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A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

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Molecular Plant 2022年第8期15卷 1268-1284页

作者： Yun Deng Shoucheng Liu Yilin Zhang Jingsheng Tan Xiaopeng Li Xiao Chu Binghua Xu Yao Tian Yudong Sun Bosheng Li YunbiXu Xing Wang Deng Hang He Xingping Zhang Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangShandong 261000China School of Advanced Agricultural Sciences and School of Life Sciences State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijing 100871China Jiangsu Xuhuai Area Huaiyin Institute of Agricultural Science HuaianJiangsu 223300China

Watermelon,Citrullus lanatus,is the world's third largest fruit crop.Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon.Here,we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies.All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps,representing the highest completeness and assembly quality to date.The G42 reference genome is 369321829 bp in length and contains 24205 predicted protein-coding genes,with all 22 telomeres and 11 centromeres characterized.Furthermore,we established a pollen-EMS mutagenesis protocol and obtained over 200000M1 seeds from G42.In a sampling pool,48 monogenic phenotypic mutations,selected from 223M1and 78 M2 mutants with morphological changes,were confirmed.The average mutation density was 1 SNP/1.69Mband1 indel/4.55 Mb per M1 plant and 1SNP/1.08Mb and 1 indel/6.25 Mb per M2 plant.Taking advantage of the gap-free G42 genome,8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100%accuracy,whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed.Using this library and the gap-free genome,two genes responsible for elongated fruit shape and male sterility(CiMs1)were identified,both caused by a single basechange from G to A.The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.

关键词： watermelon gap-free genome EMS,mutation library gene discovery genome-wide sequencing genic male sterility

SoySNP618K array:A high-resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding

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Journal of Integrative Plant Biology 2022年第3期64卷 632-648页

作者： Yan-Fei Li Ying-Hui Li Shan-Shan Su Jochen CReif Zhao-Ming Qi Xiao-Bo Wang Xing Wang Yu Tian De-Lin Li Ru-Jian Sun Zhang-Xiong Liu Ze-Jun Xu Guang-Hui Fu Ya-Liang Ji Qing-Shan Chen Ji-Qiang Liu Li-Juan Qiu The National Key Facility for Crop gene Resources and genetic Improvement(NFCRI)/Key Laboratory of Crop gene Resource andGermplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop SciencesChinese Academy ofAgricultural SciencesBeijing 100081China Beijing Compass Biotechnology Co.Ltd Beijing 102206China Department of Breeding Research Leibniz Institute of Plant Genetics and Crop Plant Research(IPK)Gatersleben 06466Germany Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/genetics ofChinese Agriculture Ministry) Northeast Agricultural UniversityHarbin 150030China School of Agronomy Anhui Agricultural UniversityHefei 230036China Xuzhou Institute of Agricultural Sciences of Xu-huai Region of Jiangsu Xuzhou 221131China Department of Plant genetics and Breeding China Agricultural UniversityBeijing 100193China Hulun Buir Institution of Agricultural Sciences ZhalantunInner Mongolia 021000China Suzhou Academy of Agricultural Sciences Suzhou 234000China

Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop science.Here,we developed and validated the Soy SNP618 K array(618,888 SNPs)for the important crop soybean.The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions;29.34%of the SNPs mapped to genic regions representing 86.85%of the 56,044annotated high-confidence genes.Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions,highlighting the potential of the Soy SNP618 K array in supporting gene bank management.The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data,suggesting that the ascertainment bias in the Soy SNP618 K array was largely compensated for.Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time,E2 and Gm PRR3 b,and of a new candidate gene,Gm VIP5.Moreover,genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate(>0.65).Thus,the Soy SNP618 K array is a valuable genomic tool that can be used to address many questions in applied breeding,germplasm management,and basic crop research.

关键词： functional single nucleotide polymorphism array gene discovery genomic selection genome-wide association studies marker-assisted selection soybean

Vegetable biology and breeding in the genomics era

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Science China(Life Sciences) 2023年第2期66卷 226-250页

作者： Hongbo Li Xueyong Yang Yi Shang Zhonghua Zhang Sanwen Huang 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 SciencesShenzhen 518120China Key Laboratory of Biology and genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Yunnan Key Laboratory of Potato Biology The CAAS-YNNU-YINMORE Joint Academy of Potato SciencesYunnan Normal UniversityKunming 650500China Engineering Laboratory of genetic Improvement of Horticultural Crops of Shandong Province College of HorticultureQingdao Agricultural UniversityQingdao 266109China Chinese Academy of Tropical Agricultural Sciences Haikou 571101China

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize,thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

关键词： vegetable genomics multi-omics gene discovery molecular breeding

Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex

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Molecular Plant 2020年第7期13卷 1027-1046页

作者： Takayuki Tohge Federico Scossa Regina Wendenburg Pierre Frasse llse Balbo Mutsumi Watanabe Saleh Alseekh Sagar Sudam Jadhav Jay C.Delfin Marc Lohse Patrick Giavalisco Bjoern Usadel Youjun Zhang Jie Luo Mondher Bouzayen Alisdair R.Fernie Max-Planck-lnstitut fiir Molekulare Pflanzenphysiologie Am Muehlenberg 114476 Potsdam-Golm.Germany Graduate School of Biological Science Nara Institute of Science and TechnologyIkoma 630-0192 Japan Council for Agricultural Research and Economics(CREA) Research Centre for Genomics and Bioinformaticsvia Ardeatina 54600178 RomeItaly Universite de Toulouse INP-ENSA ToulouseGenomique et Biotechnologie des FruitsCastanet-Tolosan 31326France Institute of Plant Systems Biology 4000 PlovdivBulgaria Max Planck Institute for Biology of Ageing Joseph Stelzmann Strasse 9b50931 CologneGermany Institute of Botany and Molecular genetics BioSCRWTH Aachen University52056 AachenGermany National Key Laboratory of Crop genetic Improvement and National Center of Plant gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China

While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species,those defining specialized metabolism are less well characterized and more highly variable across species.In this study,we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato.For this purpose,GC-MS-and LC-MS-based metabolomics of different tissues of Solatium lycopersicum and wild tomato species were carried out,in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis,and publicly available RNA-sequencing data for annotation of biosynthetic genes.The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism,allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway.The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening.Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways.

关键词： Solanumly copersicum secondary metabolism natural diversity wild accessions pathway elucidation gene discovery

Functional Genomics of Wood Quality and Properties

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Genomics, Proteomics & Bioinformatics 2003年第4期1卷 263-278页

作者： WeiTang XiaoyanLuo AaronNelsont HilaryCollver KatherineKinken DepartmentofBiology HowellScienceComplexEastCarolinaUniversityGreenvilleNC27858USA DepartmentofCellandDevelopmentalBiology UniversityofNorthCarolinaChapelHillNC27599USA

Genomics promises to enrich the investigations of biology and biochemistry. Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication. Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly. Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide. In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus. The aims of this review are to summarize the current status of functional genomics including: (1) gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling. Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense. Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.

关键词： gene discovery genomic sequencing lignin biosynthesis cell wall biogenesis expres- sion profiling

Hitchhiking Effect Mapping: A New Approach for Discovering Agronomic Important genes

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Agricultural Sciences in China 2007年第3期6卷 255-264页

作者： ZHANG Xue-yong TONG Yi-ping YOU Guang-xia HAO Chen-yang GE Hong-mei WANG Lan-fen LI Bin DONG Yu-shen LI Zhen-sheng Institute of Crop Sciences Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Germplasm ＆ Biotechnology Ministry of Agriculture/National Facility for Crop Gene Resources and Genetic Improvement Beijing 100081 P.R.China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 P.R.China

Besides the natural selection, the crops cultivated today have experienced two episodes of strong artificial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation between cultivars and their wild species, while modern breeding made further genetic structure differentiation between the modern varieties and the landraces. In a population, diversity of the loci under strong selection is significantly lower than that of other loci. At the same time, diversity in the genomic regions flanking these selected loci also declines in the process of selection. This phenomenon is called hitchhiking effects or selection sweep in genetics. Genomic regions with selection sweep （haplotype block） could be detected after draft genome scanning （genome typing） with molecular markers in a number of released varieties or natural populations. Marker/trait association analysis in these regions would detect the loci （or QTLs） even the favored alleles （genes） in breeding or natural adaptation. Fine scanning of these genomic regions would help to determine the sizes of haplotype blocks and to discover the key genes, thereby providing very valuable information for isolation of the key genes and molecular design of new varieties. Establishment of high density genetic linkage maps in the major crops and availability of high throughput genotyping platform make it possible to discover agronomic important genes through marker/trait association analysis. On the basis of available publications, we give a brief introduction of the hitchhiking effect mapping approach in this paper using plant height, 1 000-grain weight, and phosphorus-deficiency tolerance as examples in wheat.

关键词： domestication ＆ breeding hitchhiking effects marker/trait association analysis gene discovery