فصلنامه ژنتیک نوین
سال هفتم شماره 2 (پیاپی 29، تابستان 1391)

Quantitative genetic theories based on infinitesimal model have been very successful in selecting the best animals in the last century. One of the methods based on IFM that has been used widely in quantitative genetics is best linear unbiased prediction (BLUP). Despite, because of the limited amount of genetic material and finite number of loci for each trait some infinitesimal models assumptions can be violated. Since 1970, molecular genetics has opened this black box by mapping the single genes affecting the quantitative traits. Therefore in the past 15 years, the major effort in animal breeding has changed from quantitative to molecular genetics with emphasis on marker assisted selection (MAS). However, results have been modest. In 2001, based on a computer simulation study, genomic selection as markers covering the whole genome was proposed as a variant of MAS. Simulated and real results have been shown that the breeding values could be predicted with higher accuracy in genomic selection than traditional selection. According to expert assessments, genomic selection makes it possible to save 92% of the funds spent on traditional selection and it is twice as efficient as the latter. However, there is a long way for reaching to phenotype from genotype; nevertheless, new technologies such as genomics, transcriptomics, proteomics and metabolomics can be useful in this way.

Insulin-like growth factor binding protein-3 (IGFBP-3) gene is a structural gene responsible for the multiple influences of insulin like growth factors (IGFs) system. This study was carried out to determine the genetic diversity of Raeini Cashmere goat and its relationship with cashmere production, using two markers, HaeIII and XspI PCR-RFLPs for goat IGFBP-3 locus. A number of whole blood samples were randomly collected from 100 individual goats (males and females). DNA extraction from whole blood samples were done using modified salting out method. In the PCR-RFLP analysis with HaeIII, the frequencies of H1 and H2 alleles were 0.8 and 0.2 respectively and the frequencies of X1 and X2 alleles were 0.34 and 0.66 respectively. Shannon and Nei indices, observed and expected heterozygosities were 0.50, 0.32, 0.22 and 0.32 for HaeIII RFLP respectively and 0.64, 0.44, 0.24 and 0.45 for XspI RFLP respectively. The individuals with genotype H1H1 had higher cashmere yield than that of genotype H2H2 in three-year-old (P<0.05), but trend was reversed in five-year-old (P<0.05). But, XspI locus did not show significant effect. It could be concluded that Raeini Cashmere goat has high genetic diversity and the IGFBP-3 gene could be exploited as a candidate gene for marker-assisted selection in this breed.

Barley belongs to the Poaceae which is the largest monocotyledon family. Plastid single-copy gene acetyl- coAcarboxylase (ACCase) is the first step in the biosynthesis of fatty acids and therefore it is used to study the phylogenetic relationships, evolutionary and systematc of grasses. Single and low copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. In this study, phylogenetic relationship of the species of H. vulgare with its subspecies; H. spontaneum, H. distichon, H. tworow, H. hexastichon, were investigated using gene-specific primers acetyl- CoAcarboxylase, ACC1 (plastid form) and ACC2 (cytosolic form). There was high adaptation between homogeneity test and disparity index with phylogenetic trees. The homogeneity of substitution patterns between H. vulgare with its subspecies sequences has not been seen. In conclutsion the common tree between two genes revealed that ACC1 and ACC2 have the same evolution pathway.

Drought stress is one of the most important preventions in the crop production. The goal of this study was to find the new effective genes in drought stress mechanism. For this EST libraries of wheat, rice, cotton and festuca plants under drought stress were analyzed. The EST data of four libraries were collected from harvard university databank. To find similarity between libraries, all of EST sequences were assembled by EGassembler software. Then all contigs were analyzed by blast x from CLC Protein Workbench software against non redundant protein presented in gene banks with Evalue≤ 1*10-5. IDEG6 software was used for detecting genes with deferent expression pattern between libraries. The genes of lipid treansferase, phosphatase, metallothionein, dehydrin, glutathione s-transferase and LEA are important genes involved in drought stress in four libraries of wheat, rice, cotton and festuca. Four libraries showed significant differences in functional catalogues of photosynthesis, oxidative pentose phosphate, mitochondrial electron transport, cell wall, amino acid metabolism, hormone metabolism, redox regulation, misc, RNA, CHO metabolism, stress, nucleotide metabolism, secondary metabolism, protein, signaling that explaining these four catalogues response to the drought stress with using different sub functional catalogues.

ABCG2 (ATP binding cassette subfamily G member 2) gene have located in chromosome which is encoded ABCG2 protein that transports various xenobiotics, cytostatic drugs across the plasma membrane and cholesterol into milk. A single nucleotide change (A/C) in base 86 of exon 14 is capable of encoding a substitution of tyrosine to serine in the ABCG2 gene and increases milk yield and decreases fat and protein concentration. The major aim of this research is to identify ABCG2 gene polymorphism in Iranian population of Holstein bulls. Genomic DNA of 105 bulls was extracted from semen samples using high Pure PCR template preparation kit. Primers were designed with Oligo software and utilized in PCR. Then the PCR fragments were sequenced. Results of sequences were compared with NCBI sequence databases. A/C mutation in base 86 of exon 14 was observed with 2% frequency.

Tomato is one of the most important crops in the world which is vastly cultivated everywhere. This crop bears a great loss every year due to the presence of pathogenic fungi such as Fusarium species. In present study in order to strengthen defense mechanism of tomato, we transferred coincidently the genes PR1, chitinase and gluconase into tomato. To do so, first, the gene PR1 was extracted from tobacco genome and then replicated under the control of 35S promoter and Nos terminator in recombinant vector pBI121. In addition, chitinase and gluconase genes were replicated under the control of independent 35S promoter and Nos terminator in vicinity of PR1 gene. It is followed by transformation of tomato explants with PRP-1ChiGlu(-) containing PR1, chitinase and gluconase genes by using recombinant vector pBI121. In this transformation, leaf explants placed on the pre-media were inoculated by Agrobacterium tumefaciens LBA4404 containing aforementioned vector. These explants were transferred first to similar media and then to regeneration media and every seven days were subjected to subculture and after 4 weeks they were transferred to root generation media containing 200 ml/lit Cefotaxime and 25 mg/lit Kanamycin. Molecular analysis of PCR and dot blotting showed that transgenic plants had at least one copy of in question genes on their genome.

Upon infection of eukaryotic cells, Agrobacterium tumefaciens transfers a piece of its tumor inducing plasmid, T-DNA, to the host cell. The VirD2 virulence protein which is covalently bound to the T-DNA facilitates its transfer, nuclear localization and possibly integration into the host genome in collaboration with the interacting proteins of the host cell. VirD2 is essential for Agrobacterium–mediated transformation of both plants and non-plant cells. Here, using yeast Green Flourescent Protein (yGFP) technology we studied the subcellular localization of VirD2 expressed in yeast Saccharomyces cerevisiae cells. Fluorescence microscopy showed that an N-terminal yGFP fusion of VirD2, is located in the nucleus of yeast. This highlights nuclear localization of VirD2 in yeast and the importance of NLS sequences of C-terminal of VirD2 in this phenomenon.

To investigate the relationships between morphometric and molecular markers as well as introduce morphometric characters that shown most genetic variations in Siah Mahi, Capoeta capoeta gracilis, have been designed. A total 65 fish specimens were collected by electeroshocker set that 35 individual related to up stream station and 31 individual related to down stream station. From ten random 10-mer primers, 6 primers which shown polymorphic pattern repeatable, were selected and use in the final analysis of two locations. 26 morphometric factors were measured and was standardized. Totally 89 polymorphic band (marker) gained. Length of PCR products were between 50-1000 bp. In this study for first time in field aquaculture we used from Association analysis approach that in this method have been used from stepwise regression to determine relationship between each of morphometric characters and 89 genetic markers. In finally this results shown that 79 markers from 89 (86.51% of markers) shown significant relationship (P<0.05) to 18 morphometric characters that among them 9 characters shown significant relationship in high significant level (P≤0.01) that we could use from this morphometric characters in topics related to population of fishes

Leptin is a polypeptide hormone that was identified as the main secretion of adipose tissue. It involved in regulation of feed intake, energy metabolism and fertility. Purpose of this study was to identify allelic polymorphism in Leptin gene receptor. We have used a restriction fragment length polymorphism (RFLP) method. Blood samples were randomly collected from 100 native chickens in Sari fowl breeding station. The DNA extraction was based on salting – out method. The quantity and quality of extracted DNA were examined using spectrophotometric and agarose gel electrophoresis. A strategy employing polymerase chain reaction was used to amplify a 374 bp fragment of 9-11 exon Leptin gene receptor. Digestion of amplicons with HaeIII revealed Leptin gene receptor. On results of band pattern digestion with HaeIII be showed no mutation was observed in Leptin receptor gene of the Mazandaran native chickens and it is monomorph.

In order to identify effective SNP markers of barley flowering time in candidate genes Ppd-H1, CO1, and GIGANTEA, association analysis was conducted in a set of 52 Iranian and non-Iranian barley cultivars. Based on 42 EST-SSRs the genetic structure of the population was divided to two subgroups corresponding to the origin of the cultivars. High nucleotide diversity was observed in the exon region of Ppd-H1 while CO1 and GIGANTEA showed limited diversity. Within all three genes, the extent of linkage disequilibrium (LD) was variable and low, indicating that the candidate gene association approach could be a reliable tool to reach a high resolution map for flowering time in barley. Significant associations were observed for GIGANTEA and Ppd-H1 with flowering time, causing one week difference in flowering time. While no significant association was seen between nucleotide diversity in intron region of the CO1 and flowering time. The haplotypes of 3 genes showed no significant intergenic interactions. Valuable nucleotide diversity in the the mentioned candidate genes was detected in the germplasm specially within Iranian cultivars that could be applied in breeding for flowering time in barley. Some identified SNP alleles accelerating the time of flowering for one week, were detected in this study capable of being used in marker assisted selection. A novel allele was also detected in the gene GIGANTEA with important role in late flowering.

Bacterial Leaf Blight of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is an important disease throughout Asia. Yield losses of 10-70% have been recorded in severely infected fields. In this study genetic variation in 60 isolates of Xoo, investigated using random amplified polymorphic DNA (RAPD) marker. As a whole all used markers amplified 187 polymorphic bands. Analysis of molecular variance of RAPD data showed that the genetic variation within Xoo populations was greater than between populations. The similarity matrix made by Simple Matching coefficient and cluster analysis conducted by unweighted pair group method (UPGMA) with NTSYS-pc soft ware. At a similary index of 0.6 the isolates were grouped into 3 clusters. These results revealed that the RAPD markers which used in this study could differentiate nursery and field isolates from each other.

Drought stress is a major constraint to rice (Oryza sativa) production, particularly at the reproductive stage. One of the most important reasons for the effect of drought is the inhibition of peduncle elongation, resulting in panicle retention inside the flag leaf sheath so that the unexserted spikelets remain sterile. This research was focused on studying expression patterns of OsVP1 transcription factor encoding gene during drought-stress and abscisic acid -induced growth arrest at peduncles. The expression of OsVP1 gene was significantly up-regulated during the growth arrest induced by either drought stress or ABA and down-regulated again by re-watering or ABA removal and restoring the growth in the peduncles. OsVP1 transcripts were mostly observed in the young immature tissues and the expression levels were decreased from division zone to maturation zone; however it was always increased by drought stress. In the divisional zone of the peduncle, transcripts of this gene was observed in almost all cells and accumulated more in the nuclei. Therefore, based on the achieved results and that OsVP1 encodes a transcription factor, this gene probably affects the expression of many other genes, directly or indirectly, involved in drought stress and ABA induced growth arrest.