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Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Horticulture Research 2023年第11期10卷 96-105页

作者： Alan E.Yocca Adrian Platts Elizabeth Alger Scott Teresi Molla F.Mengist Juliana Benevenuto Luis Felipe V.Ferrão MacKenzie Jacobs Michal Babinski Maria Magallanes-Lundback Philipp Bayer Agnieszka Golicz Jodi L.Humann Dorrie Main Richard V.Espley David Chagné Nick W.Albert Sara Montanari Nicholi Vorsa James Polashock Luis Díaz-Garcia Juan Zalapa Nahla V.Bassil Patricio R.Munoz Massimo Iorizzo Patrick P.Edger Department of Horticulture Michigan State UniversityEast LansingMI48824United States Department of Plant Biology Michigan State UniversityEast LansingMI48824United States Genetics and Genome Sciences Michigan State UniversityEast LansingMI48824United States Plants for Human Health Institute North Carolina State UniversityKannapolisNC United States Horticultural Sciences Department University of FloridaGainesvilleFL 32611United States Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI48824United States University of Western Australia Perth 6009 Australia Justus Liebig University Giessen35390 Germany Department of Horticulture Washington State UniversityPullmanWA99163United States The New Zealand Institute for Plant and Food Research Limited(PFR) AucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) PalmerstonNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) MotuekaNew Zealand SEBS Plant BiologyRutgers UniversityNew Brunswick NJ 01019 United States Department of Viticulture and Enology University of CaliforniaDavisDavisCA 95616United States National Clonal Germplasm Repository USDA-ARSCorvallisOR 97333United States Department of Horticulture North Carolina State UniversityKannapolisNC United States MSU AgBioResearch Michigan State UniversityEast LansingMI48824United States

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide.The industry continues to face a wide variety of production challenges(e.***.disease pressures),as well as a demand for higher-yielding cultivars with improved fruit quality characteristics.Unfortunately,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops.Here,we describe the construction and analysis of the first pangenome for both blueberry and cranberry.Our analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in cranberry.Auxiliary genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality traits.The discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding efforts.The pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database.Lastly,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

关键词： breeding cultivar crops

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Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding

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aBIOTECH 2021年第4期2卷 375-385页

作者： Jun Li Yan Li Ligeng Ma College of Life Sciences State Key Laboratory of North China Crop Improvement and RegulationHebei Agricultural UniversityBaoding 071001HebeiChina College of Life Sciences Beiing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental ImprovementCapital Normal UniversityBeijing 100048China

Common wheat(Triticum aestivum L.)is one of the three major food crops in the world;thus,wheat breeding programs are important for world food security.Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding.Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools,especially CRISPR/Cas9 genome editing technology,which allows multiplex genome engineering.Here,we describe the development of CRISPR/Cas9,which has revo-lutionized the field of genome editing.In addition,we emphasize technological breakthroughs(e.***.base editing and prime editing)based on CRISPR/Cas9.We also summarize recent applications and advances in the functional annotation and breeding of wheat,and we introduce the production of CRISPR-edited DNA-free wheat.Combined with other achievements,CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.

关键词： Wheat CRISPR/Cas9 Genome editing Functional genomics breeding

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Genomic basis of selective breeding from the closest wild relative of large-fruited tomato

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Horticulture Research 2023年第8期10卷 254-264页

作者： Junwei Yang Yun Liu Bin Liang Qinqin Yang Xuecheng Li Jiacai Chen Hongwei Li Yaqing Lyu Tao Lin State Key Laborary of Agrobiotechnology Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable CropsCollege of HorticultureChina Agricultural UniversityBeijing 100193China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China.

The long and intricate domestication history of the tomato(Solanum lycopersicum)includes selection sweeps that have not been fully explored,and these sweeps show significant evolutionary trajectories of domestication traits.Using three distinct selection strategies,we represented comprehensive selected sweeps from 53 Solanum pimpinellifolium(PIM)and 166 S.lycopersicum(BIG)accessions,which are defined as pseudo-domestication in this study.We identified 390 potential selection sweeps,some of which had a significant impact on fruit-related traits and were crucial to the pseudo-domestication process.During tomato pseudo-domestication,we discovered a minor–effect allele of the SlLEA gene related to fruit weight(FW),as well as the major haplotypes of fw2.2/cell number regulator(CNR),fw3.2/SlKLUH,and fw11.3/cell size regulator(CSR)in cultivars.Furthermore,18 loci were found to be significantly associated with FW and six fruit-related agronomic traits in genome-wide association studies.By examining population differentiation,we identified the causative variation underlying the divergence of fruit flavonoids across the large-fruited tomatoes and validated BRI1-EMS-SUPPRESSOR 1.2(SlBES1.2),a gene that may affect flavonoid content by modulating the MYB12 expression profile.Our results provide new research routes for the genetic basis of fruit traits and excellent genomic resources for tomato genomics-assisted breeding.

关键词： breeding cultivar traits

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Genomewide selection for fruit quality traits in apple: breeding insights gained from prediction and postdiction

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Horticulture Research 2023年第6期10卷 238-249页

作者： Sarah A.Kostick Rex Bernardo James J.Luby Department of Horticultural Science University of MinnesotaSaint PaulMN 55108USA Department of Agronomy and Plant Genetics University of MinnesotaSaint PaulMN 55108USA

Many fruit quality traits in apple(Malus domestica Borkh.)are controlled by multiple small-effect quantitative trait loci(QTLs).Genomewide selection(genomic selection)might be an effective breeding approach for highly quantitative traits in woody perennial crops with long generation times like apple.The goal of this study was to determine if genomewide prediction is an effective breeding approach for fruit quality traits in an apple scion breeding program.Representative apple scion breeding germplasm(nindividuals=955),high-quality single nucleotide polymorphism(SNP)data(nSNPs=977),and breeding program fruit quality trait data at harvest were analyzed.breeding parents‘Honeycrisp’and‘Minneiska’were highly represented.Moderate to high predictive abilities were observed for most fruit quality traits at harvest.For example,when 25%random subsets of the germplasm set were used as training sets,mean predictive abilities ranged from 0.35 to 0.54 across traits.Trait,training and test sets,family size for within family prediction,and number of SNPs per chromosome affected model predictive ability.Inclusion of large-effect QTLs as fixed effects resulted in higher predictive abilities for some traits(e.***.percent red overcolor).Postdiction(i.***.retrospective)analyses demonstrated the impact of culling threshold on selection decisions.The results of this study demonstrate that genomewide selection is a useful breeding approach for certain fruit quality traits in apple.

关键词： breeding germplasm crops

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Enabling breeding Selection for Biomass in Slash Pine Using UAV-Based Imaging

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Plant Phenomics 2022年第1期4卷 310-323页

作者： Zhaoying Song Federico Tomasetto Xiaoyun Niu Wei Qi Yan Jingmin Jiang Yanjie Li Research Institute of Subtropical Forestry Chinese Academy of ForestryNo.73Daqiao RoadFuyangHangzhou311400 Zhejiang ProvinceChina College of Landscape and Travel Agricultural University of HebeiBaodingChina AgResearch Ltd. Christchurch 8140New Zealand Auckland University of Technology Auckland 1010New Zealand

Traditional methods used to monitor the aboveground biomass(AGB)and belowground biomass(BGB)of slash pine(Pinus elliottii)rely on on-ground measurements,which are time-and cost-consuming and suited only for small spatial scales.In this paper,we successfully applied unmanned aerial vehicle(UAV)integrated with structure from motion(UAV-SfM)data to estimate the tree height,crown area(CA),AGB,and BGB of slash pine for in slash pine breeding plantations sites.

关键词： pine breeding Biomass

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breeding crops by design for future agriculture

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2020年第6期21卷 423-425页

作者： Chengdao LI Western Barley Genetics Alliance College of ScienceHealthEngineering and EducationMurdoch UniversityMurdochWA 6150Australia

Plant breeding is both the science and art of developing elite crop cultivars by creating and reassembling desirable inherited traits for human benefit.From the bulk selection of wild plants for cultivation during early civilization to Mendelian genetics and genomics-assisted breeding in modern society,breeding methodologies have evolved over the last thousand years.In the past few decades,the“Green Revolution”through breeding of semi-dwarf wheat and rice varieties,and the use of heterosis and transgenic crops have dramatically enhanced crop productivity and helped prevent widespread famine(Hickey et al.,2019).Integration of these technologies can significantly improve breeding efficiency in the development of super crop varieties(Li et al.,2018).

关键词： breeding crops cultivar

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Cytoplasmic and nuclear genome variations of rice hybrids and their parents inform the trajectory and strategy of hybrid rice breeding

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Molecular Plant 2021年第12期14卷 2056-2071页

作者： Zhoulin Gu Zhou Zhu Zhen Li Qilin Zhan Qi Feng Congcong Zhou Qiang Zhao Yan Zhao Xiaojian Peng Bingxin Dai Rongrong Sun Yan Li Hengyun Lu Lei Zhang Tao Huang Junyi Gong Danfeng Lv Xuehui Huang Bin Han National Center for Gene Research State Key Laboratory of Plant Molecular GeneticsCenter for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China University of Chinese Academy of Sciences Beijing 100049China College of Life Sciences Anhui Normal UniversityWuhuAnhui 241000China School of Life Sciences Anhui Agricultural UniversityHefeiAnhui 230036China School of Life Science and Technology Shanghai Tech UniversityShanghai 201210China State Key Laboratory of Rice Biology China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 310006China College of Life Sciences Shanghai Normal UniversityShanghai 200234China

The male sterility(MS)line is a prerequisite for efficient production of hybrid seeds in rice,a self-pollinating species.MS line breeding is pivotal for hybrid rice improvement.Understanding the historical breeding tra-jectory will help to improve hybrid rice breeding strategies.Maternally inherited cytoplasm is an appro-priate tool for phylogenetic reconstruction and pedigree tracing in rice hybrids.In this study,we analyzed the cytoplasmic genomes of 1495 elite hybrid rice varieties and identified five major types of cytoplasm,which correspond to different hybrid production systems.As the cytoplasm donors for hybrids,461 MS lines were also divided into five major types based on cytoplasmic and nuclear genomic architecture.Spe-cific core accessions cooperating with different fertility-associated genes drove the sequence divergence of MS lines.Dozens to hundreds of convergent and divergent selective sweeps spanning several agro-nomic trait-associated genes were identified among different types of MS lines.We further analyzed the cross patterns between different types of MS lines and their corresponding restorers.This study system-atically analyzed the cytoplasmic genomes of rice hybrids revealed their relationships with nuclear ge-nomes of MS lines,and illustrated the trajectory of hybrid rice breeding and the strategies for breeding different types of MS lines providing new insights for future improvement of hybrid rice.

关键词： rice hybrid cytoplasm cytoplasmic male sterile environment-sensitive genic male sterile breeding

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breeding effects on the genotype×environment interaction for yield of durum wheat grown after the Green Revolution:The case of Spain

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The Crop Journal 2020年第4期8卷 623-634页

作者： Fadia Chairi Nieves Aparicio Maria Dolores Serret José Luis Araus Section of Plant Physiology University of BarcelonaBarcelonaSpain AGROTECNIO(Center of Research in Agrotechnology) LleidaSpain Instituto de Tecnología Agraria de Castilla y León(ITACyL) ValladolidSpain

This study evaluates the changes caused by breeding in the genotype by environment(G×E)interaction of the durum wheat varieties most widely cultivated in Spain after the Green Revolution.A set of 12 cultivars was tested in 27 environments,which are understood as the combination of different sites,years,and treatments(water regime and planting dates),representative of the durum wheat growing conditions in Spain with average grain yields(GY)ranging between 2.8 and 9.1 Mg ha^-1.The most important environmental factors affecting the G×E interaction for yield were themaximum and the mean temperature during the entire crop cycle.An improvement in genetic yield was observed in warm environments and under optimal water conditions that resemble those where the germplasm originated(essentially as advanced lines)before its release in Spain.Therefore,the adaptation of semi-dwarf durum in Spain has shown a tendency to specific adaptation rather than large-scale adaptation.Two different patterns of selection have been reported due the G×E interaction and changes in the ranking of genotypes:in the high yielding environments(GY>5 Mg ha^-1),plants favor increased water uptake,with higher levels of transpiration and more open stomata(more negative values of carbon isotope composition,δ^13 C,and higher canopy temperature depression,CTD),whereas,in low yielding environments(GY<5 Mg ha^-1)plants close their stomata and favor greater water use efficiency(less negativeδ^13 C values and lower CTD values).

关键词： breeding cultivar dwarf

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INSTRUCTION FOR CONTRIBUTORS

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Rice science 2024年第3期31卷 F0002-F0002页

SCOPE Rice Science is an international peer-reviewed journal sponsored by China National Rice Research Institute and hosting by Elsevier B V.It publishes original research papers,reviews,experimental technique as well as letters on rice science in English language.Some of the topics that may be included in each issue are:breeding and genetics,biotechnology,germplasm resources,agronomy.

关键词： breeding germplasm language

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breeding wheat for resistance to Fusarium head blight in the Global North: China, USA, and Canada

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The Crop Journal 2019年第6期7卷 730-738页

作者： Zhanwang Zhu Yuanfeng Hao Mohamed Mergoum Guihua Bai Gavin Humphreys Sylvie Cloutier Xianchun Xia Zhonghu He Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Food Crops Institute Hubei Academy of Agricultural SciencesWuhan 430064HubeiChina Department of Crop and Soil Sciences University of GeorgiaGriffinGA 30223USA US Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research UnitManhattanKS 66506USA Agriculture and Agri-Food Canada Ottawa Research and Development CentreOttawaOntario K1A 0C6Canada CIMMYT-China Office c/o CAASBeijing 100081China

The objective of this paper is to review progress made in wheat breeding for Fusarium head blight(FHB) resistance in China, the United States of America(USA), and Canada. In China,numerous Chinese landraces possessing high levels of FHB resistance were grown before the 1950 s. Later, pyramiding multiple sources of FHB resistance from introduced germplasm such as Mentana and Funo and locally adapted cultivars played a key role in combining satisfactory FHB resistance and high yield potential in commercial cultivars.Sumai 3, a Chinese spring wheat cultivar, became a major source of FHB resistance in the USA and Canada, and contributed to the release of more than 20 modern cultivars used for wheat production, including the leading hard spring wheat cultivars Alsen, Glenn, Barlow and SY Ingmar from North Dakota, Faller and Prosper from Minnesota, and AAC Brandon from Canada. Brazilian wheat cultivar Frontana, T. dicoccoides and other local germplasm provided additional sources of resistance. The FHB resistant cultivars mostly relied on stepwise accumulation of favorable alleles of both genes for FHB resistance and high yield,with marker-assisted selection being a valuable complement to phenotypic selection. With the Chinese Spring reference genome decoded and resistance gene Fhb1 now cloned, new genomic tools such as genomic selection and gene editing will be available to breeders, thus opening new possibilities for development of FHB resistant cultivars.

关键词： Fhb1 Fusarium head blight resistance Fusarium graminearum Triticum aestivum Wheat breeding

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