Identification and genetic mapping of random amplified polymorphic DNA (RAPD) markers to the sheep genome

Screening and identification of potential sex-associated sequences in Danio rerio

Current knowledge on zebrafish (Danio rerio) suggests that sex determination has a polygenic genetic basis in this species, although environmental factors may also be involved. This study aimed to identify sex-associated genomic regions using two different marker systems: inter-simple sequence repeats (ISSRs) and random-amplified polymorphic DNA (RAPDs). Two bulks were constructed: one with DNA from zebrafish females and the other from males; then, a total of 100 ISSR and 280 RAPD primers were tested. Three DNA fragments presenting sexual dimorphism (female-linked: OPA17436 and OPQ191027 ; male-linked: OPQ19951 ) were determined from sequential analysis of the bulks followed by assessment in individuals. These fragments were cloned and convert into the following sequenced characterized amplified regions (SCAR): DrSM_F1, DrSM_F2, and DrSM_M, which share identities with sequences located in chromosomes 2, 3, and 11 (Zv9), respectively. Using these potential markers in zebrafish samples it was possible to correctly identify 80% of the males (DrSM_M) and 100% of the females (DrSM_F1 + DrSM_F2) in the analyzed population.

RAPD analysis of DNA polymorphism in Turkish sheep breeds

The genetic diversity and phylogenetic relationships of 108 individual sheep from three Turkish sheep breeds (Kivircik, Gökçeada, and Sakiz) were studied using RAPD analysis. Polymorphisms within and between populations were assayed using 15 random primers, and 82 loci were amplified ranging from 250 to 2,500 bp. The percentage of polymorphic loci was found to be 80.49, 78.05, and 73.17%, for Kivircik, Gökçeada, and Sakiz sheep breeds, respectively. Total genetic diversity was 0.2265, and the average coefficient of genetic differentiation was 0.1181. Genetically, the Gökçeada breed was more closely related to the Sakiz breed than to the Kivircik breed.

Genetic diversity of nine populations of the black goat (Capra hircus) in Sichuan, PR China

Sixteen polymorphic primers screened from 100 random primers were selected to analyze the randomly amplified polymorphic DNA (RAPD) of 540 domesticated black goats (Capra hircas) from 9 different geographical populations in Sichuan Province of China. After the test, 170 entirely repeatable RAPD markers representing goat polymorphisms were obtained from the 16 polymorphic primers, the lengths of the markers ranging from 0.1 to 2.5 kb. The genetic distance among the black goat populations ranges from 0.1051 to 0.2978. The similarity coefficient (0.9002) between Jintang and Lezhi black goats was the highest in the 9 populations, followed by the coefficient (0.8953) between Jialing and Yinshan goats, while that between Jiangan and Huili goats was found to be the lowest (0.7424). The coefficient of differentiation among population genes (Gst) was 0.2766, indicating a comparatively low degree of differentiation among the black goat populations. A UPGMA dendrogram constructed from similarity coefficients showed that the two populations from Huili and Baiyu, which are found mostly on the Western Sichuan plateau and in mountainous areas, clustered together, and the other seven populations formed another group. It can also be clearly seen that the Huili and Baiyu populations are very special, and must have been closely related in the past, even though their link with the other populations is quite weak as a result of genetic communication. The results of the experiment offer some crucial scientific data useful for the breeding of black goats.

Use of RAPD markers for identifying Nelore bulls with early reproductive maturation onset

Random amplified polymorphic DNA (RAPD) markers were used for identifying animals with early (precocious) or late (non-precocious) reproductive maturation onset. Animals (n=34) were phenotyped according to spermatozoa appearance in ejaculates (group A, 20 animals) or to the expected progeny difference (EPD) values for scrotal circumference (group B, 14 animals). The RAPD markers were initially detected by amplifying two pooled samples of equimolar amounts of DNA from the eight precocious 12 and non-precocious animals of group A. Only 38 out of 320 random primers used for screening group A pooled samples detected polymorphisms. These polymorphic primers generated 443 distinguishable and reproducible bands, from which 174 were polymorphic and 269, monomorphic. These polymorphic primers were then used in RAPD reactions to amplify individual DNA samples from animals belonging to both groups, A and B. The dendrograms generated from RAPD patterns allowed phenotypic class differentiation in both cases. Therefore, RAPD markers can be used as a tool for identifying genotypes favoring early sexual maturation in Nelore breeding programs.

Male-specific DNA sequences in pigs

One hundred primers (Operon kits OPAA, OPAO, OPAV, OPC, and OPE series) were used for random amplified polymorphic DNA (RAPD) fingerprinting to determine male-specific fragments. Seventy-four percent of the primers yielded Yorkshire polymorphic fragments. One of these primers, OPAV-18, produced a novel 1098-bp DNA fragment found only in tested males. This male-specific fragment was isolated and constructed into plasmids for nucleotide sequencing. Two primers (5'-TTGCTCACGG TAGATAACAA GAGAG-3' and 5'-TTGCTCACGG ACCAGGTAGG GAATG-3') were designed according to the cloned male-specific sequence to amplify the male-specific band using polymerase chain reaction (PCR) for pig sexing. Sex-specific bands in the PCR gel products were represented in males but none were found in females when Yorkshire, Duroc, and Landrace genomic DNA samples were amplified with these two primers by PCR. The PCR products in the gel were transferred to nylon membranes and hybridized with a 32P-dCTP labeled probe of the cloned male-specific DNA fragment. There was a clear hybridization signal in samples from all of the male pigs, but not from those of female pigs. Male and female genomic DNA samples from these pigs were spotted onto nylon membranes and hybridized with the male-specific probe. The probe hybridized strongly to males only. A high degree of sequence homology was found among the novel male-specific DNA sequences in Yorkshire, Duroc and Landrace. The sex of these three breeds of pigs could be easily and effectively determined using these two primers.

Population structure in the endangered Blanca Cacereña bovine breed demonstrated by RAPD analyses

RAPD analyses have been used to determine the genetic diversity and the population structure of the endangered Blanca Cacereña bovine breed. Genetic variability was evaluated on the basis of 1048 loci produced by 71 primers. RAPD produced a number of polymorphic loci (30.44%), and it has been proved to be a useful method for evaluating polymorphisms in this breed. The dendrograms based on simililarity indexes and on Nei's genetic distances between 60 animals and the value of genetic differentiation among subpopulations (F(ST)) showed a clear population substructure defined by herds and a scarce genetic flow among herds. Analysis of molecular variance (AMOVA) showed that 32.4% of the total variance was due to differences among herds and confirmed the clustering found. The results of the present study allow us to plan more adequate mating in order to maintain the genetic diversity and to improve the efficiency of conservation for the Blanca Cacereña bovine breed.

PCR-detected genome polymorphism in malignant cell growth

In this chapter, we analyze the problem of genetic polymorphism in tumorigenesis, which determines basic capacities of tumors. The study of genome polymorphism with modified PCR methods allows the detection of various forms of polymorphism in tumor cells. This method has made it possible to determine association of DNA polymorphism with conditions of oncogenes, antioncogenes, and genes of apoptosis and with their allelic states. A special type of nonspecific DNA polymorphism that resulted from an increase in the mutation number in the cancer cell genome was discovered. This phenomenon was called the microsatellite mutator phenotype. Because the type of DNA polymorphism correlates with various biological capacities of malignant tumors and has an important prognostic significance, the analysis of DNA polymorphism in benign and malignant tumors of different histogenesis will play an important role both in theoretical studies of cancer and in oncological practice. A modified B1-PCR was used to study the genome polymorphism in the mouse tumor cells. The gain of the band 470 bp and the loss of the band 600 bp were revealed in the hepatoma cell line MH-22a as compared with liver cells of C3HA mice. The differentiation of teratocarcinoma EC F9 cells to endoderm-like cells was not accompanied by any changes in the B1-AF DNA fingerprint.

Localization and characterization of nucleotide sequences from the canine Y chromosome

We previously reported the identification of a male-specific 658-bp DNA sequence in dogs. We used a specific primer pair designed for PCR amplification of this fragment with DNA samples from 238 dogs, 6 dingoes and 12 wolves. All 133 male samples amplified the 658-bp sequence, whereas all female samples did not. The sequence was not amplified from male DNA samples representing other wild canids (jackals, coyotes, foxes). A lambda phage was isolated from a canine male genomic library that contained an insert of approximately 15 kb of canine genomic DNA, including the male-specific 658-bp sequence. This lambda phage was used in fluorescence in-situ hybridization experiments. It hybridized to the canine Y chromosome together with a lambda clone containing a segment of the SRY gene and a cosmid clone containing a portion of the pseudoautosomal region. The male-specific 658-bp sequence was located at the end opposite to the pseudoautosomal region while the SRY gene sequence hybridized near the centromere. Additionally, two (CA)-repeat sequences were identified in the lambda clone that contained the 658-bp sequence. Specific primer pairs were designed to amplify each of the repeats. Primer pair MS34 amplified three different alleles from 13 unrelated canine male DNA samples with a PIC value of 0.40. Primer pair MS41 amplified five alleles with a PIC value of 0.71. These microsatellites are the first reported polymorphic sequences in the dog located in the non-recombining portion of the Y chromosome.