• The Plant Pathology Journal
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• 제36권5호
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• pp.418-427
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• 2020

Xanthomonas campestris pv. campestris (Xcc), the pathogen of black rot which is the most destructive disease of Brassica vegetables throughout the world. Here, we reported two novel sequence-characterized amplified region (SCAR) markers (i.e., XccR6-60 and XccR6-67) for the detection of Xcc race 6 via re-alignment of the complete genome sequences of Xcc races/strains/pathovars. The specificity of SCAR primer sets was verified by mean of PCR amplification using the genomic DNA template of Xcc races/strains/pathovars and two other plant infecting bacterial strains. The PCR result revealed that the XccR6-60 and XccR6-67 primer sets amplified 692-bp and 917-bp DNA fragments, respectively, specifically from race 6, while no visible amplification was detected in other samples. In addition, the SCAR primers were highly sensitive and can detect from a very low concentration of genomic DNA of Xcc race 6. However, the complete genome sequence of Xcc race 6 is not yet publicly available. Therefore, the cloning and sequencing of XccR6-60 and XccR6-67 fragments from race 6 provide more evidence of the specificity of these markers. These results indicated that the newly developed SCAR markers can successfully, effectively and rapidly detect Xcc race 6 from other Xcc races/strains/pathovars as well as other plant pathogenic bacteria. This is the first report for race-specific molecular markers for Xcc race 6.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.151-151
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• 2017

In Asia, rice production has some difficulties with reduction of farm household population and increase of elderly population. As a result, it has resulted in inefficiency and we needs to reduce labor force and improve labor productivity. Direct-seeding in rice could reduce labor and production costs, the area of direct seeding is increasing in japonica rice production in Asia. In direct seedling cultivation competition against weeds is one of most important concern. So, low temperature germinability and mesocotyl elongation should be considered. In this study, we evaluated the mesocotyl length and low temperature germination conducted association analysis using 137 korea core collections. An average length of mesocotyl among 137 core collections was skewed range from 0mm to 43mm. we searched candidate gene around target SNP. Such related traits, genome-wide association study (GWAS) analysis was carried out using GAPIT. Also, average mesocotyl length of 394 korea landrace cultivars was measured ranging from minimum 0 mm to maximum 34mm. 30 out of 394 Korea landrace cultivar conducted re-sequencing, and haplotype analysis of candidate gene. we searched these related resources, which including germination of low temperature and mesocotyl elongation. This could be used for the development of direct-seeding cultivars. The valiated accession of core collection and landrace cultivars will be used development of direct-seedling cultivar in the future.

• Asian-Australasian Journal of Animal Sciences
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• 제25권11호
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• pp.1521-1528
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• 2012

Previously identified QTL regions on BTA1 and BTA5 were investigated to validate the QTL regions and to identify candidate genes for growth and carcass traits in commercial cattle populations from the USA and Korea. Initially, a total of 8 polymorphic microsatellite (MS) markers in the BTA1 and 5 QTL regions were used for Chi-square tests to compare the frequencies of individual alleles between high and low phenotypic groups for the US (Michigan Cattleman's Association/Michigan State University; MCA/MSU) cattle. For a subsequent study, 24 candidate genes containing missense mutations and located within the QTL regions based on bovine genome sequence data were analyzed for genotyping in the two commercial cattle populations. Re-sequencing analyses confirmed 18 public missense SNPs and identified 9 new SNPs. Seventeen of these SNPs were used for genotyping of the MCA/MSU cattle (n = 98) and Korean native cattle (n = 323). On BTA1, UPK1B, HRG, and MAGEF1 polymorphisms residing between BM1312 and BMS4048 were significantly associated with growth and carcass traits in one or both of the MCA/MSU and Korean populations. On BTA5, ABCD2, IL22 and SNRPF polymorphisms residing between BL4 and BR2936 were associated with marbling and backfat traits in one or both of the MCA/MSU and Korean cattle populations. These results suggested that BTA 1 and 5 QTL regions may be segregating in both Korean Hanwoo and USA commercial cattle populations and DNA markers tested in this study may contribute to the identification of positional candidate genes for marker-assisted selection programs.

• Asian-Australasian Journal of Animal Sciences
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• 제27권9호
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• pp.1345-1354
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• 2014

Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

• Animal Bioscience
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• 제37권7호
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• pp.1168-1176
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• 2024

Objective: As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future. Methods: Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations. Results: Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations. Conclusion: The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.

• Journal of Plant Biotechnology
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• 제45권3호
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• pp.196-206
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• 2018

고구마는 식량뿐만 아니라 전분을 비롯하여 카로티노이드, 비타민C, 비타민E, 안토시아닌과 같은 저분자 항산화물질을 생산하는 중요한 산업용 뿌리작물로 건조 등 조건 불리지역에 적용이 가능한 최고의 전분작물로 각광받고 있다. 이러한 관점에서 중국, 일본을 비롯한 세계 각국에서 오믹스 기반 유용유전자 발굴 및 활용에 대한 연구가 활발히 진행되고 있다. 또한 2014년부터 한 중 일 고구마연구협의회(TRAS)를 중심으로 Xushu 18(6배체) 고구마 유전체 해독 연구가 진행되고 있으며 거의 완성단계에 이르고 있다. 향후 고구마 유전체 해독이 완성되면 오믹스 기반 연구결과와 더불어 전분대사, 항산화물질 대사, 환경스트레스, 기능성 등의 기작에 관여하는 유용유전자 분리 및 활용 연구의 활성화에 기여할 것이며 6배체 고구마 유전체 해독 연구는 식물 유전체 해독에 있어 가장 문제시되는 다배수체 식물의 유전체 해독 문제해결에 가장 큰 기여를 할 것으로 기대 된다. 본 논문은 현재까지 연구된 고구마 생명공학 연구 현황과 조건 불리지역 분자육종 전망에 대해 기술하였다. 이러한 연구 동향 분석은 고구마를 활용한 글로벌 식량, 에너지, 환경문제 해결을 위한 실용화 연구에 도움이 될 것으로 생각된다.

• 한국육종학회지
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• 제51권4호
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• pp.318-325
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• 2019

식물은 다양한 환경 스트레스에 적응하기 위해 스트레스 내성 유전자의 발현과 자연 돌연변이를 통해 외부 환경 및 자극에 대한 반응 특성을 강화시켜 왔다 본 연구는 사료용 옥수수를 대상으로 감마선을 이용하여 돌연변이 집단을 구축하고 내염성이 증대된 계통을 개발하고자 수행되었다. 140RS516은 NaCl 처리 조건에서 대조군인 KS140과 비교하여 증가된 염 스트레스 내성을 보였다. 감마선에 의한 다양한 유전변이를 보인 140RS516 식물체는 염 스트레스 조건에서 대조군보다 높은 발아율과 생장, 기공전도도 그리고 proline함량을 나타냈으며, 내염성에 관여하는 유전자들의 발현이 증가하였다. 따라서 본 연구를 통해 개발된 140RS516 옥수수는 간척지 염화토양과 같이 불량한 환경에서 작물 재배 및 생산이 가능한 내염성 품종을 개발하기 위한 육종 소재로 활용될 수 있을 것이다.

• 한국작물학회지
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• 제65권4호
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• pp.406-415
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• 2020

본 연구는 간척지 내 재배 가능한 내염성 사료용 옥수수를 선발하기 위해 EMS를 이용하여 돌연변이 집단을 구축하고 기내 선발 방법을 통해 내염성 증진 계통을 선발하였고, 연구결과는 다음과 같다. 1. 사료용 옥수수 모본인 KS140에 다양한 조건으로 EMS를 처리하여 발아율 및 식물의 생육 상태를 조사하였고, 발아율에는 영향을 미치지 않으면서 생육에 큰 영향을 주지않는 0.5% EMS를 돌연변이 유도 적정 농도로 선정하였다. 2. 기내 선발 방법을 통해 선발된 내염성 증진 계통 140ES91 계통을 이용하여 0.5% 염분 스트레스 처리 후 표현형을 조사한 결과, 대조군인 KS140 대비 식물의 초장 및 근장의 생육이 양호하였으며, 높은 proline 함량과 기공전도도를 보였다. 따라서 염분 스트레스 시 높은 proline 함량과 기공전도도가 140ES91 계통의 증가된 내염성과 관련이 있을 것으로 판단된다. 3. 내염성 증진 140ES91 계통의 유전변이 분석을 통해 유전자 기능에 영향을 미칠 수 있는 아미노산 변이를 유발하는 39개의 변이 유전자를 확인하였고, 변이 유전자와 내염성의 관계를 증명하기 위한 유전자 기능 분석이 요구된다. 4. 기 보고된 내염성 관련 유전자들의 발현 양상을 조사한 결과 ABP9과 CIPK31 유전자는 대조군 대비 염분 스트레스 처리 전후 140ES91 계통에서 높은 발현율을 보였으며, CIPK21 유전자는 염분 스트레스 처리 후 대조군에는 발현이 감소하나 140ES91 계통에서는 발현이 유지됨을 확인하였다. 따라서 140ES91 계통에서 보이는 내염성 관련 유전자들의 높은 발현율이 140ES91 계통의 내염성에 관여할 것으로 판단된다. 5. 이상의 결과 기내 선발 방법을 통해 선발한 내염성 증진 계통은 간척지와 같은 염류집적 토양에서 작물의 안정적인 재배와 생산이 가능한 내염성 증진 품종 개발의 육종소재로 활용될 수 있을 것으로 판단된다.