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| 1 | Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China显示文摘Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes.More than 3000 wheat cultivars have been registered,released,and documented since 1949 in China.In this study,a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced.A total of 43.75 Tb of sequence data were generated with an average read depth of 17.94x for each cultivar,and more than 60.92 million SNPs and 2.54 million InDels were captured,based on the Chinese Spring RefSeq genome v1.0.Seventy years of breeder-driven selection led to dramatic changes in grain yield and related phenotypes,with distinct genomic regions and phenotypes tar-geted by different breeders across the decades.There are very clear instances illustrating how introduced Italian and otherforeign germplasm was integrated into Chinese wheat programs and reshaped the genomic landscape of local modern cultivars.Importantly,the resequencing data also highlighted significant asymmetric breeding selec-tion among the three sub-genomes:this was evident in both the collinear blocks for homeologous chromosomes and among sets of three homeologous genes.Accumulation of more newly assembled genes in newer cultivars implied the potential value of these genes in breeding.Conserved and extended sharing of linkage disequilibrium(LD)blocks was highlighted among pedigree-related cultivars,in which fewer haplotype differences were detected.Fixation or replacement of haplotypes from founder genotypes after generations of breeding was related to their breeding value.Based on the haplotype frequency changes in LD blocks of pedigree-related cultivars,we propose a strategy for evaluating the breeding value of any given line on the basis of the accumulation(pyramiding)of bene-ficial haplotypes.Collectively,our study demonstrates the influence of 'founder genotypes' on the output of breeding efforts over many decades and also suggests that founder genotype perspectives are in fact more dy-namic when applied in the context of modern genomics-informed breeding. | Chenyang Hao Chengzhi Jiao Jian Hou Tian Li Hongxia Liu Yuquan Wang Jun Zheng Hong Liu Zhihong Bi Fengfeng Xu Jing Zhao Lin Ma Yamei Wang Uzma Majeed Xu Liu Rudi Appels Marco Maccaferri Roberto Tuberosa Hongfeng Lu Xueyong Zhang | 2020 | Molecular Plant2020，13，12： | 9 |
| 2 | Late Pliocene–Quaternary evolution of redox conditions in the western Qaidam paleolake (NE Tibetan Plateau) deduced from Mn geochemistry in the drilling core SG-1显示文摘 | Yibo Yang Xiaomin Fang Erwin Appel Albert Galy Minghui Li Weilin Zhang | 2013 | Quaternary Research2013，，3： | 2 |
| 3 | Quaternary paleolake nutrient evolution and climatic change in the western Qaidam Basin deduced from phosphorus geochemistry record of deep drilling core SG-1显示文摘 | Yibo Yang Xiaomin Fang Albert Galy Erwin Appel Minghui Li | 2013 | Quaternary International2013，，： | 2 |
| 4 | Principles andpotential of the anaerobic digestion of waste-activated sludge显示文摘 | Li se Appels Jan Baeyens Jan Degrève | 2008 | Progress in Energy and Combustion Science2008，34，6： | 1 |
| 5 | Chronic aspiration of gastric fluid accelerates pulmonary allograft dysfunction in a rat model of lung transplantation 显示文摘 | Hartwig MG Appel J2 Li B | 2006 | Thorac Cardiovasc Surg2006，131，： | 1 |
| 6 | Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison显示文摘 | Chengdao Li Peixiang Ni Michael Francki Adam Hunter Yong Zhang David Schibeci Heng Li Allen Tarr Jun Wang Mehmet Cakir Jun Yu Matthew Bellgard Reg Lance Rudi Appels | 2004 | Functional & Integrative Genomics2004，，2： | 1 |
| 7 | Evidence-based guidelines for cardiovacular disease prevention in women 显示文摘 | Mosca L Appel LI Benjamin El | 2004 | Circulation2004，109，5： | 1 |
| 8 | Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation显示文摘 | Jia J Zhao SC Kong XY Li YR Zhao GY He WM Appels RD Pfeifer M Tao Y Zhang XY Jing RL Zhang C Ma YZ Gao LF Gao C Spannagl M Mayer KFX Li D Pan SK Zheng FY Hu Q Xia XC Li JW Liang QS Chen J Wicker T Gou CY Kuang HH He GY Luo YD Keller B Xia QJ Lu P Wang JY | | 0，，： | 1 |
| 9 | Chronic aspiration of gastric fluid induces the development of obliterative bronchi- olitis in rat lung transplants 显示文摘 | Li B Hartwig MG Appel JZ | 2008 | Am J Transplant2008，8，8： | 1 |
| 10 | A Novel Chimeric Low-Molecular-Weight Glutenin Subunit Gene From the Wild Relatives of Wheat Aegilops kotschyi and Ae. juvenalis: Evolution at the Glu-3 Loci显示文摘 | Li Xiaohui Ma Wujun Gao Liyan Zhang Yanzhen Wang Aili Ji Kangmin Wang Ke Appels Rudi Yan Yueming | 2008 | Genetics2008，，1： | 1 |
| 11 | Cloning and characterization of a novel low molecular weight glutenin subunit gene at the Glu-A3 locus from wild emmer wheat (Triticum turgidum L. var. dicoccoides)显示文摘 | Xiaohui Li Aili Wang Yinghua Xiao Yueming Yan Zhonghu He Rudi Appels Wujun Ma S. L. K. Hsam F. J. Zeller | 2008 | Euphytica (-)2008，，1： | 1 |
| 12 | Novel x-Type High-Molecular-Weight Glutenin Genes From Aegilops tauschii and Their Implications on the Wheat Origin and Evolution Mechanism of Glu-D1-1 Proteins显示文摘 | Zhang Yanzhen Li Xiaohui Wang Aili An Xueli Zhang Qian Pei Yuhe Gao Liyan Ma Wujun Appels Rudi Yan Yueming | 2008 | Genetics2008，，1： | 1 |
| 13 | Novel x-type high-molecular-weight glutenin genes from Aegilops tauschii and their implications on the wheat origin and evolution mechanism of Glu-D1-1 proteins显示文摘 | ZHANG Y ZH LI X H WANG A L AN X L ZHANG Q PEI Y H GAO L Y MA W J APPELS R YAN Y M | 2008 | Genetics2008，178，： | 1 |
| 14 | Chronic aspiration of gastric fluid induces the development of obliterative bron- chiolitis in rat lung transplants 显示文摘 | Li B Hartwig MG Appel JZ | 2008 | Am J Transplant2008，8，8： | 1 |
| 15 | Uranium distribution in the lacustrine calcareous clastic-evaporite sequence in the western Qaidam Basin,and implications for U behavior in concentration of closed water显示文摘Uranium(U)provides especially useful information for reconstructing paleoredox conditions due to its unique geochemical properties and behavior in supergene environments.The proxy potential under | YANG Yibo FANG Xiaomin LI Minghui APPEL Erwin ZHANG Weilin LIU Xiaoming | 2014 | Acta Geologica Sinica(English Edition)2014，88，S1： | 0 |
| 16 | Deep Drilling Campaign in the Western Qaidam Basin,NE Tibetan Plateau and their Revealed Global Temperature Forcing of Salt Formation in the Late Miocene-Quaternary显示文摘The Qaidam Basin in the NE Tibetan Plateau has contributed the largest amount of potash in China.However,how the potash was formed has long been a subject of debate.Here we carried out a deep | FANG Xiaomin LI Minghui Erwin APPEL WANG Jiuyi HAN Wenxia ZHANG Weilin YANG Yibo CAI Maotang | 2014 | Acta Geologica Sinica(English Edition)2014，88，S1： | 0 |
| 17 | The Battle to Sequence the Bread Wheat Genome:A Tale of the Three Kingdoms显示文摘In the year 2018,the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop,the common wheat.Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature.A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries,taking a conventional strategy similar to that for sequencing Arabidopsis and rice,became ferocious over time as both sequencing technologies and genome assembling methodologies advanced.At different stages,multiple versions of genome sequences of the same variety(e.g.,Chinese Spring)were produced by several groups with their special strategies.Finally,16 years after the rice genome was finished and 9 years after that of maize,the wheat research community now possesses its own reference genome.Armed with these genomics tools,wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution,domestication,genetic and epigenetic regulation of homoeolog expression,as well as defining its genetic diversity and breeding on the genome level.The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield. | Jiantao Guan Diego F.Garcia Yun Zhou Rudi Appels Aili Li Long Mao | 2020 | Genomics, Proteomics & Bioinformatics2020，18，3： | 0 |
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