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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,"respectively.We 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 B.napus by calculating the genetic diversity and linkage disequilibrium parameters.Selective-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

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Research advances on ecotype and sub-ecotype differentiation of Prochlorococcus and its environmental adaptability

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Science China Earth Sciences 2020年第11期63卷 1691-1700页

作者： Wei YAN Xuejin FENG Wei ZHANG Rui ZHANG Nianzhi JIAO College of Marine Science and Technology China University of GeosciencesWuhan 430074China State Key Laboratory of Marine Environmental Science Fujian Key Laboratory of Marine Carbon SequestrationCollege of Ocean and Earth SciencesXiamen UniversityXiamen 361102China

Prochlorococcus,a group of marine cyanobacteria,is the most abundant and smallest oxygen-producing photosynthetic microorganism.It is mainly distributed in the euphotic zone of tropical and subtropical oceans and is a key participant in the marine biogeochemical cycle.Prochlorococcus has evolved continuously to adapt to the marine environment,and can be considered a recent evolutionary form of cyanobacteria,one of the most ancient life forms.The diverse ecotypes and subecotypes of Prochlorococcus increase its genomic diversity and environmental adaptability,allowing Prochlorococcus to become a dominant species in its environment.Here we review the ecotype classification and distribution,ecotype and subecotype differentiation,and environmental adaptability of Prochlorococcus.We also evaluate the role and significance of ecotype and sub-ecotype differentiation of Prochlorococcus,and discuss future research directions on this basis.

关键词： Prochlorococcus ecotype Sub-ecotype Environmental adaptation

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Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers

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Journal of Genetics and Genomics 2009年第8期36卷 491-500页

作者： Xingyu Hu Jianfei Wang Ping Lu Hongsheng Zhang State Key Lab of Crop Genetics and Germplasm Enhancement College ofAgriculture Nanjing Agricultural University Nanjing 210095 China Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 China

The genetic diversity of 118 accessions of broomcom millet （Panicum miliaceum L.）, collected from various ecological areas, was analyzed. Using 46 SSR （Simple Sequence Repeat） polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles were found, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91. The range of polymorphism information content （PIC） was 0.2844）.980 （average, 0.793）. The expected heterozygosity （He） varied from 0.346 to 0.989, with an average of 0.834. The average coefficient of the genetic similarity of SSR markers among the 118 accessions was 0.609, and it ranged from 0.461 to 0.851. The UPGMA （Unweight Pair Group Method with Arithmetic Mean） clustering analysis at the genetic similarity value of 0.609 grouped the 118 accessions into five groups. Mantel test meant that geographical origin and genetic distance presented positive correlation. The clustering results were consistent with known information on ecological growing areas. The genetic similarity coefficient of the accessions in the Loess Plateau ecotype was significantly lower than those in the other ecotypes. It indicates that the highest level of genetic diversity occurred in the Loess Plateau, which is probably the original site of Panicum miliaceum.

关键词： Panicum miliaceum L. genetic diversity SSR marker ecotype

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Bi-directional Selection in Upland Rice Leads to Its Adaptive Differentiation from Lowland Rice in Drought Resistance and Productivity

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Molecular Plant 2019年第2期12卷 170-184页

作者： Hui Xia Zhi Luo Jie Xiong Xiaosong Ma Qiaojun Lou Haibin Wei Jie Qiu Hua Yang Guolan Liu Longjiang Fan Liang Chen Lijun Luo Shanghai Agrobiological Gene Center Shanghai China College of Plant Sciences & Tech no logy Huazho ng Agricultural University Wuhan China lnstitute of Crop Science & Institute of Bioinformatics College of Agriculture and Biotechnology Zhejiang University Hangzhou China These authors contributed equally to this article.

Drought resistance is required in rice breeding to address the challenge of frequent droughts . However, the evolutionary mechanism of rice drought resistance is not fully understood. We investigated the genetic differentiation between upland and lowland rice domesticated in agro-ecosystems with contrasting water-soil conditions using genome-wide SNPs. We estimated morphological differences among upland and lowland rice in drought resistance and productivity through common garden experiments. Upland rice had better drought resistance but poorer productivity. The negative correlations between traits of drought resistance and productivity are attributed to the underlying genetic trade-offs through tight linkages (e.g., DCA1 and OsCesA7) or pleiotropic effects (e.g., LAX1). The genetic trade-offs are comm on and greatly shape the evolutio n of drought resista nee in upland rice . In genomic regions associated with both productivity and drought resistance, signs of balancing selection were detected in upland rice, while signs of directional selection were detected in lowland rice, potentially contributing to their adaptive differentiation. Signs of balancing selection in upland rice resulted from bi-directional selection during its domestication in drought-prone upland agro-ecosystems.Using genome-wide association analysis, we ide ntified several valuable quantitative trait loci associated with drought resista nee, for which highly differentiated genes should be considered candidates. Bi-directional selection breaking tight linkages by accumulating recombination events would be applicable in breeding water-saving and droughtresistance rice.

关键词： drought resistance upland rice ecological adaptation ecotype trade-off domestication

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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) MOE Key Laboratory of Environmental Change and Natural Disasters College of Resources Science and Technology Beijing Normal University Beijing 100875 China Key Laboratory of Vegetation Ecology Ministry of Education Institute of Grassland Science Northeast Normal University Changchun 130024 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.

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Ecophysiological aspects and photosynthetic pathways in 105 plants species in saline and arid environments of Tunisia

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Journal of Arid Land 2014年第6期6卷 762-770页

作者： Abdallah ATIA Mokded RABHI Ahmed DEBEZ Chedly ABDELLY Houda GOUIA Chiraz Chaffei HAOUARI Abderrazak SMAOUI Research Unit Nutrition and Nitrogen Metabolism and Stress ProteinDepartment of BiologyFaculty of Sciences of TunisCampus Universitaire El Manar I Tunis 1060Tunisia Laboratory of Extremophile Plants Centre of Biotechnology of Borj-Cedria Hammam-Lif 2050Tunisia

In Tunisian arid regions, plant life forms, ecotypes, physiological types and photosynthetic pathways （03, 04 or CAM） remain unclear. Understanding the characters of these plant species could be important for land restoration. A literature survey was conducted for 105 plants species in arid regions of Tunisia. These plant species belong to several ecotypes： halophytes, xerophytes, gypsophytes, psamophytes, xero-halophytes, gypso-halophytes, psamo-halophytes, psamo-xerophytes, xero-gypsophytes and hygro-halophytes. The variation of photosynthetic pathway types in the 105 studied species shows that 56.2% were C3, 41.0% were C4, 1.9% were CAM and 1.0% were C3-CAM. The C3 pathway was more abundant in the halophytes, whereas the C4 one was more common in the xerophytes, gypsophytes, gyp- so-halophytes and psamo-halophytes. The ratio of C3 to C4 species （C3/C4 ratio） was 0.2 in the psamo-halophytes, 0.8 in the gypso-halophytes, 1.1 in the xerophytes, 1.6 in the xero-halophytes, 1.8 in the hygrohalophytes, 2.0 in the psamo- phytes and 3.8 in the halophytes. The annuals were mainly C3 plants whereas most of perennials were C4 ones. The C3/C4 ratio was 1.3 in succulent species and 1.4 in non-succulent species. Thus, succulence seems not to affect the distribution of C3 and C4 pathways within the studied plants. This investigation shows high percentages of C4 plants occurred in Tuni- sian arid regions. However, there were significant differences in their abundance among ecotypes. Basing on C3/C4 ratio, we can find that the abundance of the C4 pathway was in the following order： psamo-halophytes, gypso-halophytes, xe- rophytes, xero-halophytes, hygro-halophytes, psamophytes and halophytes. In Tunisian arid regions, C4 species were most abundant in xerophytes and less abundant in halophytes. In the Chenopodiaceae the number of C3 plants was 13 and the number of C4 species was 20 and in the Poaceae the number of C3 was 23 and the number of C4 was 19 species. Thus, the most C4 proportion was in the Chenopodiaceae and Poaceae s

关键词： C3 C4 CAM life form ecotype physiological type Tunisian arid regions

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Upper Darriwilian(Middle Ordovician) Radiolarians and Ostracods from the Hulo Formation, Zhejiang Provicnce, South China

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Journal of Earth Science 2018年第4期29卷 886-899页

作者： Yuhao Yi Aihua Yuan Jonathan C Aitchison Qinglai Feng School of Earth Sciences China University of Geosciences State Key Laboratory of Geological Processes and Mineral Resources China University of Geosciences School of Earth and Environmental Sciences University of Queensland

Considerable research has been done on the Ordovician marine fossils from South China, including macrofossils such as brachiopods, graptolites, bivalves, trilobites, some microfossils like conodonts and acritarches. However, radiolarians and ostracods that are also important consti- tuents of the Ordovician marine ecosystem have been paid little attention in this region. In this study, ten radiolarians species belonging to four genera and sixteen ostracods species grouped into nine genera were found from the Hulo Formation at the Hengdu Section of the Jiangshan District, west- ern Zhejiang Province, South China. The fossil-bearing strata belong to the graptolite Pterograptus elegans Zone which indicates the Late Darriwilian Age. This radiolarian fauna is the first record of the Middle Ordovician radiolarian body fossils and also the earliest Ordovician radiolarian fauna reported from South China. The occurrence of Beothuka in this fauna extends the stratigraphic range of the genus to the Upper Darriwilian. Reviews of previous literatures suggest that the diversity of Beothuka was greater during the Early Ordovician, and then declined gradually from the Early Ordovician to the Middle Ordovician before its extinction. The co-occurring ostracod fauna belongs to a shallow-water ecotype. This is contrary to the host lithofacies of the ostracod fauna which represent a deep-water environment. Therefore, these ostacods may have been transported from the shallow-water environment, most likely from the Yangtze carbonate platform. If this conjecture is the truth, then the Jiangshan District was near the shallow-water carbonate platform and received its sediments during the Darriwilian. It is still essential to do more work in the future to better understand the ecology of the Ordovician ostracod fanuas and their role in the sedimentary system of South China.

关键词： radiolarians ostracods ecotype Ordovician Hengdu Section South China.

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Does higher ploidy level increase the risk of invasion?A case study with two geo-cytotypes of Solidago gigantea Aiton(Asteraceae)

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Journal of Plant Ecology 2018年第2期11卷 317-327页

作者： David U.Nagy Szilvia Stranczinger Aliz Godi Anett Weisz Christoph Rosche Jan Suda Mark Mariano Robert W.Pal Department of Ecology Institute of BiologyFaculty of SciencesUniversity of PécsH-7624 PécsIfjúság u.6Hungary Department of Botany Institute of BiologyFaculty of SciencesUniversity of PécsH-7624 PécsIfjúság u.6Hungary Working Group:Plant Ecology Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle-WittenbergAm Kirchtor 1D-06108 HalleGermany Department of Botany Faculty of ScienceCharles University in PragueBenátská2CZ-12801 PragueCzech Republic and Institute of BotanyThe Czech Academy of SciencesZámek 1CZ-25243 PruhoniceCzech Republic Department of Biological Sciences Montana TechMontana Tech of the University of Montana1300 W Park StMT 59701 ButteUSA

Aims Understanding the role of genetics in biological invasions has become an important aspect for modern plant ecology.Many studies suggest that increased ploidy level benefits the success of an invasive species,but the basis for this phenomenon is not fully understood.in its native,North American range,Solidago gigantea has three geo-cytotypes comprising di-,tetra-and hexa-ploid populations,while in Europe,where it is highly invasive,S.gigantea stands are composed primarily of tetraploid individu-als.Our study investigates whether North American hexaploids can induce a greater risk of invasion,due to their higher perfor-mance in a non-native range,as compared to the existing tetra-ploids of that range.Methods We performed greenhouse and common garden experiments along with microsatellite analyses to test whether differences in chromo-some number and origin of the species mean superior fitness in the introduced range.Important Findings Genetic diversity was significantly higher in the native hexaploid popula-tions(A_(R)=6.04;H_(e)=0.7794),rather than the non-native tetraploid pop-ulations(A_(R)=4.83;H_(e)=0.6869).Furthermore,differentiation between geo-cytotypes was moderate(ρST=0.1838),which was also confirmed by their clear segregation in principal component analysis and structure analyses,proving their different genetic structure.in contrast to genetic diversity,the non-native tetraploid geo-cytotype performed better in the common garden experiment,implying that higher genetic diversity does not always mean better success.Our results suggest that native hexa-ploids do not present a greater risk,as assessed by their performance in the introduced range,when compared to the non-native tetraploids,as was suggested by previous studies.Nevertheless,their introduction is still undesirable due to their different genetic structure,which,through hybridization,could give a new drive to the invasion of S.gigantea.

关键词： EiCA plant invasion microsatellite ecotype polyploidy

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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.

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Analysis on the indicator species and ecological groups of pelagic ostracods in the East China Sea

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Acta Oceanologica Sinica 2008年第6期27卷 83-93页

作者： XU Zhaoli Key and Open laboratory of Marine and Estuary Fisheries of Ministry of Agriculture East China Sea Fisheries Research Insti-tute Chinese Academy of Fisheries Sciences Shanghai 200090 China

Ecological adaptation and ecological groups of pelagic ostracods were examined in the East China Sea （23°30′-33°00′N, 118°30′ -128°00′E）, in relation to temperature and salinity. The data were collected in four surveys conducted from 1997 to 2000. The density, yield density, or negative exponent models were used to determine the optimal temperature and salinity of water for the thriving growth of pelagic ostracods. Thereafter, ecological groups and potential distribution patterns of pelagic ostracods were determined based on the predicted parameters such as optimal temperature and salinity, consulting the geographic distribution. The analytical results indicate that, among the numerical dominant pelagic ostracods in the East China Sea （ECS）, Euconchoecia aculeata, E. elongata, E. chierchiae, E. maimai, and Cypridina dentata, etc. are offshore subtropical water species. These species are widely distributed in the area, and they can be brought by the warm current to north offshore during spring and winter. The predicated optimal temperature （OT） and optimal salinity （OS） for Paraconchoecia decipiens, P. echinata, P. spini- fera, P. oblonga, Conchoecia magna and Porroeciaporrecta are all greater than 25℃ and 34 separately. These species are mainly distributed in the waters of the Kuroshio, the Taiwan Warm Current, and the Taiwan Strait, and therefore are designated as ocean- ic tropical water species. On the other hand, Pseudoconchoecia concerttrica is considered as offshore subtropical water species based on its geographical distribution although its OT is 19℃. The other species, though their OSs are approximately 34 and with OTs ranging from 20° to 25℃, are considered as offshore subtropical water species because they were found to be widely distributed from the South China Sea to the East China Sea.

关键词： zooplankton pelagic ostracods ecotype temperature salinity East China Sea indicator species

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