion\/Deletion Polymorphisms in Gujjar Population of Jammu Region of (J and K) State"},"content":{"rendered":"

Introduction<\/strong><\/p>\n

Human genome contains a significant portion of repetitive DNA sequences. Alu<\/em> insertion elements are the most abundant class of short interspersed elements (SINEs) in the human genome, numbering more than million per haploid genome (Watkins et al.<\/em> 2003). The Alu<\/em> family of repetitive elements was originally defined as a fraction of renatured repetitive DNA that was distinctively cleaved with the restriction enzyme alu<\/em>I (houck et al.<\/em>1979). Alu<\/em> elements are derived from the 7sl rna gene and they share about 90% sequence homology with 150 bp in the middle that is not found in the Alu<\/em> family (Ullu et al<\/em>. 1984). These elements mobilize by retroposition through an RNA polymerase III intermediate (Rogers, 1983). Alu<\/em> elements first appeared in primate genome about 65 million years ago (Deininger and Daniels, 1986) and have since undergone amplification from a few master genes (deininger et al<\/em>. 1992) to their repetitive status today at a rate of approximately 8 x 10-3<\/sup> Alu<\/em> elements per year. Some Alu<\/em> elements have retroposed so recently that they are not yet\u00a0 fixed that is their insertion in specific location of genome is polymorphic which make them useful markers for the population structure analysis. The advantage of Alu<\/em> insertions as markers is that the ancestral state of polymorphism is always known \u2013 the absence of element since there is no mechanism for their removal after the insertion. The other advantage is uniqueness of insertion at specific location since there is no sequence specificity for insertion sites meaning that all loci carrying a particular Alu<\/em> insertion derived from unique event and hence they are identical by descent. These properties are reason that polymorphic Alu<\/em> insertions were used as markers in numerous population structure analyses even at micro-geographical scale. During the present study, a total genomic dna samples of 50 healthy individuals, randomly selected from Gujjar population from different geographic locations of Jammu region, were analyzed for the four Alu<\/em> (Alu<\/em> ACE, Alu<\/em> APO, Alu<\/em> PLAT and Alu<\/em> PV 92) insertion \/ deletion polymorphism.<\/p>\n

Material and Methods<\/strong><\/p>\n

Materials<\/strong><\/p>\n

\u00a0<\/strong>Present study is an account of the genomic diversity with respect to Alu<\/em> insertion\/ deletion polymorphism amongst the Gujjar population of Jammu region. Before collecting the blood samples of the 50 randomly selected healthy Gujjar individuals, the Gujjar community was apprised about the nature of work and outcomes of the study.<\/p>\n

Methods<\/strong><\/p>\n

5 ml of whole blood was collected randomly from 50 healthy individuals of the Gujjar community. These samples were stored at \u2013200<\/sup>C until DNA was isolated. DNA was isolated by using phenol:chloroform method (Sambrook and Russel,\u00a0 2001) and salting out method (miller et al<\/em>., 1988). Target specific Oligonucleotide primers of four Alu <\/em>(Alu<\/em> ACE, Alu<\/em> APO, Alu<\/em> PLAT and Alu<\/em> PV 92) markers were used to amplify the target loci.<\/p>\n

PCR reactions were carried out in a 25\u03bcl volume containing 100 ng DNA, 200 \u00b5M dNTPs, 1.5 mMMgCl2<\/sub>, 25 ng each primer, 1.25 U Taq polymerase,50 mM KCl 10 mm tris \u2013 HCl (pH 8.4). 30 cycles of\u00a0\u00a0\u00a0 94\u00ba C for 4 min, 58\u00ba C for 1 min, 72\u00ba C for 1 min were used for ACE in a thermocycler, 30 cycles of\u00a0\u00a0\u00a0 94\u00ba C for 4 min, 54\u00ba C for 1 min, 72\u00ba C for 1 min were used for pv92, 30 cycles of\u00a0\u00a0\u00a0 94\u00ba C for 4 min, 50\u00ba C for 1 min, 72\u00ba C for 1 min were used for apo and 30 cycles of\u00a0\u00a0\u00a0 94\u00ba C for 4 min, 60\u00ba C for 1 min, 72\u00ba C for 1 min were used for plat. pcr products of each marker was visualized in UV\u2013 light after separation in a 2% Agarose gel and ethidium bromide staining.<\/p>\n

Table 1: distribution of four Alu (Alu ACE, Alu APO, Alu PV92, Alu PLAT)<\/em> insertion genotypes and allele frequencies in Gujjar population of Jammu region of j&k state.<\/strong><\/p>\n\n\n\n\n\n\n\n\n\n\n\n
Alu markers<\/strong><\/td>\n\u00a0<\/strong><\/td>\n\u00a0\u00a0 <\/strong><\/p>\n

\u00a0 II<\/strong><\/td>\n

\u00a0<\/strong><\/p>\n

\u00a0\u00a0 ID<\/strong><\/td>\n

\u00a0<\/strong><\/p>\n

\u00a0 DD<\/strong><\/td>\n

Total <\/strong><\/td>\n\u00a0<\/strong><\/p>\n

\u00a0\u00a0 I<\/strong><\/td>\n

\u00a0<\/strong><\/p>\n

\u00a0\u00a0 D<\/strong><\/td>\n

Total<\/strong><\/td>\n<\/tr>\n
Alu ACE<\/td>\nN<\/td>\n8<\/td>\n22<\/td>\n20<\/td>\n50<\/td>\n38<\/td>\n62<\/td>\n100<\/td>\n<\/tr>\n
<\/td>\nFREQUENCY<\/td>\n0.16<\/td>\n0.44<\/td>\n0.40<\/td>\n100<\/td>\n0.38<\/td>\n0.62<\/p>\n

 <\/td>\n

100<\/td>\n<\/tr>\n
Alu APO<\/td>\nN<\/td>\nNIL<\/td>\n44<\/td>\n6<\/td>\n50<\/td>\n44<\/td>\n56<\/td>\n100<\/td>\n<\/tr>\n
<\/td>\nFREQUENCY<\/td>\nZERO<\/td>\n0.88<\/td>\n0.12<\/td>\n100<\/td>\n0.44<\/td>\n0.56<\/td>\n100<\/td>\n<\/tr>\n
Alu PV92<\/td>\nN<\/td>\n11<\/td>\n14<\/td>\n25<\/td>\n50<\/td>\n36<\/td>\n64<\/td>\n100<\/td>\n<\/tr>\n
<\/td>\nFREQUENCY<\/td>\n0.22<\/td>\n0.28<\/td>\n0.50<\/td>\n100<\/td>\n0.36<\/td>\n0.64<\/td>\n100<\/td>\n<\/tr>\n
Alu PLAT<\/td>\nN<\/td>\n16<\/td>\n25<\/td>\n9<\/td>\n50<\/td>\n57<\/td>\n43<\/td>\n100<\/td>\n<\/tr>\n
<\/td>\nFREQUENCY<\/td>\n0.32<\/td>\n0.50<\/td>\n0.18<\/td>\n100<\/td>\n0.57<\/td>\n0.43<\/td>\n100<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

allele frequencies of all the four Alu<\/em> polymorphic markers were calculated by gene counting method. the estimated allele frequencies were then used to apply the chi-square test to calculate whether the difference between the observed frequencies and the expected frequencies was significant or not. Heterozygosity of each individual Alu<\/em> marker was calculated using Nei\u2019s 1973 method. Average heterozygosity was also calculated.<\/p>\n

Table 2: Showing heterozygosity and average heterozygosity of four Alu<\/em> (Alu ACE, Alu APO, Alu PV92 and Alu PLAT) <\/em><\/strong>polymorphic loci in 50 individuals of Gujjar population of Jammu region of J&K.<\/strong><\/p>\n\n\n\n\n\n\n\n\n
Alu marker<\/strong><\/td>\nHeterozygosity<\/strong><\/td>\n<\/tr>\n
Alu ACE<\/td>\n0.4712<\/td>\n<\/tr>\n
Alu APO<\/td>\n0.4928<\/td>\n<\/tr>\n
Alu PV92<\/td>\n0.4608<\/td>\n<\/tr>\n
Alu PLAT<\/td>\n0.4920<\/td>\n<\/tr>\n
Average<\/p>\n

heterozygosity<\/td>\n

0.4805<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

Results<\/strong><\/p>\n

Distribution of four Alu <\/em>(Alu<\/em> ACE, Alu<\/em> APO, Alu<\/em> PV-92, Alu<\/em> plat) insertion\/deletion genotypes and allele frequencies in Gujjar population of Jammu region of j&k state are given in table 1.The heterozygosity values in all the four markers and average heterozygosity value are given in table 2.The observed frequencies and expected frequencies in all four Alu<\/em> (Alu<\/em> ace, Alu<\/em> apo, Alu<\/em> pv92, Alu<\/em> plat) markers with corresponding \u03c7\u00b2 values at one degree of freedom studied are given in table 3.<\/p>\n

Table 3: showing the observed frequencies and expected frequencies in all four Alu<\/em> (Alu<\/em> ace, Alu<\/em> apo, Alu<\/em> pv92, Alu<\/em> plat) markers with corresponding \u03c7\u00b2 values studied in Gujjar population of Jammu region of j&k.<\/strong><\/p>\n\n\n\n\n\n\n\n
Alu<\/em><\/strong> marker<\/strong><\/td>\nPhenotypes<\/strong><\/td>\nObserved frequencies<\/strong><\/td>\nExpected frequencies<\/strong><\/td>\n<\/tr>\n
Alu<\/em> ace<\/td>\nID<\/p>\n

DD<\/p>\n

II<\/td>\n

8<\/p>\n

22<\/p>\n

20<\/td>\n

7.22<\/p>\n

22.56<\/p>\n

19.22<\/p>\n

\u03a72 <\/sup>= 0.22<\/p>\n

(0.70 > p > 0.05)<\/p>\n

 <\/td>\n<\/tr>\n

Alu<\/em> apo<\/td>\nII<\/p>\n

ID<\/p>\n

DD<\/td>\n

0<\/p>\n

44<\/p>\n

6<\/td>\n

9.68<\/p>\n

24.64<\/p>\n

15.68<\/p>\n

\u03a72 <\/sup>= 30.87<\/p>\n

(p < 0.001)<\/p>\n

 <\/td>\n<\/tr>\n

Alu <\/em>pv92<\/p>\n

 <\/td>\n

II<\/p>\n

ID<\/p>\n

DD<\/td>\n

11<\/p>\n

14<\/p>\n

25<\/td>\n

6.48<\/p>\n

23.04<\/p>\n

20.48<\/p>\n

\u03a72<\/sup> = 7.70<\/p>\n

(0.01 > P >0.001)<\/p>\n

 <\/td>\n<\/tr>\n

Alu<\/em> PLAT<\/td>\nII<\/p>\n

ID<\/p>\n

DD<\/td>\n

16<\/p>\n

25<\/p>\n

9<\/td>\n

16.24<\/p>\n

24.51<\/p>\n

9.25<\/p>\n

\u03a72<\/sup> = 0.02<\/p>\n

(0.90 > P > 0.80)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Discussion<\/strong><\/p>\n

In the present study Alu<\/em> ace frequency was calculated to be 0.38 and on making a comparison of the present findings with the available data on other different Indian populations it was found to be lower than the Alu<\/em> ace frequency as reported by Majumder et al<\/em>. (1999) in 14 ethnic populations of India. Alu <\/em>ace frequency observed in the present study was also found lower when compared with the four ethnic populations groups from Punjab (kaur et al<\/em>., 2002), two tribal populations of south India (veerraju et al<\/em>., 2001), two caste populations of Tamil Nadu except gavara naidu which had the Alu<\/em> ace insertion frequency of 0.379 (Vijaya et al.,<\/em> 2007). It was also lower than the Yadava population of Andhra Pradesh (ravindrnath et al<\/em>., 2005). Alu<\/em> ace heterozygosity was calculated to be 0.4712 which was close to the heterozygosity values reported by kaur et al<\/em>. (2002) in four ethnic populations of Punjab India. Alu <\/em>ace heterozygosity value was higher than the value reported from two tribal populations of south India by veerraju et al<\/em>. (2001) and it was close to the values reported by majumder et al<\/em>. (1999) in 14 ethnic populations of India. Alu<\/em> apo marker showed 0.44 insertion frequency which was higher than only one population (munda) group and lower than 11 populations studied by majumder et al.<\/em> (1999). Alu<\/em> apo insertion frequency was also lower when compared with other Indian populations (kaur et al<\/em>., 2002; ravindranath et al<\/em>., 2005; vijaya et al.,<\/em> 2007; Veerraju et al<\/em>., 2001).<\/p>\n

Alu<\/em> apo marker showed highest value of heterozygosity (0.4928) which was close to the heterozygosity values in other Indian populations (majumder et al<\/em>., 1999; kaur et al<\/em>., 2002; ravindranath et al<\/em>., 2005; vijaya et al<\/em>., 2007). This marker showed highest level of heterozygosity among the four markers used in the study of the genomic diversity of Gujjar population during the present study.<\/p>\n

Alu<\/em> pv92 insertion frequency was found to be 0.36 in Gujjar population. It was higher than Brahmins but lower than other three populations of Punjab (kaur et al.,<\/em> 2002). Alu<\/em> pv92 insertion frequency was also higher than reddiyar and Tamil yadaver population groups of Tamil Nadu (vijaya et al.,<\/em> 2007) and 4 (Brahmins (up), gaud, Muslims and Rajputs) of total populations studied by majumder et al.<\/em> (1999). Alu<\/em> pv92 insertion frequency was also lower than the two tribal populations studied by veerraju et al., <\/em>(2001).<\/p>\n

In the present study insertion frequency was highest in Alu<\/em> plat marker which was found to be 0.57. This value is close to the insertion values of Alu<\/em> plat in other Indian populations (majumder et al<\/em>., 1999; kaur et al., <\/em>.2002; ravindranath et al<\/em>., 2005; Vijaya\u00a0 et al<\/em>.,\u00a0 2007).<\/p>\n

Alu<\/em> plat marker was found to be the second most diverse marker among the four markers used for the study of genomic diversity in Gujjar population and showed heterozygosity value 0.4920 which was almost\u00a0 similar to the heterozygosity values reported by kaur et al.<\/em> (2002) in four ethnic populations of Punjab.<\/p>\n

After studying the allele frequencies and heterozygosity values for four Alu<\/em> (Alu<\/em> ace, Alu<\/em> apo, Alu <\/em>PV92, and Alu<\/em> plat) polymorphic loci, all the markers showed insertion frequencies lower than or equal to those found in other populations of India studied by previous workers (Majumder et al.,<\/em> 1999; Kaur et al.,<\/em> 2002; ravindranath et al<\/em>., 2005; Vijaya et al<\/em>., 2007) but in comparison to other world populations, the insertion frequencies in the present population are quite high. The average heterozygosity in the present population was recorder as 0.4792. It may be pertinent to point out here that Majumder et al. <\/em>(1999) reported consistently high levels of average heterozygosity in 14 ethnic populations from India ranging from 0.351 to 0.499. The present study population also exhibits high levels of heterozygosity thus showing that Gujjar population is highly diverse with respect to these markers because high values of heterozygosity accounts for high diversity. But Gujjar population is a strictly endogamous population and therefore should have more of homozygotes as compared to heterozygotes i.e. should have low levels of heterozygosity as against the present finding. The reason behind the high heterozygosity levels of studied markers and thus high genomic diversity in Gujjar population may be the derivation of this strictly endogamous population from the non-endogamous Hindus who adopted Islam as their religion during the reign of aurengjeb and became Muslims. This suggests the effect of recent historic events on the distribution of Alu<\/em> specific markers on the present day Gujjar population of Jammu region of J&K state. Chi- square test revealed that in two markers Alu<\/em> ACE and Alu<\/em> plat the chi square value was below the tabulated value at one degree of freedom which showed that the differences between the observed frequencies and the expected frequencies was not significant and the population was in hardy-Weinberg equilibrium with respect to Alu<\/em> ace and Alu<\/em> plat markers (table 3). But in case of Alu<\/em> apo and Alu<\/em> pv92 the chi- square value calculated was higher than the tabulated value at one degree of freedom which revealed that there was significant difference between observed frequencies and the expected frequencies and the population was not in hardy\u2013Weinberg equilibrium with respect to Alu<\/em> apo and Alu<\/em> pv92 marker. The unexpected results obtained for Alu<\/em> APO and Alu<\/em> PV92 markers may be due to sampling error as the population size used in the present study was quite small.<\/p>\n

References<\/strong><\/p>\n

    \n
  1. Deininger, P. L., and Daniels, G. R. (1986). The recent evolution of mammalian repetitive DNA elements. Trends Genet<\/em>. 2: 76\u201380.<\/li>\n
  2. Deininger, P. L., Batzer, M. A., Hutchison, C. A., and Edgell, M. H. (1992). Master genes in mammalian repetitive DNA amplification. Trends Genet<\/em>. 8: 307\u2013311.<\/li>\n
  3. Houck, C. M., Rinehart, F. P., and Schmid, C. W. (1979). A ubiquitous family of repeated DNA sequences in the human g J. Mol. Biol. <\/em>132: 289\u2013306.<\/li>\n
  4. Kaur, I., Roy, S., Chakrabarti, S., Sarhadi, V.K., Majumder, P.P., Bhanwer, A.J.S. and Singh, J. (2002). Genomic diversities and affinities among four endogamous groups of Punjab (India) based on autosomal and mitochondrial DNA polymorphisms. Human Biology <\/em>74(6): 819\u2013836.<\/li>\n
  5. Majumder, P.P., Roy, B., Banerjee, S., Chakraborty, M. and Dey, B., et al.<\/em>\u00a0\u00a0\u00a0\u00a0\u00a0 (1999) Human-specific insertion\/deletion polymorphisms in Indian populations and their possible evolutionary implications. J. Hum. Genet<\/em>. 7<\/strong>: 435-446.<\/li>\n
  6. Miller, s., dykes, d. d., and polesky, h. f. (1988). A simple salting out procedure of extracting dna from human nucleated cells. Nucleic acid res<\/em>. 16: 1215-1216.<\/li>\n
  7. Ravindranath, V. M., Lakshmi, N., Ramesh,\u00a0M. and Veerraju, P. (2005). Alu<\/em> insertion \/ deletion polymorphisms in Yadava population of Andhra Pradesh, South India. J. Hum. Genet<\/em>. 5(3): 223-224.<\/li>\n
  8. Rogers, J. (1983). Retroposons defined. Nature, <\/em>301: 460.<\/li>\n
  9. sambrook, , and Russell, d.w. (2001). molecular cloning, a laboratory manual. cold spring harbor laboratory press, cold spring harbor, New York, usa.<\/li>\n
  10. Ullu, E., and Tschudi, C. (1984). Alu<\/em> sequences are processed 7SL RNA genes. Nature, <\/em>312: 171\u2013172.<\/li>\n
  11. Veerraju, P., Rao, T.V., Lakshmi, N., Reshmi, S., Dey, B. and\u00a0Majumder, P.P. (2001). Insertion \/ Deletion DNA polymorphisms in two South Indian tribal populations. IJHG<\/em> 1(2): 129-132.<\/li>\n
  12. vijaya, m., kanthimathi, , srikumari, c. r., reddy, p. g., majumder, m. m., and ramesh, a. (2007). A study on telugu \u2013 immigrants of Tamil Nadu, south India. Int j hum genet<\/em>. 7(4): 303-306.<\/li>\n
  13. Watkins, W.S., Rogers, A.R., Ostler, C.T., Wooding, S., Bamshad, M.J., Brassington, A.E., Carroll, M.L., Nguyen, S.V., Walker, J.A., Prasad, B.V.R., Reddy, P.G., Das, P.K., Batzer, M.A. and Jorde, L.B. (2003). Genetic variation among world populations: Inferences from 100 Alu<\/em> insertion polymorphisms. Genome Res<\/em>. 13: 1607-1618.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    Introduction Human genome contains a significant portion of repetitive DNA […]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[],"class_list":["post-1184","post","type-post","status-publish","format-standard","hentry","category-vol3no1"],"_links":{"self":[{"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/posts\/1184","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/comments?post=1184"}],"version-history":[{"count":4,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/posts\/1184\/revisions"}],"predecessor-version":[{"id":12627,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/posts\/1184\/revisions\/12627"}],"wp:attachment":[{"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/media?parent=1184"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/categories?post=1184"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/tags?post=1184"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}