• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.219-219
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• 2022

Granule-bound starch synthase I (GBSSI), encoded by the waxy gene, is responsible for the accumulation of amylose during the development of starch granules in rice endosperm. Despite many findings on waxy alleles, the genetic diversity and evolutionary studies are still not fully explored regarding their functional effects. Comprehensive evolutionary analyses were performed to investigate the genetic variations and relatedness of the GBSSI gene in 374 rice accessions composed of 54 wild accessions and 320 bred cultivars (temperate japonica, tropical japonica, indica, aus, aromatic, and admixture). GBSS1 coding regions were analyzed from a VCF file retrieved from whole-genome resequencing data, and eight haplotypes were identified in the GBSSI coding region of 320 bred cultivars. The genetic diversity indices revealed the most negative Tajima's D value in the tropical-japonica, followed by the aus and temperate-japonica, while Tajima's D values in indica were positive, indicating balancing selection. Diversity reduction was noticed in temperate japonica (0.0003) compared to the highest one (wild, 0.0044), illustrating their higher genetic differentiation by F_ST-value (0.604). The most positive Tajima's D value was observed in indica (0.5224), indicating the GBSSI gene domestication signature under balancing selection. In contrast, the lowest and negative Tajima's D value was found in tropical japonica (-0.5291), which might have experienced a positive selection and purified due to the excess of rare alleles. Overall, our study offers insights into haplotype diversity and evolutionary fingerprints of GBSSI. It ako provides genomic information to increase the starch content of cooked rice.

• Fisheries and Aquatic Sciences
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• 제26권12호
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• pp.752-761
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• 2023

Genetic diversity serves as the basis for selecting and genetically enhancing any culturable species in aquaculture. Here, two different strains of wild (River Ravi and River Kabul) and six captive-bred strains of Labeo rohita from various provinces were se- lected, and genetic diversity among them was evaluated using three different microsatellite markers, i.e., Lr-28, Lr-29, and Lr-37, and one mitochondrial CO1 (Cytochrome c oxidase subunit 1) gene. Different strains of L. rohita were collected, and part of their caudal fin was cut and preserved in ethanol for DNA extraction and determination of genetic diversity among them. Results in- dicated that selected markers were polymorphic with polymorphic information content (PIC) content values above 0.5 with the highest in Lr-28 followed by Lr-29 and then Lr-37. The observed heterozygosity (Ho) of all strains was higher (Avg: 0.731) but less than the expected heterozygosity (He). Moreover, TMs and WRs showed the highest He, while TKs showed the lowest, He. Over- all, inbreeding coefficient (FIS) values observed for all strains with selected markers were positive. The DNA barcoding with the CO1 gene revealed genetic variation among various strains, as demonstrated by the clades in the phylogenetic tree separating the strains into two distinct clusters that then divided into sub-clusters. In conclusion, TMs showed the highest heterozygosity as compared to other strains. Overall results provide the baseline data for the initiation of the genetic improvement program.

• The Plant Pathology Journal
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• 제32권2호
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• pp.102-111
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• 2016

Olive culture is very important in the Mediterranean Basin. A severe outbreak of Olive Quick Decline Syndrome (OQDS) caused by Xylella fastidiosa infection was first noticed in 2013 on olive trees in the southern part of Apulia region (Lecce province, southern Italy). Studies were carried out for detection and diversity evaluation of the Apulian strain of Xylella fastidiosa. The presence of the pathogen in olive samples was detected by PCR amplifying the 16S rDNA, gyrase B subunit (gyrB) and HL hypothetical protein genes and single nucleotide polymorphisms (SNPs) assessment was performed to genotype X. fastidiosa. Twelve SNPs were recorded over gyrB and six SNPs were found for HL gene. Less variations were detected on 16S rDNA gene. Only gyrB and HL provided sufficient information for dividing the Apulian X. fastidiosa olive strains into subspecies. Using HL nucleotide sequences was possible to separate X. fastidiosa into subspecies pauca and fastidiosa. Whereas, nucleotide variation present on gyrB gene allowed separation of X. fastidiosa subsp. pauca from the other subspecies multiplex and fastidiosa. The X. fastidiosa strain from Apulia region was included into the subspecies pauca based on three genes phylogenetic analyses.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2004년도 International Meeting of the Microbiological Society of Korea
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• pp.42-44
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• 2004

• Journal of Microbiology and Biotechnology
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• 제21권10호
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• pp.1001-1011
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• 2011

To explore bacterial diversity for elucidating genetic variability in acylhomoserine lactone (AHL) lactonase structure, we screened 800 bacterial strains. It revealed the presence of a quorum quenching (QQ) AHL-lactonase gene (aiiA) in 42 strains. These 42 strains were identified using rrs (16S rDNA) sequencing as Bacillus strains, predominantly B. cereus. An in silico restriction endonuclease (RE) digestion of 22 AHL lactonase gene (aiiA) sequences (from NCBI database) belonging to 9 different genera, along with 42 aiiA gene sequences from different Bacillus spp. (isolated here) with 14 type II REs, revealed distinct patterns of fragments (nucleotide length and order) with four REs; AluI, DpnII, RsaI, and Tru9I. Our study reflects on the biodiversity of aiiA among Bacillus species. Bacillus sp. strain MBG11 with polymorphism (115Alanine > Valine) may confer increased stability to AHL lactonase, and can be a potential candidate for heterologous expression and mass production. Microbes with ability to produce AHL-lactonases degrade quorum sensing signals such as AHL by opening of the lactone ring. The naturally occurring diversity of QQ molecules provides opportunities to use them for preventing bacterial infections, spoilage of food, and bioremediation.

• Parasites, Hosts and Diseases
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• 제53권2호
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• pp.177-187
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• 2015

Merozoite surface proteins (MSPs) of malaria parasites play critical roles during the erythrocyte invasion and so are potential candidates for malaria vaccine development. However, because MSPs are often under strong immune selection, they can exhibit extensive genetic diversity. The gene encoding the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum displays 2 allelic types, K1 and 3D7. In Thailand, the allelic frequency of the P. falciparum msp-3 gene was evaluated in a single P. falciparum population in Tak at the Thailand and Myanmar border. However, no study has yet looked at the extent of genetic diversity of the msp-3 gene in P. falciparum populations in other localities. Here, we genotyped the msp-3 alleles of 63 P. falciparum samples collected from 5 geographical populations along the borders of Thailand with 3 neighboring countries (Myanmar, Laos, and Cambodia). Our study indicated that the K1 and 3D7 alleles co-existed, but at different proportions in different Thai P. falciparum populations. K1 was more prevalent in populations at the Thailand-Myanmar and Thailand-Cambodia borders, whilst 3D7 was more prevalent at the Thailand-Laos border. Global analysis of the msp-3 allele frequencies revealed that proportions of K1 and 3D7 alleles of msp-3 also varied in different continents, suggesting the divergence of malaria parasite populations. In conclusion, the variation in the msp-3 allelic patterns of P. falciparum in Thailand provides fundamental knowledge for inferring the P. falciparum population structure and for the best design of msp-3 based malaria vaccines.

• The Plant Pathology Journal
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• 제37권6호
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• pp.619-631
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• 2021

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

• 미생물학회지
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• 제44권2호
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• pp.147-155
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• 2008

한국의 시화호와 중국의 Aha호 저질토에서 서식하는 황산염 환원세균(sulfate reducing bacteria, SRB)의 깊이에 따른 군집구조를 비교하기 위하여, 이화성 아황산염 환원효소(EC 1.8.99.1; dissimilatory sulfite reductase, dsr) 유전자를 대상으로, polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE) 및 클론 라이브러리를 이용하여 미생물의 군집구조를 분석하였다. DGGE band 양상을 분석한 결과, Aha호 보다는 시화호에서 더 맡은 밴드를 보여 다양성이 높았고, 깊이별 차이는 나타나지 않았다. 두 서식지에서 얻은총68개 클론의 염기서열을 가지고 계통학적 분석을 한 결과 시화호에서는 Deltaproteobacteria 그룹, Firmicutes 그룹에 속해있는 Desulfotomaculum 종과 archaeal thermophilic SRB 그룹에 속해있는 Archaeoglobus 종이, Aha호에서는 Desulfotomaculum 그룹과 유사성이 높았다. 분리된 대부분의 클론들(59%)은 배양된 황산염 환원세균과는 매우 낮은 유사도를 보였고, 환경에서 분리된 클론들과도90% 이하의 유사도를 나타냈다. 총 클론을 88% 유사도를 기준으로 9그룹으로 나뉘었을 때 시하호와 Aha호의 각 클론은 서로 다른 그룹으로 존재하였다. 이러한 결과는 두 서식지의 이화성 아황산염 환원효소를 가지고 있는 미생물의 군집구조는 확연히 다르고 각 서식지에 특이적인 황산염 환원 미생물이 존재함을 시사한다.

• 생명과학회지
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• 제18권2호
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• pp.175-179
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• 2008

Cornus controversa is a long-lived woody species mostly distributed in East Asia. Random amplified polymorphic DNA (RAPD) markers were used to investigate the genetic diversity and population structure of Korean populations of this species. A high level of genetic variation was found in seven populations of C. controversa. The mean genetic diversity (H) was 0.222 across populations, varying from 0.200 to 0.238. Eighty of the 93 loci (86.0%) showed detectable polymorphism in at least one population. Total genetic diversity values ($H_T$) varied between 0.192 and 0.231, giving an average overall polymorphic loci of 0.212. The interlocus variation of genetic diversity within populations ($H_S$) was high (0.167). Mean of genetic diversity in C. controversa was higher than average values for species with similar life history traits. The sexual reproduction, perennial habitat, and longevity are proposed as possible factors contributing to high genetic diversity. On a per locus basis, the proportion of total genetic variation due to differences among populations ($G_{ST}$) ranged from 0.169 to 0.278 with a mean of 0.216, indicating that about 21.6% of the total genetic variation was among populations. An indirect estimate of the number of migrants per generation (Nm=1.893) indicated that gene flow was extensive among Korean populations of C. controversa.

• Ocean and Polar Research
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• 제31권4호
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• pp.319-326
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• 2009

Analysis of four microsatellite markers from Mud Crab Scylla serrata revealed that there is high level of genetic diversity within this species. Genetic diversity of S. serrata was calculated using allele diversity, observed heterozygosity, expected heterozygosity (Het-exp), polymorphic information content, gene differentiation and Nei's $D_{A}$ distance. Mean polymorphic information content value was 0.797, which reflected high level of polymorphism across the loci of S. serrata. The Palau population has the highest genetic diversity (Het-exp=0.871), while the Kosrae population has the lowest genetic diversity (Hetexp=0.806). However, the geographical genetic distance among S. serrata populations from Yab, Chuuk, Pohnpei, Kosrae, and Palau were low (0.2009${\sim}$0.3350). These results suggest that despite their wide distribution, S. serrata are no different in geographical genetic diversity within the five sampled locations.