Evaluation of SSR and SNP Markers for Molecular Breeding in Rice

( Zennia Jean Gonzaga ),( Kashif Aslam ),( Endang M. Septiningsih ),( Bertrand C. Y. Collard ) 한국육종학회 2015 Plant Breeding and Biotechnology Vol.3 No.2

Simple sequence repeats (SSRs) have been the marker of choice for rice molecular breeding due to the high level of polymorphism, technical simplicity and low cost. Recent advances in rice genomics have led to the discovery of abundant single nucleotide polymorphism (SNPs) which have enormous potential for rice molecular breeding. To assess both marker systems for molecular breeding in rice, SSR and SNP markers were evaluated on a set of 23 genotypes representing indica germplasm for their usefulness in molecular research and breeding program. Seven hundred SSR and sequence tagged sites (STS) markers and 384 SNPs were screened for polymorphism. Highly polymorphic markers based on polymorphic information content (PIC) values were identified, which will be useful for molecular breeding. Data was used to identify an “indica genotyping set” based on high level of polymorphism, chromosome position and marker quality which will provide kits of markers for marker assisted selection (MAS). Genetic diversity analysis using SSR data was more consistent with pedigrees compared to analysis with SNP data indicating that more than 384 SNPs are required when elite indica breeding material is used. The results also indicated that there were polymorphic “blind spots” for the fixed SNP set suggesting that SSRs could still be used to complement fixed-SNP genotyping platforms for some molecular breeding applications.

Molecular Markers and Their Usefulness in Rice Breeding

( Neeraj Kumar Tyagi ),( Bandarupalli Ramesh ),( Kuldeep Tyagi ) 전북대학교 농업과학기술연구소 2009 농업생명과학연구 Vol.40 No.2

Molecular markers are extensively used for improving and sustaining the rice productivity. A variety of molecular genetic markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), microsatellites or simple sequence repeats (SSRs), expressed sequence tags (EST) and single nucleotide polymorphism (SNP) have been developed providing new tools for rice breeding. The major advantages of the molecular markers over the other classes of markers are their number is potentially unlimited, spanning across the genome, their expression is unaffected by the environment and their assessment is independent of the stage of plant development. Molecular markers are landmarks in the chromosome maps that can be used to monitor the transfer of specific chromosome segments known to carry useful agronomic traits. Breeders use these molecular markers to increase the precision of selection for the best trait combinations. Molecular markers have large number of applications ranging from diversity analysis to the improvement of rice varieties by marker assisted selection. This review describes the usefulness of some important DNA markers in rice improvement.

감귤 분자육종을 위한 분자표지 개발 현황 및 전망

김호방,김재준,오창재,윤수현,송관정,Kim, Ho Bang,Kim, Jae Joon,Oh, Chang Jae,Yun, Su-Hyun,Song, Kwan Jeong 한국식물생명공학회 2016 식물생명공학회지 Vol.43 No.3

세계적인 과수작물로서의 경제적 중요성에도 불구하고, 감귤 생산은 주로 자연교잡 실생이나 눈 돌연변이로부터의 선발 또는 단순 품종 도입 등을 통해 이루어지고 있는 실정이다. 긴 유년기, 다배성, 자가불화합성과 같은 감귤 고유의 식물학적 특성, 주요 형질들(병저항성, 수량성, 품질 등)의 QTL에 의한 조절 등은 전통 육종을 통한 우수 품종의 개발을 어렵게 하는 요인이다. 지구 온난화에 의한 생산 여건의 급격한 변화, 소비자 요구 다양화 등은 고품질 감귤의 조기 선발과 안정적 생산, 품종 다양화, 육종 비용 절감 등을 위한 체계적인 감귤 분자육종 프로그램의 도입을 요구하고 있다. 동위효소를 이용한 최초의 감귤 연관지도 작성이 이루어진 이래, 다양한 분자표지를 이용한 연관지도 작성, 생물(CTV, CiLV, ABS, 선충] 및 비생물적(염분, 저온) 스트레스, 아포믹시스, 다배성, 과실착색(카로티노이드, 안토시아닌), 무종자, 웅성불임, 신맛 적음, 생식, 형태(나무, 잎, 꽃, 열매 등), 과실 품질, 종자수, 수량성, 조기 착과 등과 연관된 분자표지 발굴, QTL 맵핑 등이 이루어졌다. CTV 저항성과 적육(안토시아닌 축적) 형질에 대해서는 유전자 클로닝이 이루어졌고, 교배 육종 효율 증대 및 비용 절감을 위해 교잡배와 주심배를 구분하기 위한 다수의 simple sequence repeat (SSR) 분자표지가 개발되었다. 최근, 스위트오렌지와 '클레멘타인' 만다린에 대한 고품질의 표준 유전체가 완성되어 유전체 기반 감귤 분자육종을 위한 토대가 마련되었다. 표준 유전체 정보를 토대로 대규모 분자표지(SNP, SSR, InDel) 기반의 표준 연관 및 물리지도 작성, 비교 유전체 지도 작성, gene annotation, 전사체 분석 등이 활발히 이루어지고 있다. 감귤 유전자원 및 핵심집단에 대해 표준 유전체 기반 비교 유전체 분석, GBS (genotyping-by-sequencing), GWAS (genome wide association study) 등을 통해 감귤의 다양한 형질과 연관된 분자마커 발굴 및 개발, 유용/변이 유전자 클로닝 등에 관한 연구가 가속화될 것으로 전망된다. 또한 표적 유전체 교정 및 VIGS (virus-induced gene silencing) 기술도 유전자 마커의 검증을 비롯한 감귤 분자육종 프로그램에 활발히 이용될 것이다. Citrus is an economically important fruit crop widely growing worldwide. However, citrus production largely depends on natural hybrid selection and bud sport mutation. Unique botanical features including long juvenility, polyembryony, and QTL that controls major agronomic traits can hinder the development of superior variety by conventional breeding. Diverse factors including drastic changes of citrus production environment due to global warming and changes in market trends require systematic molecular breeding program for early selection of elite candidates with target traits, sustainable production of high quality fruits, cultivar diversification, and cost-effective breeding. Since the construction of the first genetic linkage map using isozymes, citrus scientists have constructed linkage maps using various DNA-based markers and developed molecular markers related to biotic and abiotic stresses, polyembryony, fruit coloration, seedlessness, male sterility, acidless, morphology, fruit quality, seed number, yield, early fruit setting traits, and QTL mapping on genetic maps. Genes closely related to CTV resistance and flesh color have been cloned. SSR markers for identifying zygotic and nucellar individuals will contribute to cost-effective breeding. The two high quality citrus reference genomes recently released are being efficiently used for genomics-based molecular breeding such as construction of reference linkage/physical maps and comparative genome mapping. In the near future, the development of DNA molecular markers tightly linked to various agronomic traits and the cloning of useful and/or variant genes will be accelerated through comparative genome analysis using citrus core collection and genome-wide approaches such as genotyping-by-sequencing and genome wide association study.

감귤 분자육종을 위한 분자표지 개발 현황 및 전망

김호방,김재준,오창재,윤수현,송관정 한국식물생명공학회 2016 JOURNAL OF PLANT BIOTECHNOLOGY Vol.43 No.3

Citrus is an economically important fruit crop widely growing worldwide. However, citrus production largely depends on natural hybrid selection and bud sport mutation. Unique botanical features including long juvenility, polyembryony, and QTL that controls major agronomic traits can hinder the development of superior variety by conventional breeding. Diverse factors including drastic changes of citrus production environment due to global warming and changes in market trends require systematic molecular breeding program for early selection of elite candidates with target traits, sustainable production of high quality fruits, cultivar diversification, and cost-effective breeding. Since the construction of the first genetic linkage map using isozymes, citrus scientists have constructed linkage maps using various DNA-based markers and developed molecular markers related to biotic and abiotic stresses, polyembryony, fruit coloration, seedlessness, male sterility, acidless, morphology, fruit quality, seed number, yield, early fruit setting traits, and QTL mapping on genetic maps. Genes closely related to CTV resistance and flesh color have been cloned. SSR markers for identifying zygotic and nucellar individuals will contribute to cost-effective breeding. The two high quality citrus reference genomes recently released are being efficiently used for genomics-based molecular breeding such as construction of reference linkage/ physical maps and comparative genome mapping. In the near future, the development of DNA molecular markers tightly linked to various agronomic traits and the cloning of useful and/or variant genes will be accelerated through comparative genome analysis using citrus core collection and genome-wide approaches such as genotyping-by-sequencing and genome wide association study. 세계적인 과수작물로서의 경제적 중요성에도 불구하고, 감귤 생산은 주로 자연교잡 실생이나 눈 돌연변이로부터의선발 또는 단순 품종 도입 등을 통해 이루어지고 있는 실정이다. 긴 유년기, 다배성, 자가불화합성과 같은 감귤 고유의식물학적 특성, 주요 형질들(병저항성, 수량성, 품질 등)의QTL에 의한 조절 등은 전통 육종을 통한 우수 품종의 개발을 어렵게 하는 요인이다. 지구 온난화에 의한 생산 여건의급격한 변화, 소비자 요구 다양화 등은 고품질 감귤의 조기선발과 안정적 생산, 품종 다양화, 육종 비용 절감 등을 위한체계적인 감귤 분자육종 프로그램의 도입을 요구하고 있다. 동위효소를 이용한 최초의 감귤 연관지도 작성이 이루어진 이래, 다양한 분자표지를 이용한 연관지도 작성, 생물(CTV, CiLV, ABS, 선충] 및 비생물적(염분, 저온) 스트레스, 아포믹시스, 다배성, 과실착색(카로티노이드, 안토시아닌), 무종자, 웅성불임, 신맛 적음, 생식, 형태(나무, 잎, 꽃, 열매등), 과실 품질, 종자수, 수량성, 조기 착과 등과 연관된 분자표지 발굴, QTL 맵핑 등이 이루어졌다. CTV 저항성과 적육(안토시아닌 축적) 형질에 대해서는 유전자 클로닝이 이루어졌고, 교배 육종 효율 증대 및 비용 절감을 위해 교잡배와주심배를 구분하기 위한 다수의 simple sequence repeat (SSR) 분자표지가 개발되었다. 최근, 스위트오렌지와 ‘클레멘타인’ 만다린에 대한 고품질의 표준 유전체가 완성되어 유전체 기반 감귤 분자육종을 위한 토대가 마련되었다. 표준 유전체 정보를 토대로 대규모 분자표지(SNP, SSR, InDel) 기반의 표준 연관 및 물리지도 작성, 비교 유전체 지도 작성, gene annotation, 전사체 분석 등이 활발히 이루어지고 있다. 감귤유전자원 및 핵심집단에 대해 표준 유전체 기반 비교 유전체 분석, GBS (genotyping-by-sequencing), GWAS (genome wide association study) 등을 통해 감귤의 다양한 형질과 연관된 분자마커 발굴 및 개발, 유용/변이 유전자 클로닝 등에 관한 연구가 가속화될 것으로 전망된다. 또한 표적 유전체 교정 및 VIGS (virus-induced gene silencing) 기술도 유전자 마커의 검증을 비롯한 감귤 분자육종 프로그램에 활발히 이용될 것이다.

주요 박과작물의 유전체 및 분자마커 연구 현황

박기림(Girim Park),김나희(Nahui Kim),박영훈(Younghoon Park) 한국생명과학회 2015 생명과학회지 Vol.25 No.9

수박과 멜론은 경제적 중요성을 지니는 대표적인 박과 작물이다. 최근 유전자 지도 작성 및 차세대 유전체 염기서열 분석에 기반한 분자마커 개발과 염기서열변이 탐색은 마커 이용 선발 및 여교잡 등 분자육종을 통한 품종육성에 필수적 기술이다. 본 연구에서는 이들 작물에 대한 국내외 유전체 분석 과 분자마커 개발 현황에 대해 분석 · 정리함으로서 향후 분자육종에 활용할 수 있는 정보를 제공하고자 하였다. 수박과 멜론은 참조유전체의 염기서열이 밝혀졌으며 다수의 유전자 지도가 작성되어 수량, 과특성, 내병성과 같은 주요 형질과 연관된 마커의 개발과 관련 유전자의 탐색이 꾸준히 진행되고 있다. 현재까지 해외에서 보고된 유전자지도는 수박 멜론 각 각 16종 이상이며, 40개 이상의 주요형질에 대한 유전자좌와 연관 마커들이 존재한다. 더욱이 고밀도 유전자 지도와 유전자지도 기반 클로닝을 통해 이러한 형질을 조절하는 기능 유전자에 정보가 밝혀지고 있다. 또한 참조게놈정보를 기반으로 한 다양한 유전자원의 전장유전체염기서열 재분석이 꾸준히 이루어지고 있다. 새로운 분자마커의 자체적 개발과 더불어 이와 같이 현재 활용 가능한 공개된 마커들의 정보를 통해 유전체학 이용 육종과정을 크게 앞당길 수 있을 것이다. Watermelon and melon are economically important Cucurbitaceae crops. Recently, the development of molecular markers based on the construction of genetic linkage maps and detection of DNA sequence variants through next generation sequencing are essential as molecular breeding strategies for crop improvement that uses marker-assisted selection and backcrossing. In this paper, we intended to provide useful information for molecular breeding of watermelon and melon by analyzing the current status of international and domestic research efforts on genomics and molecular markers. Due to diverse genetic maps constructed and the reference genome sequencing completed in the past, DNA markers that are useful for selecting important traits including yield, fruit quality, and disease resistances have been reported and publicly available. To date, more than 16 genetic maps and loci and linked markers for more than 40 traits have reported for each watermelon and melon. Furthermore, the functional genes that are responsible for those traits are being continuously discovered by high-density genetic map and map-based cloning. In addition, whole genome resequencing of various germplasm is under progress based on the reference genome. Not only by the efforts for developing novel molecular markers, but application of public marker information currently available will greatly facilitate breeding process through genomics-assisted breeding.

Miniature Inverted-repeat Transposable Elements (MITEs) as Valuable Genomic Resources for the Evolution and Breeding of Brassica Crops

( Perumal Sampath ),( Tae Jin Yang ) 한국육종학회 2014 Plant Breeding and Biotechnology Vol.2 No.4

Transposable elements (TEs) play important roles in structural and functional diversification, genome enlargement, and speciation in plant genome. Their derivatives or small non-autonomous TEs play important roles in the alteration of homologous genes by epigenetic control or structural modification. The miniature inverted-repeat transposable element (MITE) is one of the representative non-autonomous class II TEs. MITEs include high copy members that are widely distributed and in close association with genic regions, which make MITEs useful targets and resources for in-depth understanding of genome evolution, as well as practical applications in molecular breeding. Here, we discuss the important features of MITEs, such as the identification tools of a novel MITE family, structural characterization, distribution pattern analysis, and impact on evolution in highly duplicated Brassica genome. We show the characteristics, copy numbers, and distribution patterns of 20 novel MITE families, and represent their putative roles in the evolution of the triplicated Brassica genome. We also introduce our MITE database, and discuss the utility of MITEs for developing MITE-derived markers that are useful for molecular breeding of Brassica crops.

채소 품종육종 과거 현재 미래

조명철(Myeong Cheoul Cho),곽정호(Jung-Ho Kwak),정효봉(Hyo Bong Jeong),장석우(Suk Woo Jang),박수형(Su Hyoung Park),권영석(Young Seok Kwon),김철우(Chul Woo Kim),최민선(Min Seon Choi),한지원(Ji Won Han),문지혜(Ji Hye Moon),김대영(Dae Yo 한국육종학회 2020 한국육종학회지 Vol.52 No.S

Nowadays most parts of vegetable breeding in Korea have been conducted by private seed companies. However, in the beginning stages of breeding research, Horticulture Experiment Station played a crucial role. Major vegetable varieties that are distributed from Korea are produced as F1 hybrids. Korea has developed leading techniques and human infrastructure for vegetable breeding. Such brilliant developments have resulted from three major factors: changes in the composition of varieties, the establishment of year-round vegetable production, and the development of the seed export market. First, an F1 hybrid system increased seed performance more than traditional open pollinated (OP) varieties with respect to productivity, uniformity and disease resistance. Moreover, an F1 hybrid system required repetitive seed production and provision, which increased the economic growth of seed companies. Second, vegetables tend to be consumed fresh instead of dried or processed. Finally, vegetable seed exports have continuously increased with the aid of R&D projects such as the Golden Seed Project (GSP). Therefore, for further progress of the vegetable industry, new varieties that can meet consumers’ demands, as well as the stable provision of fresh vegetables, are required. Contrary to the past, the future focus must be concerned with productivity and cultivation stability, the development of high value, functional, eco-friendly vegetables, and high quality vegetables. To cope with this, every breeding subject, including industry, universities, and institutes, have to collaborate with the aim of advancing vegetable breeding in Korea.

고구마 생명공학연구 현황과 조건 불리지역 분자육종 전망

김호수,윤웅한,이찬주,김소은,지창윤,곽상수 한국식물생명공학회 2018 JOURNAL OF PLANT BIOTECHNOLOGY Vol.45 No.3

Dramatic increase in global population accompanied by rapid industrialization in developing countries has led to serious environmental, food, energy, and health problems. The Food and Agriculture Organization of the United Nations has estimated world population will increase to 9.7 billion by 2050 and require approximately 1.7 times more food, and more than 3.5 times energy than that of today. Particularly, sweetpotato is easy to cultivate in unfavorable conditions such as heat, drought, high salt, and marginal lands. In this respect, sweetpotato is an industrially valuable starch crop. To replace crops associated with these food and energy problems, it is necessary to develop new crops with improved nutrients and productivity, that can be grown on marginal lands, including desertification areas using plant biotechnology. For this purpose, exploring useful genes and developing genetically modified crops are essential strategies. Currently, sweetpotato [Ipomoea batatas (L.) Lam.] have been re-evaluated as the best health food and industrial crop that produces starch and low molecular weight antioxidants, such as vitamin A, vitamin E, anthocyanins and carotenoids. This review will focus on the current status of research on sweetpotato biotechnology on omics including genome sequencing, transcriptome, proteomics and molecular breeding. In addition, prospects on molecular breeding of sweetpotato on marginal lands for sustainable development were described.

고구마 생명공학연구 현황과 조건 불리지역 분자육종 전망

김호수,윤웅한,이찬주,김소은,지창윤,곽상수,Kim, Ho Soo,Yoon, Ung-Han,Lee, Chan-Ju,Kim, So-Eun,Ji, Chang Yoon,Kwak, Sang-Soo 한국식물생명공학회 2018 식물생명공학회지 Vol.45 No.3

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. Dramatic increase in global population accompanied by rapid industrialization in developing countries has led to serious environmental, food, energy, and health problems. The Food and Agriculture Organization of the United Nations has estimated world population will increase to 9.7 billion by 2050 and require approximately 1.7 times more food, and more than 3.5 times energy than that of today. Particularly, sweetpotato is easy to cultivate in unfavorable conditions such as heat, drought, high salt, and marginal lands. In this respect, sweetpotato is an industrially valuable starch crop. To replace crops associated with these food and energy problems, it is necessary to develop new crops with improved nutrients and productivity, that can be grown on marginal lands, including desertification areas using plant biotechnology. For this purpose, exploring useful genes and developing genetically modified crops are essential strategies. Currently, sweetpotato [Ipomoea batatas (L.) Lam.] have been re-evaluated as the best health food and industrial crop that produces starch and low molecular weight antioxidants, such as vitamin A, vitamin E, anthocyanins and carotenoids. This review will focus on the current status of research on sweetpotato biotechnology on omics including genome sequencing, transcriptome, proteomics and molecular breeding. In addition, prospects on molecular breeding of sweetpotato on marginal lands for sustainable development were described.

Recent research on enhanced resistance to parasitic nematodes in sweetpotato

김윤희,양정욱 한국식물생명공학회 2019 Plant biotechnology reports Vol.13 No.6

Sweetpotato yields are affected by diverse environmental factors, such as viruses, fungal diseases, and parasitic nematodes. In particular, plant–parasitic nematodes are major pathogenic factors affecting sweetpotato cultivation regionally. Seden-tary endoparasitic nematodes, including root-knot nematodes and cyst nematodes, cause serious sweetpotato yield losses in northeast Asia, including South Korea, China, and Japan. In this review, we describe the current status of research on nematode resistance in sweetpotato and molecular methods for resolving these cultivation problems. Conventional breed-ing and molecular techniques, including genome-editing-based transgenic technology and omics-based analyses, should be combined to develop sweetpotato cultivars with improved resistance to various important nematodes.