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Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of ecotype Divergence

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Molecular Plant 2019年第1期12卷 30-43页

作者： Dezhi Wu Zhe Liang Tao Yan Ying Xu Lijie Xuan Juan Tang Gang Zhou Ulrike Lohwasser Shuijin Hua Haoyi Wang Xiaoyang Chen Qian Wang Le Zhu Antony Maodzeka Nazim Hussain Zhilan Li Xuming Li Imran Haider Shamsi Ghulam Jilani Linde Wu Hongkun Zheng Guoping Zhang Boulos Chalhoub Lisha Shen Hao Yu Lixi Jiang institute of Crop Science Zhejiang UniversityHangzhou 310058China Temasek Life Sciences Laboratory and Department of Biological Science National University of SingaporeSingapore 117543Singapore Biomarker Technologies Corporation Beijing 101300China Department of Genebank Leibniz institute of Plant Genetics and Crop Plant Research06466 Stadt SeelandGermany Institute of Crop and Nuclear Agricultural Sciences Zhejiang Academy of Agricultural SciencesHangzhou 310021China Office of Research Innovation & CommercializationPMAS-Arid Agricultural University Rawalpindi46300 RawalpindiPakistan Institute of Crop Science Jinhua Academy of Agncultural SciencesJinhua 321017China

Rapeseed (Brassica napus),an important oilseed crop,has adapted to diverse climate zones and latitudes by forming three main ecotype groups,namely winter,semiwinter,and spring types. However,genetic variations underlying the divergence of these ecotypes are largely unknown. Here,we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions.A total of 5.56 and 5.53 million singlenucleotide polymorphisms (SNPs)as Well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of "Darmor-bzh"and "Tapidor,"*** generated a map of allelic drift paths that shows splits and mixtures of the main populations,and revealed an asymmetric evolution of the two subgenomes of *** by calculating the genetic diversity and linkage disequilibrium ***-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses.A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups,and will facilitate screening of molecular markers for accelerating rapeseed breeding.

关键词： Brassica napus genome resequencing selective sweep ecotype divergence GWAS floweringtime trait

Genetic Diversity of Seed Storage Proteins in Different ecotype Varieties of japonica Rice and Its Application

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Rice science 2006年第2期13卷 85-92页

作者： JIN Wei-dong LI Na HONG De-lin National Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural University Nanjing 210095 China Suzhou Institute of Rural Cadre Suzhou 215011 China

One hundred and fifteen varieties （including cultivars and lines） with different ecotypes in japonica rice （Oryza sativa L.） were analyzed for endosperm storage proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis （SDS-PAGE） to estimate their genetic diversity for the purpose of genetic improving and variety identification. Nineteen types of profile were identified according to 1） presence/absence of 65 kDa bands, 2） staining intensity of 70, 60, 57, 37-39, 22-23, 13 and 10 kDa bands, 3） migration velocity of 35 kDa （α-4） and 4） band number at 57 kDa location. An unweighted-pair group average method with arithmetic mean （UPGMA） dendregram based on the cluster analysis of genetic similarity of the protein bands showed a small genetic variation among the tested materials, with the similarity coefficients varying between 0.75 and 1.00. Three distinct groups were identified from the cluster analysis of the rice varieties studied at the similarity coefficient level of 0.894. The first group included eight varieties with high amylose content, the second group contained fifteen varieties with high protein content, and the third group had the remaining ninety-two varieties, which accounted for 80% of the total materials. Clear relationship between ecotypes distinguished by maturity and groups revealed by cluster analysis was not found in this study. Only the group of high amylose linked with medium-maturity medium japonica ecotype. The bands of 70 kDa and 65 kDa can be used as protein markers to identify F1 seed purity of japonica hybrid rice Liuyanyou 422.

关键词： genetic diversity japonica rice ecotype storage protein electrophoresis

Morphological and Anatomical Variations in Rheophytic ecotype of Violet, Viola mandshurica var. <i>ikedaeana</i>(Violaceae)

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American Journal of Plant Sciences 2013年第4期4卷 859-865页

作者： Ryosuke Matsui Shogo Takei Kyohei Ohga Hiroshi Hayakawa Masataka Yoshida Jun Yokoyama Katsura Ito Ryo Arakawa Toshiro Masumoto Tatsuya Fukuda Faculty of Agriculture Kochi University Kochi Japan Faculty of Science Yamagata University Yamagata Japan Graduate School of Integrated Arts and Sciences Kochi University Kochi Japan Graduate school of Science and Engineering Yamagata University Yamagata Japan

We compared the leaf morphology and anatomy of the putative rheophytic ecotype of Viola mandshurica W. Becker var. ikedaeana (W. Becker ex Taken.) F. Maek. and its closely related variety, V. mandshurica var. mandshurica. We showed that the leaf of the rheophytic ecotype of V. mandshurica var. ikedaeana was narrower than that of V. mandshurica var. mandshurica. Moreover, the leaf thickness and guard cell size of the rheophytic ecotype of V. mandshurica var. ikedaeana were significantly larger than those of V. mandshurica var. mandshurica. We further showed that leaves of the rheophytic ecotype of V. mandshurica var. ikedaeana contained fewer cells than did those of V. mandshurica var. mandshurica. Our results suggest that the narrower leaves of V. mandshurica var. ikedaeana are caused by a decrease in the number of cells. A narrower leaf may enable the rheophytic ecotype of V. mandshurica var. ikedaeana to resist the strong flow of water that occurs after heavy rainfall, while a thicker leaf may enhance tolerance to desiccation and high- intensity light.

关键词： ecotype Leaf Rheophyte Stenophyllization Viola mandshurica

ecotype and Regional Division of Afforestation Plants in China

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Agricultural Science & Technology 2010年第1期11卷 173-175,185页

作者：徐毅常根柱中国农业科学技术出版社北京100081 中国农业科学院兰州畜牧与兽药研究所甘肃兰州730050

The selection of afforestation plants,which is based on the ecotype of afforestatioin plant,is the key of plant engineering. There is not final verdict yet on the standard of ecotype of afforestation plant. According to the presentational feature （regional distribution,Climatic indicator）,ecotype （climatoecological type,edaphic ecotype and biota ecotype） and genetic association of afforestation plant,combined with the experience in the greening practice,the afforesting nursery stock （Arbor and Shrub ） is divided into five ecotypes while the herbaceous plant are divided into three ecotypes.

关键词： Afforestation plant ecotype Division research

Edaphic factors determining variation of two ecotypes of Leymus chinensis in North China

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Progress in Natural Science:Materials International 2006年第11期16卷 1150-1155页

作者： ZHOU Chan~1 and YANG Yunfei~2**(1. MOE Key Laboratory of Environmental Change and Natural Disasters, College of Resources Science and Technology, Beijing Normal University, Beijing 100875, China 2. Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China) [a]MOE Key Laboratory of Environmental Change and Natural Disasters College of Resources Science and Technology Beijing Normal University Beijing China [b]Key Laboratory of Vegetation Ecology Ministry of Education Institute of Grassland Science Northeast Normal University Changchun China

To identify ecotypic variation of L. chinensis, the physiological characteristics and environmental factors were measured and assessed for grey-green and yellow-green ecotypes of L. chinensis grown in the salt-alkalized and aeolian sandy soils. Although both ecotypes presented a similar salt-alkaline tolerance under the experimental conditions, they differed in several aspects. The L. chinensis grown in the aeolian sandy soils had higher water potential and chlorophyll content and lower proline content in their leaves than those grown in the salt-alkalized habitat, and the grey-green ecotype of L. chinensis in both types of soils had higher water potential, chlorophyll and proline contents than the yellow-green ecotype. Besides, grey-green ecotypes had higher salt-alkaline tolerance than the yellow-green ecotype. The stepwise regression analysis showed that soil conductance and pH value were the main ecological factors affecting the physiology of L. chinensis. From the natural distribution of the two ecotypes, we considered that salt-alkaline in the soils is the leading factor in determining ecotypic variation of L. chinensis. The two ecotypes were first named grey-green and yellow-green ecotypes respectively.

关键词： L.chinensis ecotype adaptability variation ecological factor salt-alkaline in soil.

Seasonal changes of endogenous ABA and cytokinins in environmental adaptation of different ecotypes of reed plants

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Journal of Environmental Sciences 1995年第4期7卷 449-454页

作者： Wang Hongliang , Zhang Chenglie(Department of Biology, Lanzhou University , Lanzhou 730000 , China)

ＳｅａｓｏｎａｌｃｈａｎｇｅｓｏｆｅｎｄｏｇｅｎｏｕｓＡＢＡａｎｄｃｙｔｏｋｉｎｉｎｓｉｎｅｎｖｉｒｏｎｍｅｎｔａｌａｄａｐｔａｔｉｏｎｏｆｄｉｆｆｅｒｅｎｔｅｃｏｔｙｐｅｓｏｆｒｅｅｄｐｌａｎｔｓＷａｎｇＨｏｎｇｌ... 详细信息

ＳｅａｓｏｎａｌｃｈａｎｇｅｓｏｆｅｎｄｏｇｅｎｏｕｓＡＢＡａｎｄｃｙｔｏｋｉｎｉｎｓｉｎｅｎｖｉｒｏｎｍｅｎｔａｌａｄａｐｔａｔｉｏｎｏｆｄｉｆｆｅｒｅｎｔｅｃｏｔｙｐｅｓｏｆｒｅｅｄｐｌａｎｔｓＷａｎｇＨｏｎｇｌｉａｎｇ，ＺｈａｎｇＣｈｅｎｇｌｉ...

关键词： ABA cytokinin ecotype environmental adaptation Phragmites communis T.

Intraspecific diversity: adaptive differentiation of Picea mongolica W. D. Xu ecotypes

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Forestry Studies in China 2011年第3期13卷 189-197页

作者： LIU An-tian ZOU Chun-jing ZHANG Chao ZHENG Yuan-run Hideyuki SHIMIZU XU Wen-duo Shanghai Key Laboratory of Urbanization ＆ Ecological Restoration School of Life Science East China Normal University Shanghai 200062 P. R. China State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing 100093 P. R. China National Institute for Environmental Studies 16-2 Onogawa Tsukuba Ibaraki 3005-8056 Japan Institute of Applied Ecology Chinese Academy of Sciences Shenyang 110016 P. R. China

Picea mongolica W. D. Xu is an endemic and endangered species which is only found in semi-arid areas of northern China. It has been widely used as an afforestation tree in the establishment of the Three-North Shelterbelt System for its adaptation to arid soils and as a virescent tree in urban gardens and streets for its beautiful shape. Due to different microenvironments, P. mongolica populations may differentiate into many ecological groups with different adaptive abilities. Long-term adaptation to a dry environment makes P. mongolica differentiate into different ecotypes. Typical ecotypes are P. mongolica f. purpurea （Fp）, P. mongolica f. rubra （Fr） and P. mongolica f. viridis （Fv）. Our results show that cone size is clearly not uniform among different ecotypes; the largest cones are found in the Fv ecotype and the smallest in Fp. There were also distinct differences between these ecotypes in terms of height and length of squama. At the molecular level, the zymograms of peroxidase and lipase prove the existence of different ecotypes in P. mongolica. The results are useful for investigating and managing this rare spruce species in China.

关键词： Picea mongolica W. D. Xu intraspecific diversity adaptive differentiation ecotype

Yellowing of disease? Or differentiating for adaptation? Study on Cinnamomum camphora ecotypes

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Forestry Studies in China 2010年第2期12卷 67-73页

作者： LI Qing ZOU Chun-jing XU Ying Shimizu HIDEYUKI Shanghai Key Laboratory of Urbanization ＆ Ecological Restoration School of Life Science East China Normal University Shanghai 200062 P. R. China National Institute for Environmental Studies 16-20nogawa Tsukuba Ibaraki 305-8506 Japan

Cinnamomum camphora （L.） Presl is an evergreen broad-leaved tree of the Lauraceae family, widely distributed in the sub-tropical areas in the south of China and used as a virescent tree in urban gardens and streets in Shanghai for its beautiful shape and intensive stress-resistance. However, yellowing of C camphora in recent years casts doubt about its significance. We believe the green-leaved and yellow-leaved C camphora might be two different ecotypes, and tentatively refer to the green-leaved C camphora as C camphora f. viridis f. nov （CCV） and the yellow-leaved as C camphora *** f. nov （CCF）. We studied their differences and arrived at the following conclusions： 1） compared with CCF, the area of lamina of CCV is significantly larger and the amount of chlorophyll （Chl） significantly higher; 2） the lamina and palisade tissues of CCV are significantly thicker than those of CCF, but its cuticle is significantly thinner; 3） the shape of the stomata of CCV is different from that of the CCF; the stomatal density and stomatal index of CCV are significantly lower than those of CCF. These results show that C camphora might evolve adaptive dif- ferentiation in some aspects which can be used in virescence in urban streets and gardens.

关键词： Cinnamomum camphora ecotype differentiation chlorophyll stomatal parameters

The adaptive significance of differences of root morphology, anatomy and physiology from three ecotypes of reed(Phragmites communis Trin.)

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Research in Cold and Arid Regions 2016年第3期8卷 196-204页

作者： YuBing Liu XinRong Li ZhiShan Zhang XiaoJun Li Jin Wang Shapotou Desert Research & Experiment Station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences

Reeds are widely distributed in drought and high salt conditions of northwestern China. Leaf epidermal micromorphology, anatomy, chloroplast ultrastructure and physio-chemical characteristics due to long-term adaptation in the natural habitats of common reed （Phragmites communis Trin.） contrasted considerably among three different ecotypes： dune reed （DR）, Gobi salt reed （GSR） and swamp reed （SR）. The main objective of the present study is to determine the adapting characteristics of morphology, anatomy and physiological responses of thin roots in DR, GSR and SR. The results show that root length density was higher in SR and few root hairs were observed in DR. Cross-section anatomical features show that each ecotype has an endodermis and exodermis, while cortex thickness and proportion of root cortical aerenchyma and stele in root structure varied among the three ecotypes. The stele and xylem share a larger area in DR compared to GSR and SR. GSR has a large proportion of the cortex with radialized distribution of aerenchyma cells spacing, and the cortex has a peripheral, mechanically stiff ring in the exodermis. SEM and TEM microscope images show that GSR has a scle- renchyma ring with high lignification in the exodermis. The physio-chemical parameters show that GSR had a higher level of stress tolerance than DR. These findings indicate that developed water-absorbing tissues were largely distributed in the root structure of DR, and a main framework with supporting function spacing with aerenchyma was dominant in GSR in the long term adaptation to their natural habitats, respectively.

关键词： Phragmites communis ecotype root morphology cross-section anatomy physio-chemical parameters