Genotyping-by-sequencing (GBS) is a robust and rapid tool to develop SNP markers. Reduced sequencing complexity and multiplex sequencing of GBS has reduced genotyping cost for complex genome. However multiplex sequencing brings low sequencing depth which can lead to reduced number of markers. Therefore to find the appropriate condition for GBS is needed. In this research we demonstrated the use of ApeKI and selective primers for GBS of pepper (Capsicum spp.). Selective primers which amplify the GBS library with one or two flanking sequences to ApeKI site were used to increase sequencing depth. By in silico digestion, we developed six different selective primers amplify 4,000-400,000 regions. We made the GBS library with eight pepper accessions in four species using six selective primers and sequenced. Proper selective primers and pooling rate for each species will be determined. This approach will be useful for genotyping Capsicum breeding lines or populations by developing high quality SNP markers.

Capsicum diversity is getting lower in modern crops because of the genetic erosion. In Capsicum, breeders have been mainly focused on agriculturally important traits such as disease resistances, high yield and pungency. This narrow breeding pool hampered to develop improved cultivars. It has become a hot issue to conservation of genetic diversity and exploitation of wild germplasm in Capsicum. However, although a large number of accessions are maintained in Capsicum germplasm collections, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of core samples. We investigated patterns of molecular diversity at 48 single nucleotide polymorphisms (SNPs) in 4056 accessions from 11 Capsicum species from 89 different countries. Using these genetic variations and 32 different morphological traits, 250 core set was selected in whole Capsicum germplasm. The core collection could be a primary source for distributing germplasm to pepper breeders and other national programs as well as for evaluation

GM콩은 사료용으로 2004년 Monsanto사의 제초제 저항성 콩 승인을 시작으로 11개 이벤트와 3개의 후배교배종들 이 Monsanto Korea, Bayer Crop Science, DuPont Korea, BASF 4개의 회사에서 개발되어 국내로 수입되고 있다. 단일 이벤트는 7개의 제초제저항성, 1개의 해충저항성, 3개의 기능성을 강화한 특성들이 있다. 기능성 강화에는 올레산 함량 증가와 SDA 생성하는 특성들이 DuPont사와 Monsanto사에서 개발되었다. 2011년부터는 후대교배종이 신청 되어 2가지 특성을 모두 지니고 있는 이벤트들이 수입되고 있다. 이와 같이 GM통이 사료용으로 대량 수입됨에 따 라 비의도적 소실로 인한 자연계 방출 가능성을 염두해 두고, 미리 국내에서의 유전자 이동성 평가를 하기 위하여 콩의 화분 특성과 교잡율을 GM콩의 모본으로 사용된 non-GM 모본을 협조 받고, 3개의 국내 야생콩(IT 184230, IT 183042, IT 236804)과 3개의 국내 장려품종(IT 212859, IT 212860, IT 178684)과 함께 개화시기를 맞춰 화분특성과 교잡율을 조사하고자 2014년 전남대학교 60평 격리온실에서 1주인 간격으로 파종하여 재배하고 있다. 개화기간 동안에 화분비산거리, 화분량, 화분형태 및 크기, 화분 발아력, 화분 수명과 교잡율을 조사하여 국내 야생콩과 GM 콩 모본과의 교잡 가능성에 대한 기초 자료를 생성하여 향후 GM콩 환경위해성 심사 과정에 참고하고자 연구를 진 행하고 있다.

B;ue GM 카네이션 8품종을 개발한 일본 Florigene사는 미국, 네덜란드를 포함한 10개국에서 상용화하고 있다. 국 내에서는 집약적으로 시설내에서 재배되는 화훼류가 유망한 GMO개발 작물이 될 것으로 인식되고 있다. 따라서 저온성 작물인 Alstroemeria를 이용한 실질적 동등성 평가 지침서를 개발하고자 식물학적․원예산업적 자료를 조사 하였다. Alstroemeria의 노지 월동성을 확인하기 위하여 재식 깊이별 생존율을 전남대학교 포장에서 측정하였다. 지표면에서 5cm 이내로 가까이 식재된 경우 모두 고사하였으며, 그 이상의 깊이로 식재된 경우 높은 생존율을 보 여, 국내 노지에서의 월동 가능성을 보여주었고 5월부터 개화하여 정원용으로 개발이 가능할 것으로 판단되었다. 화분비산특성을 조사하고자 측정한 1 anther당 화분 수는 대략 25,000-28,000개로 특정되었으며 화분활력은 30-60%로 다양하였다. 화분 발아력 기준을 설정하기 위하여 화분 발아배지 자당의 농도를 10, 15, 20, 25%로 다양 하게 처리한 결과 배지 내 자당이 가장 낮은 배지(10%)에서 가장 높은 발아율을 보여 추후 더 낮은 농도의 자당처리 가 필요한 것으로 추정되었다. Alstroemeria의 화분 비산 거리를 측정하기 위하여 슬라이드그라스를 이용한 포집 후 측정 방식을 이용하여 측정 중에 있다. 2014년도에는 재배적 측면에서 실질적 동등성 평가기준을 위한 실험을 진행 중에 있다

Rice is the staple food for more than half the world’s population. It is known that Zinc is one of the most important essential micronutrient for human About thirty percentage world’s population doesn’t still get enough zinc through their diets. As a staple food of over half world’s population, rice should take the responsibility to provide much more zinc in the future. Here, we performed Genome-Wide Association Study(GWAS) with high-resolution density SNPs and InDels to identify natural allelic variation in zinc increase from Heuristic or core rice set, which is derived from a total 24,368 rice germplasms. The range of the concentration and distribution of zinc in 137 core accessions of brown rice grain were wide, from 7.86ppm to 31.76ppm, with mean 18.97ppm. In particular, GWAS result show that the high peak found in Chromosomes (1, 4, 6, 8). The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular breeding.

GM 유채는 2013년 국내에서 비의도적으로 방출되어 5곳에서 발견되었다고 추정되고 있다. 봄철 경관용으로 전국 지자체에서 유채를 식재하고 유채 축제 면적이 늘어남에 따라 2013년부터 본연구진은 국내에서의 유채 화분 비산 에 관한 연구와 환경위해성 평가 가이드라인 기초DB 준비를 진행 중에 있다. 이에 따라 최근까지의 GM유채의 국 제적 상용화 현황과 국내 수입 승인 현황이 조사되었다. 2013년까지의 GMO식물의 국내유출 추정 현황을 조사하 과 유채의 유전자 이동 가능성을 제고하기 위하여 식물학적․농업적 특성이 조사되었다. 유채의 표현형 검증에 필 요한 비교지표를 설정하고 실험방법에 대한 기준을 제시하였다. 유채의 재식 깊이별 생존 능력을 측정하여, ‘유달’ 과 ‘영산’ 품종 모두 3cm 깊이에서는 40-65% 정도의 종자 발아율을 보이고, 10cm 깊이에서는 급격이 저하되어 1-17% 정도의 종자 발아율을 보였다. 또한 20cm 깊이부터는 발아가 어려운 것으로 판단되었다. 유채의 결실 특성 을 조사하기 위하여 ‘내한’, ‘탐미’, ‘탐라’ 품종들을 대상으로 노지에서의 결실율은 96-98%를 보였으며, 바람과 곤 충이 없는 격리온실상에서는 68-78%의 결실율을 보여 격리온실 내에서의 비의도적인 결실 유도 매개를 고려하고 분재배로 생육상태가 노지보다 저조한 상황을 고려하면 대단히 높은 자가 결실율을 보여주고 있다. 비의도적 봄 철 종자 비산으로 인한 결실 여부를 확인하기 위하여 ‘유달’, ‘영산’ 품종을 3월 초에 파종한 결과 ‘유달’은 결실이 가능하고 ‘영산’은 결실 불능인 결과가 나와 품종에 따른 차이가 큰 것으로 판단되었다. 이에 따라 유채의 비의도적 유전자 이동과 잡초화 가능성에 관련한 기초자료 수집이 필요한 것으로 보인다.

Chrysanthemum (Dendranthema grandiflorum Ramat.) is a member of the Asteraceae and 588 varieties obtained Plant Variety Protection and 601 varieties were registered to Korea Seed & Variety Service for marketing. Thus, chrysanthemum is one of the important horticultural crop and having a possibility for infringement of Plant Breeder’s Rights. We investigated the genetic relationship of 20 chrysanthemum varieties using simple sequence repeat (SSR) markers. A total 335 SSR primer sets were screened for identification of 20 varieties. With 335 SSR primers, seventeen SSR primers showed polymorphism and reproducibility between 20 varieties. A total of 77 polymorphic fragments were identified by 17 SSR markers. Two to eight SSR alleles were detected for each SSR locus with an average of 4.53 alleles per locus. The polymorphism information content values ranged from 0.408 to 0.825 with an average of 0.45. Genetic distance of 20 varieties ranged from 0.36 to 0.73 by unweighted pair-group method with arithmetical average based on Jaccard’s distance coefficients. All of twenty varieties were distinguished by 17 marker genotypes. Future work will be investigated to construct DNA profile database for large number of chrysanthemum varieties using DNA sequencer.

Gamma irradiation has been used as a tool for plant mutation breeding to select new cultivar with improved characteristics. Generally, the irradiation of seeds with high doses of gamma rays disturbs the synthesis of protein, hormone balance, and enzyme activity. And also, high dose of gamma rays to reduce plant height, number of tiller, and root length, although the effect of gamma-irradiated plants may depend on the species and cultivar or stress conditions. Biological effects of radiations can be divided into two types according to dose range and periods of exposure. Acute irradiation represents exposure to high-dose of irradiation over short period time, whereas the chronic irradiation is comprised of exposure to low doses of radiation over extended period of time. To compare the effects of acute and chronic exposure to ionizing radiation on two wheat cultivars (K4191 and Geumgangmil), we measured their germination rate, seedling height, and root length. In order to understand the influence of antioxidant-related genes and DNA repair-related genes, we used qRT-PCR methods to identify their expression levels. To study the behavior of a radiation-induced free radical, gamma-irradiated seeds were used for ESR spectroscopy. Plant growth pattern was showed positive correlation with ESR results. This study indicates that low level chronic radiation exposure is even more serious effects than short doses of high level radiation according to different wheat cultivar.

Seed & Variety Service for Plant Variety Protection (PVP). We previously constructed DNA profile database for identifying 159 lettuce varieties using 60 simple sequence repeat (SSR) markers. In this study, we selected optimum markers from previously applied markers and new SSR markers for the standardization of DNA profile database of 65 commercial lettuce varieties containing 18 PVP varieties distributed in Korea. Twenty-eight SSR markers from 60 SSR markers were selected for characterization with 65 commercial lettuce varieties according to the reproducibility, polymorphism, band pattern of marker and easiness of scoring. Out of 156 SSR primers, we additionally selected 11 new SSR primer pairs showed polymorphisms between 8 varieties and repetitive reproducibility on capillary electrophoresis system. Totally 127 polymorphic amplified fragments were obtained using 39 SSR markers. Two to seven SSR alleles were detected for each locus with an average of 3.3 alleles per locus. Average polymorphism information content was 0.517, ranging from 0.281 to 0.771. Genetic distance of clusters ranged from 0.29 to 0.96 by unweighted pair-group method with arithmetical average based on Jaccard’s distance coefficients. A total of 65 commercial lettuce varieties were discriminated by 39 SSR marker genotypes. These SSR profile database developed will be continually characterized for the standardization of DNA profiles for lettuce commercial varieties

Plant bZIP transcription factors play crucial roles in biological processes. In this study, 136 putative bZIP transcription members were identified in Brassica rapa. The bZIP family can be divided into nine groups according to the specific amino acid rich domain in Brassica rapa. To screen the cold stress responsive BrbZIP genes, we evaluated whether the transcription patterns of the BrbZIP genes were enhanced by cold treatment in the inbred lines, Chiifu and Kenshin, by microarray data analysis and qRT-PCR. The expression level of six genes increased significantly in Kenshin, but these genes were unchanged in Chiffu. Additionally, homo- and hetero-dimerization test between selected bZIP proteins indicated the Bra020735 is a key regulator in cold response. These findings suggest that the six genes that encoded proteins containing N-rich regions might be involved in cold stress response. These results presented herein provide valuable information regarding the molecular basis of the bZIP transcription factors and their potential function in regulation growth and development, particularly in cold stress response.

Recently, the importance of food safety is increasing due to numerous junk food. Junk food means to violate the law in stage such as production, manufacture, distribution, and sale of food. Many crop plants are processing as foods including bread, noodle, and other foods for supporting nutrition to human. For example, rice is one of the most well-known food crops in the world, and processed rice is being mixed with other processed crops to health food. The object of this study is to detect amount of specific grains, i.e. rice from processed foods mixed with other cereals. This experiment was performed to the following two steps: 1) designed the specific primer sets based on chloroplast DNAs, 2) amplified products using real-time PCR. We designed eleven primer sets within chloroplast DNA of rice, and then the confirmation of primer efficiency was to amplified with rice genomic DNA using real-time PCR. In addition, these primer sets were applied in other crops such as wheat, maize, and adlay to confirm specificity to rice. The rice specific primer sets were determined by the number of amplification and the melting peak through real-time PCR. As a result, five primer sets were confirmed to uniqueness in the rice genome. In conclusion, the specific primer sets would be useful for identifying rice grain from the processed foods to eliminate junk foods and for contribution of food safety.

Even rice is one of the most important food crops in the world, its micronutrient contents including iron is not enough to solve mineral malnutrition which is a significant public health issue in most developing countries. Iron deficiency is probably the most widespread micronutrient deficiency in humans. Experts estimate that a rice based diet should contain 14.5 ppm iron in endosperm. However, Cesar P et al reported that average iron content in milled rice was 2 ~ 3 ppm, whease it was 10 ~ 11 ppm in brown rice. Fe content of rice is usually measured by inductively plasma spectrometry (ICP). It takes times and could make error while sample processing. To breed high iron contained rice variety, the effective screen method for select high iron contained elite line is essential. To develop more effective method in screening high Fe contained brown rice, we investigate the relation the leaf chlorophyll content with iron content in brown rice. Result of analyzing leaf chlorophyll content of OsNAS3-OX which contain more Fe than wild-type plant after cultivated on Fe limited MS medium, those of OsNAS3-OX was higher than those of wild-type plant in 0 and 20 % Fe contained MS medium. After measured Fe content in twenty kinds of brown rice, we cultivated those in Fe limited MS medium then investigate the relation of leaf chlorophyll content with Fe content of brown rice. In 0 and 5 % Fe contained MS medium, the leaf chlorophyll content was highly related with Fe content of brown rice as 0.66 and 0.79. Though these result, analyze of leaf chlorophyll content cultivated in 5 % Fe content in MS media was effect on screening high Fe contained.

Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA sequences in the specific region of the chromosomes. As well as for the integrated physical mapping, FISH karyotype analysis has to be preceded. The detailed karyotypes of two onion cultivars, which are resources for onion genome sequencing project (‘Eumginara’ and ‘Sinsunhwang’), were constructed based on triple color fluorescence in situ hybridization (FISH) using 5S rDNA, 45S rDNA, and tandem repeat sequence. All used our materials showed 2n=2x=16 with x=8 as basic chromosome number. 5S rDNAs were located on 4 loci in one pair of interstitial region of short arm chromosome in both onion cultivars. Two pairs of 45S rDNAs were positioned in distal region of short arm chromosome in ‘Eumginara’. Otherwise 5 loci of 45S rDNAs were located in distal region of two pairs of short arm chromosome in ‘Sinsunhwang’. Among them, two signals of 45S rDNAs were co-localized in distal part of short arm and long arm chromosome, respectively. In case of tandem repeat sequence was detected on telomeric region of 8 pairs of chromosomes except on 45S ribosomal DNA sites. These results will provide a valuable background for physical mapping and help to further more understand the genome sequencing project in Allium cepa.

Chrysanthemums (Asteraceae) are important ornamental crops in worldwide that are well known as commercial valuable cultivars for cut flowers, potted plants, and garden flowering plants. Genus chrysanthemum consisted of 41 species that are mostly distributed in East Asia. Chrysanthemum has diverse ploidy levels with the basic chromosome number of x=9 from 2n=2x=18 (diploid) to 2n=10x=90 (decaploid). Fluorescence in situ hybridization (FISH) is a useful tool for studying the distribution of ribosomal DNAs. In this study, we have confirmed ploidy level by chromosome counting method. The somatic metaphase chromosome numbers were observed 2n=2x=18 in Chrysanthemum boreale, and 2n=6x=54 in C. indicum and C. zawadskii. More detailed Karyotype was constructed based on FISH method using 5S and 45S rDNA probes. Two (2) loci of 5S rDNA signals were detected in interstitial region of long arm chromosome in C. boreale and six (6) loci were in C. indicum and C. zawadskii. All of 45S rDNAs were located in terminal region of short arm chromosome which were visualize in six (6) loci in C. boreale and C. indicum and twelve(12) loci in C. zawadskii. In this study, it was the main topic to perform physical mapping of the location of 5S and 45S rDNA. Three of wild chrysanthemum showed variations in number of ribosomal DNAs. In the present investigation will help to further study of genome sequencing project in chrysanthemum.

Legume and rhizobia symbiosis plays an important role in conversion of atmospheric dinitrogen to ammonia. On a global scale, this interaction represents a key entry point for reduced nitrogen into the biosphere, and as a consequence this symbiosis is important in both natural and agricultural systems. Symbiotic development of nodule organ is triggered by chito-oligosaccharide signals (Nod factors) from the bacterium which are perceived by the legume root. Understanding the molecular and cellular processes that underlie Nod factor perception is one focus of legume biology. Although forward genetics has proved to be an important tool to identify key players in Nod factor perception, we still know relatively little regarding the functional networks of genes and proteins that connect the earliest steps of Nod factor perception to immediate downstream outcomes. To elucidate genes and proteins that link Nod factor perception to cellular and physiological responses we are taking a discovery-based strategy based on whole transcriptome profiling using RNA-seq analysis in the roots of Medicago truncatula in response to Sinorhizobium meliloti. Functional characterization of a number of candidate genes is currently in progress to further examine their role in nodulation such as generating transgenic plants

Phytochemical in purple percarp of wheat seed consist of high phenolic content including ferulic acid, caffeic acid, vanilic acid and anthocyanins which not only perform as source of distinctive red to purple pigmentation but also high antioxidative material. Previous work has demonstrated that certain pigmentation can be generally regarded as good dietary source of food supplement. Yet, its physiological function in other various aspects has been not thoroughly understood. In this study, we organized fundamental experiment which could evaluate germinating ability of different-colored segregated wheat population. Total of five segregated lines were recognized by assist of CIELAB coordinates. After assessing initial content of total phenol, flavonoid, monomeric anthocyanin and ORAC assay for antioxidant activity from each population, germination assay was taken place in vitro. From germinating grains, sample was taken every 6 hours for measurement of alpha amylase enzyme activity. Discernible difference in chemical constituent was recognized among population along with disparity in ORAC assay. Alpha amylase activity and germination assay showed that darkening of pericarp was related to inhibition of germination. Pigmentation in wheat is important for its physiological role and commodity value which should be considered as critical factor to be integrated in breeding program

We investigated the genetic diversity and structure of the 239 fixed lines with 47 simple sequence repeat (SSR) and 109 NGS-generated SNP markers evenly distributed in B. rapa genome. Phylogenetic analysis classified the vegetable fixed lines to four subgroups, with the three types forming a separate and relatively farther cluster. Population structure analysis identified four sub-populations corresponding to geographic origin and morphological traits, and revealed extensive admixture. The vegetable B. rapa fixed lines successfully developed in our study would be valuable materials for multinational B. rapa diversity resources establishment. Understanding the genetic diversity and population structure could be useful for utilization of the representing genetic variation and further genetic and genomic analysis.

2011년 종자산업의 세계시장 규모는 450억 달러이고, 농산물을 이용하는 식품산업의 세계시장 규모는 5조 2천억 달러에 이른다. 이러한 거대 농식품산업의 시작은 종자부터라 할 것이다. 종자의 산업적 가능성을 꿰뚫어 본 미국 과 유럽은 종자기업 중심으로 국내시장을 넘어 세계시장의 개척에 주력하여 왔다. 2011년 현재 전체 종자시장의 75%를 장악하고 있는 세계 10대 종자기업의 1~8위가 모두 이들 나라의 기업들이다. 과거 IMF 구제금융 당시, 우리 는 이러한 종자의 중요성을 제대로 인식하지 못한 채, 국내 5대 종자기업 중 4개가 외국계 기업에 인수합병되는 것 을 그냥 지켜보았다. 그 결과 많은 종자가 외국기업에 넘어가 버렸다. 농촌진흥청에 따르면 외국 품종의 재배로 인 해 우리나라가 외국에 지불한 로열티는 2009년 이후 매년 150억원이 넘고 앞으로 국내 대체 품종을 개발하지 못한 다면 향후 10년간 로열티가 2900억원에 이를 것으로 추산된다. 지재권이 설정된 종자를 사용하는 대가로 엄청난 로열티가 외국으로 빠져나가고 있는 것이다. 종자산업이 로열티를 창출하고 글로벌 경쟁력을 확보하기 위해서는 개발․개량된 종자를 품종보호권이나 특허권과 같은 지재권으로 보호하는 것이 무엇보다도 중요하다. 몬산토, 신 젠타와 같은 다국적 기업들은 국내에서 토마토, 파프리카, 시금치 등 글로벌 작물의 품종은 품종보호로 출원하고, 한편으로 육종소재, 유전자, 육종방법 등은 특허로 출원하고 있다. 이들은 양 제도의 장점을 활용한 지재권 획득전 략을 구사하여 로열티를 창출하고 있다. 2003년부터 2013년까지의 특허출원 동향을 분석한 결과를 살펴보면 생명 공학 기술을 활용한 육종기술의 발달과 함께 2009년 이후 식물분야 특허출원이 꾸준히 증가하고 있고, 이 중 60% 가 GMO 식물 개발관련 내용이나, 2013년 식물분야 출원은 총 258건으로 전체 특허출원건수 대비로는 0.1%에 불 과하다. 이에 종자, 식물, 육종과 관련된 기술을 통해 식물이 갖는 산업적 가치를 높일 수 있는 특허획득 방안과 외 국기업의 특허전략, 식물품종보호와 다른 점, 식물관련 특허출원 시 알아야 할 사항 등을 사례를 중심으로 살펴보 고자 한다.

The last decade has witnessed tremendous progress in genome sequencing and explosion of genome sequence information. This remarkable advancement in genomics provides unprecedented opportunities for crop improvement. Pepper (Capsicum spp.) is an important vegetable crop worldwide. Pepper production is constantly challenged by various pathogens and developing cultivars harnessing multiple disease resistance genes are ever increasing. Molecular markers linked to disease resistance genes will expedite the gene pyramiding. Here, I introduce genome-assisted development of molecular markers linked to resistance genes, in pepper. Phytophthora capsici L. is one of the most destructive pathogens of pepper (Capsicum spp.). Resistance of Capsicum annuum against P. capsici is controlled by quantitative trait loci (QTL), including a major QTL on chromosome 5 that is the predominant contributor to resistance. Here, to maximize the effect of this QTL and study its underlying genes, an F2 population and recombinant inbred lines were inoculated with P. capsici strain JHAI1-7 zoospores at a low concentration (3 x 103 /mL). Resistance phenotype segregation ratios for the populations were close to 3:1 and 1:1 (resistant:susceptible), respectively, consistent with a single dominant gene model. Bulked segregant analysis (BSA) using Affymetrix GeneChips revealed a single position polymorphism (SPP) marker mapping to the major QTL. When this SPP marker (Phyto5SAR) together with other SNP markers located on chromosome 5 were used to confirm the position of the major QTL, Phyto5SAR showed the highest LOD value at the QTL. A scaffold sequence (scaffold194) containing Phyto5SAR was identified from the C. annuum genome database. The scaffold contained two putative NBS-LRR genes and one SAR 8.2A gene as candidates for contributing to Phytophthora resistance. Markers linked to these genes were developed and validated by testing 100 F1 commercial cultivars. Among the markers, Phyto5NBS1 showed about 90% accuracy in predicting resistance phenotypes to a low-virulence Phytophthora isolate. These results suggest that Phyto5NBS1 is a reliable marker for Phytophthora resistance and can be used for identification of a gene(s) underlying the major QTL on chromosome 5

Genome polyploidization has provided significant sources of genetic variation for plant adaptive evolution and new species formation. However, the way in which molecular evolution of polyploid genomes builds up genetic architecture underlying speciation is unclear and whether there are any differences in polyploidsubgenomes’s responses to selection is unknown. Brassica is an ideal model to address these questions. Here, we used Arabidopsis thaliana as an outgroup to conduct comparative genome analysis of newly sequenced Brassica oleracea, B. rapaand B. napus. We revealed multi-layered modes of asymmetrical interspecific and intraspecific genome evolution. Between parallel species B. oleracea and B. rapa, these layers include: asymmetrical gene retention rates,asymmetrical TE amplification, asymmetrical tandem duplication of genes and asymmetrically alternative splicing variantsbetween the two sister species; Between subgenomes within species, these layers include: massive and asymmetrical subgenomic gene loss, great variations between paralogs at the DNA sequence level, expression differentiation of triplicated, α-duplicated and tandem duplicated genes across different tissues in the two diploid species, asymmetrical recombination on A and C in B. napus. In addition, the predominant mechanism for gene loss is small deletion, rather than asymmetrical cross-over. These patterns provide new insight into genome evolution underlying speciation and trait formation and will underpin research into genetic improvement of these important crops