• Journal of Plant Biotechnology
• /
• v.47 no.1
• /
• pp.15-25
• /
• 2020

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima's D and -1.19 for Fu's Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

• Korean Journal of Breeding Science
• /
• v.41 no.4
• /
• pp.397-402
• /
• 2009

Self-incompatibility (SI) prevents self-fertilization by inhibiting the pollen tube growth of self-pollen. Molecular analysis has revealed that the S locus comprises a number of genes, such as the S-locus glycoprotein (SLG), the S-locus receptor kinase (SRK), and SP11 (SCR). Although molecular markers related to those genes have been developed, a simple S-haplotype detecting method has not been reported due to the highly polymorphic and relatively small coding regions. In this study, the sequence characterized amplified region (SCAR) markers were used to establish an efficient radish genotyping method. We identified the S-haplotypes of 192 radish accessions using 19 different markers, which proved to be highly reliable. The accessions were assigned to 17 types of S-haplotypes, including 8 types of SRKs and 9 types of SLGs. Since the developed SCAR markers are based on their gene sequences, we could easily identify the S-haplotypes by a single specific band, with the highest frequencies detected for SLG 5, SRK 1, and SLG 1, in order. Among the tested markers, the SLG 1, SRK 1, and SRK 5 markers exhibited high reliability, compared to phenotypic results. Furthermore, we identified the seven types of unreported SLGs using SLG Class -I and -II specific markers. Although the developed SCAR markers still need to be improved for the genotyping of all S-haplotypes, these markers could be helpful for monitoring inbred lines, and for developing the MAS in radish breeding programs.

• Korean Journal of Agricultural Science
• /
• v.48 no.2
• /
• pp.283-297
• /
• 2021

Investigation of genetic diversity and molecular characterization in high yielding rice varieties is important for their identification. The experiment was conducted during 2016 - 2017 to analyse the genetic diversity of fifteen high yielding rice varieties in Bangladesh by using random amplification of polymorphic DNA (RAPD) markers. Polymorphism was revealed in 12 RAPD primers out of 30, whereas no other reaction was detected on the remaining 18 primers. The 40 out of 45 bands (88.89%) polymorphics were produced by the primers and ranged from 50 to 100%. The maximum number of polymorphic bands was produced by the primer OPB-18 whereas the lowest number of polymorphic bands belonged to OPC-12. The genetic similarity coefficients were determined with the RAPD data, which ranged from 0.47 to 0.94. The unweighted paired group of arithmetic means (UPGMA) dendrogram presented the studied rice varieties into two major clusters. Moreover, the value of Nei's genetic diversity is 0.26 and the Shanon information index is 0.41. The study produced distinct positions, suggesting that the genotypes were different from each other. The results indicated that these markers could be efficient for comparing the genetic relationships, patterns of variation, and measurement of genetic distance among rice varieties. Considering all of these results, RAPD analysis is found to be an effective tool for estimating the genetic diversity of different rice varieties. The outcomes of this research may contribute to the germplasm data of rice accessions and a future breeding program of rice genotypes.

• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.10
• /
• pp.1565-1574
• /
• 2018

Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits. Results: Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin 'eye' area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism. Conclusion: This study's results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.

• Asian-Australasian Journal of Animal Sciences
• /
• v.33 no.11
• /
• pp.1725-1731
• /
• 2020

Objective: An initial RNA-Sequencing study revealed that UDP-galactose-4-epimerase (GALE) was one of the most promising candidates for milk protein concentration in Chinese Holstein cattle. This enzyme catalyzes the interconversion of UDP-galactose and UDP-glucose, an important step in galactose catabolism. To further validate the genetic effect of GALE on milk protein traits, genetic variations were identified, and genotypes-phenotypes associations were performed. Methods: The entire coding region and the 5'-regulatory region (5'-UTR) of GALE were re-sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed linear animal model with a population encompassing 1,027 Chinese Holstein cows. Results: A total of three variants in GALE were identified, including two novel variants (g.2114 A>G and g.2037 G>A) in the 5'-UTR and one previously reported variant (g.3836 G>C) in an intron. All three single nucleotide polymorphisms (SNPs) were associated with milk yield (p<0.0001), fat yield (p = 0.0006 to <0.0001), protein yield (p = 0.0232 to <0.0001) and protein percentage (p<0.0001), while no significant associations were detected between the SNPs and fat percentage. A strong linkage disequilibrium (D' = 0.96 to 1.00) was observed among all three SNPs, and a 5 Kb haplotype block involving three main haplotypes with GAG, AGC, and AGG was formed. The results of haplotype association analyses were consistent with the results of single locus association analysis (p<0.0001). The phenotypic variance ratio above 3.00% was observed for milk protein yield that was explained by SNP-g.3836G >C. Conclusion: Overall, our findings provided new insights into the polymorphic variations in bovine GALE gene and their associations with milk protein concentration. The data indicate their potential uses for marker-assisted breeding or genetic selection schemes.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.9
• /
• pp.1319-1326
• /
• 2007

Fructose-1,6-bisphosphatase (FBP1) is a key regulatory enzyme of gluconeogenesis that catalyzes the hydrolysis of fructose-1,6-bisphosphate to generate fructose-6-phosphate and inorganic phosphate. Deficiency of fructose-1, 6-bisphosphatase is associated with fasting hypoglycemia and metabolic acidosis. The enzyme has been shown to occur in bacteria, fungi, plants and animals. The bovine FBP1 gene was cloned and characterized in this study. The full length (1,241 bp) FBP1 mRNA contained an open reading frame (ORF) encoding a protein of 338 amino acids, a 63 bp 5' untranslated region (UTR) and a 131 bp 3' UTR. The bovine FBP1 gene was 89%, 85%, 82%, 82% and 74% identical to the orthologs of pig, human, mouse, rat and zebra fish at mRNA level, and 97%, 96%, 94%, 93% and 91% identical at the protein level, respectively. This gene was broadly expressed in cattle with the highest level in testis, and the lowest level in heart. An intronic single nucleotide polymorphism (SNP) (A/G) was identified in the $5^{th}$ intron of the bovine FBP1 gene. Genotyping of 133 animals from four beef breeds revealed that the average frequency for allele A (A-base) was 0.7897 (0.7069-0.9107), while 0.2103 (0.0893-0.2931) for allele B (G-base). Our preliminary association study indicated that this SNP is significantly associated with traits of Average Daily Feed Intake (ADFI) and Carcass Length (CL) (p<0.01). In addition, the FBP1 gene was assigned on BTA8 by a hybrid radiation (RH) mapping method.

• The Plant Pathology Journal
• /
• v.30 no.4
• /
• pp.343-354
• /
• 2014

Rice blast disease caused by Magnaporthe oryzae is one of the most serious diseases of cultivated rice (Oryza sativa L.) in most rice-growing regions of the world. In order to investigate early response genes in rice, we utilized the transcriptome analysis approach using a 300 K tilling microarray to rice leaves infected with compatible and incompatible M. oryzae strains. Prior to the microarray experiment, total RNA was validated by measuring the differential expression of rice defense-related marker genes (chitinase 2, barwin, PBZ1, and PR-10) by RT-PCR, and phytoalexins (sakuranetin and momilactone A) with HPLC. Microarray analysis revealed that 231 genes were up-regulated (>2 fold change, p < 0.05) in the incompatible interaction compared to the compatible one. Highly expressed genes were functionally characterized into metabolic processes and oxidation-reduction categories. The oxidative stress response was induced in both early and later infection stages. Biotic stress overview from MapMan analysis revealed that the phytohormone ethylene as well as signaling molecules jasmonic acid and salicylic acid is important for defense gene regulation. WRKY and Myb transcription factors were also involved in signal transduction processes. Additionally, receptor-like kinases were more likely associated with the defense response, and their expression patterns were validated by RT-PCR. Our results suggest that candidate genes, including receptor-like protein kinases, may play a key role in disease resistance against M. oryzae attack.

• Journal of Microbiology and Biotechnology
• /
• v.13 no.6
• /
• pp.881-891
• /
• 2003

Paenibacillus polymyxa is a plant growth-promoting rhizobacterium (PGPR) which can be used for biological control of plant diseases. Several bacterial strains were isolated from rotten roots of Korean ginseng (Panax ginseng C. A. Meyer) that were in storage. These strains were identified as P. polymyxa, based on a RAPD analysis using a P. polymyxa-specific primer, cultural and physiological characteristics, an analysis utilizing the Biolog system, gas chromatography of fatty acid methyl esters (GC-FAME), and the 16S rDNA sequence analysis. These strains were found to cause the rot in stored ginseng roots. Twenty-six P. polymyxa strains, including twenty GBR strains, were phylogenetically classified into two groups according to the ERIC and BOX-PCR analyses and 16S rDNA sequencing, and the resulting groupings systematized to the degrees of virulence of each strain in causing root rot. In particular, highly virulent GBR strains clustered together, and this group may be considered as subspecies or biovar. The virulence of the strains seemed to be related to their starch hydrolysis enzyme activity, but not their cellulase or hemicellulase activity, since strains with reduced or no starch-hydrolytic activity showed little or no virulence. Artificial inoculation of the highly virulent strain GBR-1 onto the root surfaces of Korean ginseng resulted in small brown lesions which were sunken and confined to the outer portion of the root. Ginseng root discs inoculated in vitro or two-year-old roots grown in soil drenched with the inoculum developed significant rot only when the inoculum density was $10^{6}-10^{7}$ or more colony-forming units (CFU) per ml. These results suggest that P. polymyxa might induce ginseng root rot if their population levels are high. Based on these results, it is recommended that the concentration of P. polymyxa should be monitored, when it is used as a biocontrol agent of ginseng, especially in the treatment of stored roots.

• Animal Bioscience
• /
• v.34 no.12
• /
• pp.1940-1950
• /
• 2021

Objective: The objective of this study was to explore the effects of maize straw treated with calcium oxide (CaO) and various moisture, on the composition and molecular structure of the fiber, and gas production by fermentation in an in vitro rumen environment. Methods: The experiment used 4×3 Factorial treatment. Maize straws were treated with 4 concentrations of CaO (0%, 3%, 5%, and 7% of dry straw weight) and 3 moisture contents (40%, 50%, and 60%). Scanning electron microscopy, Fourier transform infrared spectroscopy and X-ray fluorescence spectroscopy were employed to measure the surface texture, secondary molecular structure of carbohydrate, and calcium (Ca) content of the maize straw, respectively. The correlation of secondary molecular structures and fiber components of maize straw were analyzed by CORR procedure of SAS 9.2. In vitro rumen fermentation was performed for 6, 12, 24, 48, and 72 h to measure gas production. Results: Overall, the moisture factor had no obvious effect on the experimental results. Neutral detergent fiber (NDF), acid detergent fiber, acid detergent lignin, hemicellulose and cellulose contents decreased (p<0.05) with increasing concentrations of CaO treatment. Surface and secondary molecular structure of maize straw were affected by various CaO and moisture treatments. NDF had positive correlation (p<0.01) with Cell-H (H, height), Cell-A (A, area), CHO-2-H. Hemicellulose had positive correlation (p<0.01) with Lignin-H, Lignin-A, Cell-H, Cell-A. Ca content of maize straw increased as the concentration of CaO was increased (p<0.01). Gas production was highest in the group treated with 7% CaO. Conclusion: CaO can adhere to the surface of the maize straw, and then improve the digestibility of the maize straw in ruminants by modifying the structure of lignocellulose and facilitating the maize straw for microbial degradation.

• Asian-Australasian Journal of Animal Sciences
• /
• v.29 no.9
• /
• pp.1256-1264
• /
• 2016

Adrenergic, alpha-1B-, receptor (ADRA1B) and peroxisome proliferator-activated receptor gamma, coactivator 1 beta (PPARGC1B) genes are involved in regulation of hen ovarian development. In this study, these two genes were investigated as possible molecular markers associated with hen-housed egg production, egg weight (EW) and body weight in Chinese Dagu hens. Samples were analyzed using the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique, followed by sequencing analysis. Two novel single nucleotide polymorphisms (SNPs) were identified within the candidate genes. Among them, an A/G transition at base position 1915 in exon 2 of ADRA1B gene and a T/C mutation at base position 6146 in the 3'- untranslated region (UTR) of PPARGC1B gene were found to be polymorphic and named SNP A1915G and T6146C, respectively. The SNP A1915G (ADRA1B) leads to a non-synonymous substitution (aspartic acid 489-to-glycine). The 360 birds from the Dagu population were divided into genotypes AA and AG, allele A was found to be present at a higher frequency. Furthermore, the AG genotype correlated with significantly higher hen-housed egg production (HHEP) at 30, 43, 57, and 66 wks of age and with a higher EW at 30 and 43 wks (p<0.05). For the SNP T6146C (PPARGC1B), the hens were typed into TT and TC genotypes, with the T allele shown to be dominant. The TC genotype was also markedly correlated with higher HHEP at 57 and 66 wks of age and EW at 30 and 43 wks (p<0.05). Moreover, four haplotypes were reconstructed based on these two SNPs, with the AGTC haplotype found to be associated with the highest HHEP at 30 to 66 wks of age and with higher EW at 30 and 43 wks (p<0.05). Collectively, the two SNPs identified in this study might be used as potential genetic molecular markers favorable in the improvement of egg productivity in chicken breeding.