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Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

Molecular Plant 2024年第6期17卷 867-883页

作者： Fan Zhang Ruicai Long Zhiyao Ma Hua Xiao Xiaodong Xu Zhongjie liu Chunxue Wei Yiwen Wang Yanling Peng Xuanwen Yang Xiaoya Shi Shuo Cao Mingna li Ming Xu Fei He Xueqian Jiang Tiejun Zhang Zhen Wang xianran li Long-Xi Yu Junmei Kang Zhiwu Zhang Yongfeng Zhou Qingchuan Yang Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China National Key Laboratory of Tropical Crop Breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China School of Grassland Science Beijing Forestry UniversityBeijing 100083China Department of Agronomy and Horticulture University of Nebraska-LincolnLincolnNE 68583USA Department of Crop and Soil Sciences Washington State UniversityPullmanWA 99163USA U.S.Department of Agriculture-Agricultural Research Service Plant Germplasm Introduction and Testing ResearchProsserWA 99350USA National Key Laboratory of Tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural SciencesHaikou 571101China

Given the escalating impact of climate change on agriculture and food security,gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate ***(Medicago sativa ***),the queen of forages,shows remarkable adaptability across diverse global environments,making it an excellent model for investigating species responses to climate *** this study,we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa’s climatic adaptation and genetic susceptibility to future climate *** found that interspecific genetic exchange has contributed to the gene pool of alfalfa,particularly enriching defense and stress-response *** introgression between *** ***(***)and alfalfa not only aids alfalfa’s climatic adaptation but also introduces genetic burden.A total of 1671 genes were associated with climatic adaptation,and 5.7%of them were introgressions from *** integrating climate-associated variants and climate data,we identified populations that are vulnerable to future climate change,particularly in higher latitudes of the Northern *** findings serve as a clarion call for targeted conservation initiatives and breeding *** also identified preadaptive populations that demonstrate heightened resilience to climate fluctuations,illuminating a pathway for future breeding ***,this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars,contributing to effective agricultural strategies for facing future climate change.

关键词： Medicago local adaptation population genetics adaptive introgression genetic vulnerability alfalfa breeding

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Unraveling the sorghum domestication

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Molecular Plant 2022年第5期15卷 791-792页

作者： xianran li Jianming Yu USDA Agricultural Research ServiceWheat HealthGeneticsand Quality Research UnitPullmanWA 99164USA Department of Agronomy Iowa State UniversityAmesIA 50011USA

Sorghum,the fifth major cereal crop,was domesticated in Africa and expanded *** with many other crops,this process can be generally separated into two stages:the first stage from wild ancestors to landraces,and the se... 详细信息

关键词： crops expanded globally

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Retrofitting elite cultivars with an ancestral allele for sustainable agriculture

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Science China(life Sciences) 2021年第6期64卷 1029-1030页

作者： xianran li Jianming Yu Department of Agronomy Iowa State UniversityAmesIowa 50011USA

Gene and environment interplay has always been a fascinating topic in biology and *** the consensus has gradually emerged that what we observe is not decided by one side alone,there is still debate on the relative magnitude of individual contribution,or whether our understanding of the whole system,assuming achievable eventually,can be approximated by some findings of the parts.

关键词： eventually elite alone

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Genetics-inspired data-driven approaches explain and predict crop performance fluctuations attributed to changing climatic conditions

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Molecular Plant 2022年第2期15卷 203-206页

作者： xianran li Tingting Guo Guihua Bai Zhiwu Zhang Deven See Juliet Marshall Kimberly A.Garland-Campbell Jianming Yu USDA Agricultural Research ServiceWheat HealthGeneticsand Quality Research UnitPullmanWA 99164USA Department of Agronomy Iowa State UniversityAmesIA 50011USA USDA Agricultural Research ServiceHard Winter Wheat Genetics Research UnitManhattanKS 66506USA Department of Crop and Soil Sciences Washington State UniversityPullmanWA 99164USA Department of Plant Sciences University of Idaho Research and ExtensionIdaho FallsID 83402USA

Dear Editor,Genetics-focused approaches have been widely used to uncover major genetic variants associated with performance ***,manipulating,and editing genetic variants significantly improve crop ***,the genetic component explains a portion of performance variation,and the environ-mental component contributes to the remaining,often large,portion(Laidig et al.,2017;Bonecke et al.,2020;li et al.,2021).To ensure superior and robust performance,elite varieties are extensively tested across multiple years and *** extensive performance records,coupled with climatic profiles,could be leveraged to understand climate's impact on agriculture through approaches parallel to quantitative genetics approaches(Figure 1A).

关键词： performance attributed Figure

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Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes

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Molecular Plant 2023年第6期16卷 975-978页

作者： Bosen Zhang Haiyan Huang Laura E.Tibbs-Cortes Adam Vanous Zhiwu Zhang Karen Sanguinet Kimberly A.Garland-Campbell Jianming Yu xianran li Department of Crop and Soil Sciences Washington State UniversityPullmanWA99164USA USDA-ARS Wheat HealthGeneticsand Quality Research UnitPullmanWA 99164USA USDA-ARS Corn Insects and Crop Genetics Research UnitAmesIA 50011USA USDA-ARS Plant Introduction ResearchAmesIA 50011USA Department of Agronomy lowa State UniversityAmesIA 50011USA

Dear Editor,Pan-genomes with high quality de novo assemblies are shifting the paradigm of biology research in genome evolution,speciation,and function annotation(Shi et al.,2023).An all-vs.-all comparison across assemblies potentially overcomes the limitation of mapping short reads to a single assembly in cataloging polymorphisms,especially large insertions and deletions(indels)contributing to phenotypic variations through altering gene structure or expression(Chen et al.,2021).

关键词： overcome shifting insertion

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High-efficiency plastome base editing in rice with TAL cytosine deaminase

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Molecular Plant 2021年第9期14卷 1412-1414页

作者： Riqing li Si Nian Cha Bo liu Hua liu xianran li Bing Yang Division of Plant Sciences Bond Life Sciences CenterUniversity of MissouriColumbiaMO 65211USA USDA-ARS Wheat HealthGenetics and Quality Research UnitPullmanWA 99164USA Donald Danforth Plant Science Center St.LouisMO 63132USA

Dear Editor,Genome editing has been widely applied in nuclei but not so in organelles such as the mitochondria and *** challenge for organelle genome editing is the limited accessibility of editing reagents to the compartments of organelles(Zhu et al.,2020).Recently,fusion proteins of cytidine deaminase domain(DddAtox)and transcription activator-like effectors(TALEs)have been developed for DNA base editing in mitochondria of human cells and mice(Mok et al.,2020;Lee et al.,2021).

关键词： base editing organelle

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Optimal Designs for Genomic Selection in Hybrid Crops

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Molecular Plant 2019年第3期12卷 390-401页

作者： Tingting Guo Xiaoqing Yu xianran li Haozhe Zhang Chengsong Zhu Sherry Flint-Garcia Michael D.McMullen James B.Holland Stephen J.Szalma Randall J.Wisser Jianming Yu Department of Agronomy Iowa State UniversityAmesIA50011USA Department of Statistics Iowa State UniversityAmesIA50011USA USDA-ARS and Division of Plant Sciences University of MissouriColumbiaMO65211USA USDA-ARS and Department of Crop and Soil Sciences North Carolina State UniversityRaleighNC27695USA Department of Plant and Soil Sciences University of DelawareNewarkDE19716USA

Improved capacity of genomics and biotechnology has greatly enhanced genetic studies in different areas. Genomic selection exploits the geno type-to-phe no type relationship at the whole-ge nome level and is being implemented in many crops? Here we show that design-thinking and data-mining techniques can be leveraged to optimize genomic prediction of hybrid performance? We phenotyped a set of 276 maize hybrids generated by crossing founder inbreds of nested association mapping populations for flowering time, ear height, and grain yield? With 10 296 310 SNPs available from the parental inbreds, we explored the pat? terns of genomic relati on ships and phenotypic variation to establish training samples based on clustering, graphic n etwork analysis, and genetic mating scheme ? Our analysis showed that training set desig ns outperformed random sampling and earlier methods that either minimize the mean of prediction error variance or maximize the mean of generalized coefficient of determination. Additional analyses of 2556 wheat hybrids from an early-stage hybrid breeding system and 1439 rice hybrids from an established hybrid breeding system validated the approaches. Together, we dem on strated that effective genomic predicti on models can be established with a training set 2%-13% of the size of the whole set, enabling an efficient exploration of enormous inf ere nee space of gen etic combi nations.

关键词： data mining molecular breeding genomic relationship genomic selection optimal design

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An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops

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Molecular Plant 2021年第6期14卷 874-887页

作者： xianran li Tingting Guo Jinyu Wang Wubishet ABekele Sivakumar Sukumaran Adam EVanous James PMcNellie Laura Tibbs Cortes Marta SLopes Kendall RLamkey Mark EWestgate John KMcKay Sotirios VArchontoulis Matthew PReynolds Nicholas ATinker Patrick SSchnable Jianming Yu Department of Agronomy Iowa State UniversityAmesIA 50011USA Ottawa Research and Development Centre Agriculture and Agri-Food CanadaOttawaONCanada International Maize and Wheat Improvement Center(CIMMYT) Mexico CityMexico Department of Bioagricultural Sciences and Pest Management Colorado State UniversityFort CollinsCO 80523USA

Identifying mechanisms and pathways involved in gene–environment interplay and phenotypic plasticity is a long-standing *** is highly desirable to establish an integrated framework with an environmental dimension for complex trait dissection and prediction.A critical step is to identify an environmental index that is both biologically relevant and estimable for new *** extensive field-observed complex traits,environmental profiles,and genome-wide single nucleotide polymorphisms for three major crops(maize,wheat,and oat),we demonstrated that identifying such an environmental index(i.e.,a combination of environmental parameter and growth window)enables genome-wide association studies and genomic selection of complex traits to be conducted with an explicit environmental ***,genes identified for two reaction-norm parameters(i.e.,intercept and slope)derived from flowering time values along the environmental index were less colocalized for a diverse maize panel than for wheat and oat breeding panels,agreeing with the different diversity levels and genetic constitutions of the *** addition,we showcased the usefulness of this framework for systematically forecasting the performance of diverse germplasm panels in new *** general framework and the companion CERIS-JGRA analytical package should facilitate biologically informed dissection of complex traits,enhanced performance prediction in breeding for future climates,and coordinated efforts to enrich our understanding of mechanisms underlying phenotypic variation.

关键词： phenotypic plasticity genotype by environment interaction gene-environment interplay genomewide association studies genomic selection flowering time reaction norm

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Calibration of local chemical pressure by optical probe

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National Science Review 2023年第9期10卷 258-269页

作者： Xiao Zhou Mei-Huan Zhao Shan-Ming Yao Hongliang Dong Yonggang Wang Bin Chen xianran Xing Man-Rong li Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education School of ChemistrySun Yat-sen University Center for High Pressure Science and Technology Advanced Research School of Materials Science and Engineering Peking University Beijing Advanced Innovation Center for Materials Genome Engineering Institute of Solid State Chemistry University of Science and Technology Beijing School of Science Hainan University

Chemical stabilization of a high-pressure metastable state is a major challenge for the development of advanced *** chemical pressure(Pchem) can effectively simulate the effect of physical pressure(Pphy)) experimental calibration of the pressure passed to local structural motifs,denoted as local chemical pressure(Pchem-△) which significantly governs the function of solid materials,remains absent due to the challenge of probing *** we establish an innovative methodology to experimentally calibrate the Pchem-△and build a bridge between Pchemand Pphyvia an optical probe ***-selective Bi3+-traced REVO4(RE=Y,Gd) is adopted as a prototype to introduce Bi3+optical probes and on-site sense of the Pchem-△experienced by the *** cell compression of RE0.9gBi0.02VO4under Pphyis chemically simulated by smaller-ion substitution(Sc3+→RE3+) in *** consistent red shift(△λ) of the emission spectra of Bi3+,which is dominated by locally pressure-induced REO8dodecahedral variation in RE0.98Bi0.02VO4(Pphy) and RE0.98-xScxBi0.02VO4(Pchem-△),respectively,is evidence of their similar pressure-dependent local structure *** innovative △λ-based experimental calibration of Pchem-△in the crystal-field dimension portrays the anisotropic transmission of Pchemto the local structure and builds a bridge between Pchem-△and Pphyto guide a new perspective for affordable and practical interception of metastable states.

关键词： chemical pressure high pressure ion substitution optical parameter spectra shift pressure calibration

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Chemical order-disorder nanodomains in Fe3Pt bulk alloy

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National Science Review 2022年第12期9卷 211-219页

作者： Qiang li Yang Ren Qinghua Zhang lin Gu Qingzhen Huang Hui Wu Jing Sun Yili Cao Kun lin xianran Xing Beijing Advanced Innovation Center for Materials Genome Engineering Institute of Solid State Chemistry University of Science and Technology Beijing X-Ray Science Division Argonne National Laboratory Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences NIST Center for Neutron Research National Institute of Standards and Technology

Chemical ordering is a common phenomenon and highly correlated with the properties of solid *** means of the redistribution of atoms and chemical bonds,it invokes an effective lattice adjustment and tailors corresponding physical *** date,however,directly probing the 3D interfacial interactions of chemical ordering remains a big *** this work,we deciphered the interlaced distribution of nanosized domains with chemical order/disorder in Fe3pt bulk *** F-STEM images evidence the existence of such *** reverse Monte Carlo method with the X-ray pair distribution function data reveal the 3D distribution of local structures and the tensile effect in the disordered domains at the single-atomic *** chemical bonding around the domain boundary changes the bonding feature in the disordered side and reduces the local magnetic moment of Fe *** results in a suppressed negative thermal expansion and extended temperature range in Fe3Pt bulk alloy with *** study demonstrates a local revelation for the chemical order/disorder nanodomains in bulk *** understanding gained from atomic short-range interactions within the domain boundaries provides useful insights with regard to designing new functional compounds.

关键词： Fe3Pt alloy chemical order nanodomain local structure pair distribution function

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