جستجوی مقالات مرتبط با کلیدواژه "snp" در نشریات گروه "بیوتکنولوژی و ژنتیک گیاهی"

Using the appropriate statistical method in genome wide association studies is one of the main factors for identifying genomic regions related to important economic traits. Therefore, the purpose of the present study was to calculate the explained genetic variance of Bayesian multi-step methods including BayesA, BayesB and BayesCπ for traits related to body conformation traits in crossbreed dairy cattle that were genotyped with 50K cattle chips. For each animal, five traits, body length, wither height, chest depth, chest circumference, and hip width, were collected. The analyses were performed using package hibayes in R software by fitting covariates for either SNPs alleles in Bayes A, Bayes B, or Bayes Cπ models. The lowest and highest amount of explained variance was obtained for chest circumference (12.5%) and body length (21.7%), respectively. The markers obtained from BayesA with the highest additive genetic variance were located in the chromosomes 4, 5, 6, 7, 10, 11, 16 and 23. In the present study, the genes related to body conformations traits in our study included PRDX6, ATF3, ARAP2, PDE1B, CHCHD3, TBPL2, SYN3, and PTBP1. The functional aspects of these candidate genes suggested their potential role in body growth. Moreover, pleiotropic effects were observed for some SNPs for conformation traits. The present results show when the genetic architecture of quantitative traits follows infinitesimal model assumptions, BayesA method usually performs better than Bayes. Moreover, considering the identification of new genome regions and the key role of the mentioned genes in development of body conformation, the Bayes A method can be validated for GWAS in body conformation traits.

Drought is one of the major environmental stresses that adversely affect the growth and development of wheat. This study aimed to determine the structure of the population and to identify markers associated with physiological and agronomic traits in bread wheat under drought stress conditions.

A total of 238 bread wheat genotypes were evaluated using a randomized complete block design with two replications under drought stress conditions. Various physiological traits, including carbon dioxide exchange, photosynthesis rate, and chlorophyll content, as well as agronomic traits such as days to heading, days to maturity, flag leaf length and width, plant height, seed weight per plant, number of seeds per unit area, seed yield, and biological yield, were measured. Genotyping was performed using 9K SNP array. The population structure analysis was conducted using 17,093 SNP markers in R software. Marker-trait association (MATs) was carried out using GLM model in TASSEL.

The analysis of population structure divided the 238 wheat genotypes into five subgroups. A total of 132 MTAs were identified for different traits. Notably, four SNPs, on chromosomes 6B, 4A and 6A exhibited pleiotropic effects on traits such as seed number per unit area, seed weight, and yield. Furthermore, eight MTAs for seed weight were identified on chromosomes 4B, 5B, 6B, and 7A. Chromosome 6B contained the highest number of SNPs, covering a region between 481-519 Mbp. For the number of seeds per unit area, 12 MTAs were located on chromosomes 3B, 4A, 5A, 6A, and 6B. The region with the highest number of SNPs was found between 561-492 Mbp on chromosome 6B, which overlapped with the region associated with seed weight per plant. These findings highlight the significance of this specific region in the wheat genome for improving bread wheat yield.

The results of this research provide valuable insights for breeders seeking to enhance wheat yield potential. Identified markers associated with key agronomic traits can be utilized in marker-assisted selection programs, aiding in the selection of desired traits.

Honeybees, as pollinating insects, are an important part of nature. Because behavioral traits are so important in honeybees, comparing brain tissue transcriptomes of the two subspecies with aggressive and calm behavioral characteristics makes it possible to understand this behavioral difference genetically. This study aimed to investigate to gene expression profile and identify the key genes in brain tissue in Italian (Apis Mellifera Ligustica) and African (Apis mellifera Scutellata) honeybees concerning behavioral traits. The Italian honeybee has calm behavioral characteristics, while the African is known as an aggressive honeybee.

RNA-Seq data were obtained from the NCBI  (GEO) database, and after pre-processing of reads, the brain tissue transcriptomes of both subspecies were aligned and mapped on the honey bee reference genome (v A.mel 4.5), and then data qualification, transcriptome assembly, differential expression analysis, and gene ontology were performed.

Differential gene expression analysis identified 16,701 genes on the honeybee reference genome, of which 22 genes in brain tissue between the two subspecies had significant differential expression (adj p-value <0 .05 and Log2FC>2). As well, some of these genes were first identified. Gene ontology analysis showed that among these 22 genes, such as ITPR, MRJP, HSP70Ab, MBS, GB45410, and Def1 are directly or indirectly involved in the occurrence of various traits such as defensive, health behavior, reproductive, heat, light, and smell sensitivity. In addition, the SNPs encoding the honeybee brain tissue genome were identified in both subspecies, and 99636 SNPs were identified in the Italian, and 92514 SNPs were identified in the African subspecies.

RNA-seq data, due to its high throughput, can provide us with accurate information about the expression of genes in different tissues in various subspecies. In this study, genes involved in honeybee behavioral traits and the SNPs in these genes were identified

Akhal-Teke horse is one of the oldest breeds in the south of Turkmenistan and north of Iran, which has been adapted to live in the harsh environmental conditions of Central Asia. This breed has been selected for speed for nearly 100 years; therefore, investigation of its genetic structure could improve breeding programs. The sequenced data of 86 horses from 16 breeds were downloaded from NCBI and used in this study. The phylogeny tree for the individual genome sequences was constructed. The PCA was performed using the software GCTA. In order to visualize population structure between different horse breeds, ADMIXTURE was used. The parsimony analysis revealed all breeds were divided base on geographical origins. Principal component analysis illustrated highest genetic distance among Akhal-Teke with Thoroughbred and Standard bred. Results of admixture demonstrated all individuals of Akhal-Teke assign strongly to one cluster in hypothetical population of k=4 and k=5. However, when the hypothetical population of k=2 and k=3 were done, the individual were appeared in 2 or 3 color. The mean number of ROH in Akhal-Teke was lower than Thoroughbred, Sorraia, Standard bred and Quarter and ROH>1000kb was more. Therefore, comparing to these breeds the inbreeding was lower in Akhal-Teke. The highest value of linkage disequilibrium in all bean distance was detected in Thoroughbred. After that, two breeds of Akhal-Teke and Standard bred had similar pattern. In conclusion, comparing to Thoroughbred and Standard bred, Akhal-Teke was less influenced by breeding program and the level of heterozygosity was moderate. Therefore, considering the use of this breed in the disciplines of sprinting, endurance, jumping and dramatic movements, it seems that the genetic diversity at the genome level of this breed can be used in the breeding program in this field.

The objective of this study was the detection of polymorphism in ATP1A1 gene and its association with conception rates in Holstein and Sarabi cows by PCR-SSCP method. For this purpose, blood samples were taken from 124 cows. DNA was extracted from whole blood using modified salting-out method and polymerase chain reactions were performed for amplification of 330bp fragment of the bovine ATP1A1gene. The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was used to scan for the mutations within the amplified regions. Subsequently, a numbers of samples per each band pattern were sequenced for identification of Single Nucleotide Polymorphism (SNP). The results of the sequencing and alignment using available sequences in NCBI two SNPs in the ATP1A1 gene that one of those was located in exon14 and another one in intron14 area and the mutation located in exon area was along with no changes in amino acid and obtained protein of this gene. For evaluating of association between this locations and conception rate trait, the band pattern (haplotype) were considered in the model. The results showed that the observed haplotypes in the ATP1A1 gene is not significantly correlated with conception rate.

One of the most important approaches in animal breeding is identification of structural variations responsible for economical important traits. Next generation sequencing technologies are provided accurate tools for this purpose. In the present study, Fars province native poultry genome was analyzed using genome sequencing approach. Paired-end sequencing of the whole genome was conducted by Illumina Company in China. Data quality was determined by FastQC software. Short reads of sequences were mapped with the reference genome with the BWA program. Single nucleotide polymorphisms and small deletions and insertions were identified with the GATK program. The short sequences were compared with the reference genome of over 99% and with the mean depth of the X8 coverage. In this study, 8858153 single nucleotide polymorphisms and 895378 small deletions and insertions were identified with the lowest counts in the exon region. Since the results of identifying the variants showed that the most frequent variant is related to single nucleotide polynomials¡ in this study, heterozygous loci were higher than homozygous loci indicating the high diversity of the population under study. Given the history of several thousand years of chicken domestication in Iran, one can expect that adaptation to the environment has occurred in the population studied. As a result of genomic changes in order to adapt to the environment, it has created a diversity in the population.

To identify single nucleotide polymorphisms (SNPs) in eugenol O-methyl transferase (EOMT) and Chavicol O-methyl transferase (CVOMT) genes, cleaved amplified polymorphic sequence (CAPS) markers and direct sequencing were used in different basil populations. Fragments with sizes of 571 and 908 bp of coding regions of both genes were amplified and digested with restriction enzymes Pst1 and MseI. In silico digestion of the coding region of the genes by Pst1 produced fragments of 480 and 91 bp in EOMT and 621 and 287 bp in CVOMT. However, no polymorphic restricted patterns were produced in 80 basil individuals using Pst1 digestion. In silico MseI digestion of EOMT and CVOMT gene sequences produces fragments of 59, 135 and 377 bp, and 275, 302 and 331 bp, respectively. Digestion of the amplified fragments of both genes generated polymorphic banding patterns in studied basil genotypes. One out of each different restriction patters which is produced for both genes in basil genotypes, was selected for sequencing. Sequences obtained, were aligned for both genes using Clustal Omega and SNPs were identified. The results of EOMT alignment revealed transition mutations TC and AG, but no transversion was observed in this gene. Mutations AG, TC, AC and AT were found in CVOMT gene with the highest frequency of AG. In conclusion, the results of the current investigation revealed low polymorphism in coding regions of the studied genes and demonstrated the conservity of the coding regions of both genes during basil evolution.

In this research the relationship of functional SNP of Hd5 and Hd6 genes with heading date was investigated in rice. For this purpose, 45 local and improved rice cultivars were phenotypically evaluated in Gorgan condition, and were genotyped using primer pairs specific to the genes. Association analysis in total population showed that Hd5 SNP explained 4.8% of variations in heading date and its additive effect was estimated equal to 2.6 days. However, Hd6 SNP explained equal to 5.5 % of variations in heading date and its additive effect was estimated equal to -2.4 days. After subdividing the population into two local and improved groups association analysis showed that effect of Hd5 SNP on heading date of improved cultivars wasn’t significant. However, in local cultivars, the SNP explained a relatively high portion (16.2%) of variations in heading date and its additive effect was estimated equal to 4.4 days. Effect of Hd6 SNP on heading date wasn’t significant in local cultivars, but in improved cultivars the SNP explained a relatively high portion (17.6%) of variations in heading date and its additive effect was estimated equal to -3.8 days. On the basis of the results of this research it can be concluded that improving cultivars with earliness alleles of both Hd5 and Hd6 genes is possible.

In order to detect QTLs for yield and some important agronomic traits via association mapping, 100 cultivars of winter barley (Hordeum vulgare) were evaluated in a lattice design with two replications. Yield, kernel per spike, thousand kernel weight, heading date, harvest index and plant height were measured. The population was genotyped using 3964 SNPs with minor allele frequency (MAFs) more than 10 percent. Molecular analysis of the population structure appeared two subpopulations consistent with ear row number. Average LD was observed to decay with distance increase and in the subpopulations was more than of that in the whole genome. Using a mixed linear model with kinship for controlling spurious LD effects, a total of 103 significant marker trait associations were found. 47 of the significant associations had previously been reported and 56 QTLs were reported for the first time. SNP_3660 linked with the yield and SNP_1432 associated with the kernel per spike, the thousand kernel weight and the spike morphology (two rows and six rows) had maximum -Log P and could be considered for marker assisted selection. This study showed that association mapping is a powerful tool for quantitative trait loci localization.

Copy number variation (CNV) is important on biological mechanism. For CNV detection and distribution, three bovine autosomal chromosomes, BTA6, BTA14 and BTA6 that improved for quantitative trait loci (QTL) previously, were investigated. Blood sample we obtained from 580 animals and after DNA extraction the samples were genotyped by Illumina BovineSNP50v2 BeadChip. Three hundred eighty three samples were remained for further analysis, after correction for signal intensity and GC content. Data were analyzed based on UMD3.1 bovine genome assembly for BTA6, BTA14 and BTA20. After filtration 199 CNV were detected (132 losses and 67 gains) with 0.5 CNV per animal and mean and medium of 147.3 kb and 139.4 kb respectively. A proportion of loss to gain was 1.97 fold. The Max and Min Number of CNV detected on BTA6 and BTA20 respectively. The bioinformatics analysis showed CNV region's coverage some part of 77 reference gene in bovine genome. These results showed that CNV coverage remarkable part of the three chromosomes that contain several QTL. Because of the influence of CNV on gene dosage and gene structure, it can cause phonotypic variation in quantitative traits, so probably it can be useful on livestock breeding programs.

The objective of the present study was to determine single nucleotide polymorphisms (SNP) located in the promoter region of the bovine heat shock protein 70 (Hsp70) gene. And evaluate associations between Hsp70 SNP with conception rates in Holstein and Sarabi cows. Blood samples were collected from 124 cows. The Cows were Holstein (n=72) and Sarabi (n=52). Genomic DNA was extracted using modified salting-out method. The quantity and quality of extracted DNA were examined with spectrophotometery and gel electrophoresis. Specific primers were designed for PCR amplification of a 539 base segment of the bovine Hsp70 promoter. The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was used to scan for mutations within the amplified regions. The polymorphisms were confirmed by direct sequencing. Seven single nucleotide polymorphisms were detected; one deletion at base position 895 four transitions (G1045A, G1117A, 1134C and T1204C), and two transversions (A1125C, G1128T). And also four haplotypes were detected (CAAAGCC, DGGCTTC, CDGGCTTT, CGGAGTT). Statistical analysis showed polymorphism in the promoter region of the bovine heat shock protein 70 region significantly correlated with conception rate (P <0.0001). Interestingly in Holstein breed the haplotype (CGGAGTT) of the significant mean conception rate heavier than had haplotypes (DGGCTTC, CDGGCTTT) and in Sarabi breed the haplotypes (CGGAGTT,CAAAGCC) of the significant mean conception rate heavier than had haplotype (DGGCTTC) (P< 0.01). The result of present study verified candidate SNPs within the promoter region of the bovine Hsp70 gene may be useful in selecting cows with a greater fertility.

The Insulin-Like Growth Factor I (IGF-I) Gene has a similar structure with Insulin hormone. That has an important functional in growth and development different tissue and transcribe. The IGF-I gene coded this hormone which located on Chromosome five which has six exons and five introns. The single nucleotide polymorphism was occurred in IGF-I gene and that associated with carcass traits in Zel (tailed) and Lori-Bakhtiari (fat-tailed) breed sheep with using PCR-SSCP marker. For this purpose, 4 mL of total blood was collected from the left jugular vein using vacuum tubes from Zel and Lori-Bakhtiari sheep breeds. Genomic DNA was purified from 1000-μl of blood samples that using the salting-out procedure and amplified region is located in the 5’ flanking region of the ovine IGF-I Gene. The IGF-I gene 5’flanking fragment was amplified which investigated with Single-Strand Conformational Polymorphism (SSCP) method for genotyping. Electrophoresis of PCR products were done on acrylamide gel that observed the polymorphic in this region. The frequency of patterns in Zel and Lori-Bakhtiari breeds were A (37.40%), B (41.98%), C (2.29%), D (18.32%) and A (58%), B (32%), C (4%), D (6%) respectively. Finally, for analysis of some traits was used SAS program. No significant associations of the SNPs in the 5’ flanking region of the ovine IGF-I Gene were observed for any trait.