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BnVIR:bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus

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Molecular Plant 2022年第5期15卷 779-782页

作者： Zhiquan Yang Congyuan Liang LuLu Wei Shengbo Wang Feifan Yin Dongxu Liu Liang Guo Yongming Zhou Qing-Yong Yang National Key Laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China

Dear Editor,Genetic variations,which range from single nucleotide polymor-phisms(SNPs)and short insertion/deletions(InDels)to large-scale structural variations(SVs),are the basis of phenotypic diversity.Understanding the effect of genetic variations on traits is critical for uncovering the genetic architecture of various phe-notypes.

关键词： agronomic traits InDel

Telomere-to-telomere genome assembly of melon(Cucumis melo L.var.inodorus)provides a high-quality reference for meta-QTL analysis of important traits

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Horticulture Research 2023年第10期10卷 202-214页

作者： Minghua Wei Ying Huang Changjuan Mo Haiyan Wang Qingguo Zeng Wenli Yang Jihao Chen Xuejun Zhang Qiusheng Kong National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China Hami-melon Research Center Xinjiang Academy of Agricultural SciencesUrumqi 830091China Hainan Sanya Experimental Center for Crop Breeding Xinjiang Academy of Agricultural SciencesSanya 572014China

Melon is an important horticultural crop with extensive diversity in many horticultural groups.To explore its genomic diversity,it is necessary to assemble more high-quality complete genomes from different melon accessions.Meanwhile,a large number of QTLs have been mapped in several studies.Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning.To address these problems,a telomere-to-telomere(T2T)genome of the elite melon landrace Kuizilikjiz(Cucumis melo L.var.inodorus)was de novo assembled and all the published QTLs were projected onto it in this study.The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads,PacBio high-fidelity long reads,Hi-C data,and a high-density genetic map.Each chromosome contained the centromere and telomeres at both ends.A large number of structural variations were observed between Kuizilikjiz and the other published genomes.A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome.Several clustered,co-localized,and overlapped QTLs were determined.Furthermore,20 stable meta-QTLs were identified,which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes.Collectively,the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.

关键词： Cucumis elite traits

Deciphering the enigmatic spikelet traits:Resolving trade-offs for enhancing rice yield

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Molecular Plant 2024年第5期17卷 694-695页

作者： Hideki Yoshida Makoto Matsuoka Institute of Fermentation Sciences Fukushima UniversityFukushima 960-1248Japan

Increasing the yield is one of the most important goals of crop improvement.Since the beginning of rice cultivation thousands of years ago,many efforts have been made to increase rice yield.One of the successes in this history was the Green Revolution.This tremendous improvement in the 1960s was achieved by increasing rice and wheat production through the development and widespread adoption of semi-dwarf varieties with the extensive use of fertilizers(Hedden,2003).Dwarfism in crops lowers the center of gravity of the plant body,reducing the risk of lodging and enabling farmers to use more fertilizer to increase yields.Semi-dwarf mutations in both rice and wheat created during the Green Revolution are related to the plant growth hormone gibberellin(GA).Although other mechanisms cause dwarf mutants,only GA-related semi-dwarf mutants were selected during the Green Revolution(Wang et al.,2021).While GA-related abnormalities only make plants shorter,most cases caused by other mechanisms involve not only dwarfism but also other morphological abnormalities.

关键词： dwarf crops traits

Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea(Hydrangea macrophylla)and insights into Asterid evolution

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Horticulture Research 2023年第12期10卷 45-57页

作者： Xingbo Wu Sheron A.Simpson Ramey C.Youngblood Xiaofen FLiu Brian E.Scheffler Timothy A.Rinehart Lisa W.Alexander Amanda M.Hulse-Kemp Department of Environmental Horticulture Tropical Research and Education CenterUniversity of FloridaHomesteadFL 33031United States Genomics and Bioinformatics Research Unit USDA-ARSRaleighNC 27695United States Genomics and Bioinformatics Research Unit USDA-ARSStonevilleMS 38776United States Institute for Genomics Biocomputing and BiotechnologyMississippi State UniversityStarkvilleMS 39762United States Crop Production and Protection USDA-ARSBeltsvilleMD 20705United States Floral and Nursery Plants Research Unit U.S.National ArboretumUSDA-ARSMcMinnvilleTN 37110United States Department of Crop and Soil Sciences North Carolina State UniversityRaleighNC 27695United States

The Hydrangea genus belongs to the Hydrangeaceae family,in the Cornales order of flowering plants,which early diverged among the Asterids,and includes several species that are commonly used ornamental plants.Of them,Hydrangea macrophylla is one of the most valuable species in the nursery trade,yet few genomic resources are available for this crop or closely related Asterid species.Two high-quality haplotype-resolved reference genomes of hydrangea cultivars‘Veitchii’and‘Endless Summer’[highest quality at 2.22 gigabase pairs(Gb),396 contigs,N5022.8 megabase pairs(Mb)]were assembled and scaffolded into the expected 18 pseudochromosomes.Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants,nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids.Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape,CYP78A5 located on chromosome 4,and a novel gene,BAM3 located on chromosome 17,for causing double flower.Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants,the Asterids.

关键词： Hydra traits resolved

Genome-wide association analysis identified molecular markers and candidate genes for flower traits in Chinese orchid (Cymbidium sinense)

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Horticulture Research 2023年第11期10卷 193-207页

作者： Fengxi Yang Yudi Guo Jie Li Chuqiao Lu Yonglu Wei Jie Gao Qi Xie Jianpeng Jin Genfa Zhu Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization Environmental Horticulture Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China

The orchid,the champagne of f lowers,brings luxury,elegance,and novelty to nature.Cymbidium sinense is a symbol of gigantic floral variability on account ofwavering shapes and sizes of f loral organs,althoughmarker-trait association(MTA)has not been studied for its f loral traits.We evaluated markers associated with 14 f loral traits of C.sinense through a genome-wide association study(GWAS)of 195 accessions.A total of 65318522 single-nucleotide polymorphisms(SNPs)and 3906176 insertion/deletion(InDel)events were identified through genotyping-by-sequencing.Among these,4694 potential SNPs and 477 InDelswere identified as MTAs at−log10 P>5.The genes related to these SNPs and InDels were largely associated with f loral regulators,hormonal pathways,cell division,and metabolism,playing essential roles in tailoring f loral morphology.Moreover,20 candidate SNPs/InDels linked to 11 genes were verified,8 of which were situated on exons,onewas located in the 5-UTR and twowere positioned in introns.Here,themultitepal trait-related gene RABBIT EARS(RBE)was found to be the most crucial gene.We analyzed the role of CsRBE in the regulation of flower-related genes via efficient transient overexpression in C.sinense protoplasts,and found that the floral homeotic genes CsAP3 and CsPI,as well as organ boundary regulators,including CsCUC and CsTCP genes,were regulated by CsRBE.Thus,we obtained key gene loci for important ornamental traits of orchids using genome-wide association analysis of populations with natural variation.The findings of this study can do a great deal to expedite orchid breeding programs for shape variability.

关键词： traits analysis breeding

Postharvest Variations of Rice Physicochemical traits and Volatile Compounds under Granary Conditions During Long-Time Storage

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Rice science 2023年第2期30卷 92-95,I0007-I0009页

作者： HU Hao LIU Xingquan HE Yukai JIN Jiande WU Fenghua HUANG Shiwen ZHANG Jiaojiao College of Food and Health Zhejiang Agriculture and Forest UniversityHangzhou 311300China China National Rice Research Institute Hangzhou 310006China Zhejiang Province Grain Reserve Management Co.LTD Hangzhou 310006China

Rice quality is influenced by many factors,viz.,temperature,humidity,atmosphere and storage time.To uncover quality variations of rice after postharvest,we estimated the physicochemical properties and volatile compounds of an indica rice Zhongzheyou 8 under granary conditions(20ºC-25ºC in summer and 10ºC-15ºC in other seasons)for three years.

关键词： traits humidity harvest

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Additive Effects of QTLs/Genes on Rice Grain Size traits Revealed by Genetic Comparisons

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Rice science 2023年第3期30卷 171-175,I0002-I0013页

作者： HE Lei LIANG Wenhua HU Jiang ZHAO Chunfang YAO Shu CHEN Tao ZHU Zhen ZHAO Qingyong LU Kai ZHAO Ling ZHOU Lihui QIAN Qian WANG Cailin ZHANG Yadong Institute of Food Crops Jiangsu Academy of Agricultural Science/Key Laboratory of Jiangsu Province for Agrobiology/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River(Nanjing)Ministry of Agriculture and Rural AffairsNanjing 210014China East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice Nanjing 210014China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 311400China

Grain size is controlled by many QTLs and/or genes.Despite intensive study,the genetic interactions between these QTLs/genes remain largely unclear.We previously found that the japonica large-grain rice cultivar TD70 with 1000-grain weight of 68.6 g carries superior alleles at the loci GW2,GS3,qGL3,GS5 and GW8,all of which are known to control grain size,while the indica rice variety Kasalath with 1000-grain weight of 19.1 g has normal alleles at these loci.

关键词： cultivar alleles traits

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Understanding divergent domestication traits from the whole-genome sequencing of swamp-and river-buffalo populations

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National Science Review 2020年第3期7卷 686-701页

作者： Xier Luo Yu Zhou Bing Zhang Yi Zhang Xiaobo Wang Tong Feng Zhipeng Li Kuiqing Cui Zhiqiang Wang Chan Luo Hui Li Yanfei Deng Fenghua Lu Jianlin Han Yongwang Miao Huaming Mao Xiaoyan Yi Cheng Ai Shigang Wu Alun Li Zhichao Wu Zijun Zhuo Do Da Giang Bikash Mitra Mohammad Farhad Vahidi Shahid Mansoor Sahar Ahmed Al-Bayatti Eka Meutia Sari Neena Amatya Gorkhali Sigit Prastowo Laiba Shafique Guoyou Ye Qian Qian Baoshan Chen Deshun Shi Jue Ruan Qingyou Liu Animal Biotechnology Department Agricultural Biotechnology Research Institute of Iran-North Region 11. National Institute for Biotechnology and Genetic Engineering 12. Animal Genetic Sources DepartmentDirectorate of Animal Resources Ministry of Agriculture 13. Department of Animal Science Faculty of Agriculture Syiah Kuala University 14. Animal Breeding DivisionNational Animal Science Research Institute Nepal Agriculture Research Council 15. Animal Science Department Universitas Sebelas Maret 16. International Rice Research Institute State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangxi University CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics Breeding and Reproduction of Ministry of Agriculture and Rural AffairsCollege of Animal Science and Technology China Agricultural University Guangdong Laboratory for Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources Institute of Animal ScienceChinese Academy of Agricultural Sciences International Livestock Research Institute Faculty of Animal Science and Technology Yunnan Agricultural University Bacgiang Agriculture and Forestry University Cellular Immunology Lab Department of Zoology University of North Bengal

Domesticated buffaloes have been integral to rice-paddy agro-ecosystems for millennia, yet relatively little is known about the buffalo genomics. Here, we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals(132 swamp buffaloes and 98 river buffaloes)sampled from across Asia and Europe. Beyond the many actionable insights that our study revealed about the domestication, basic physiology and breeding of buffalo, we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior, digestion metabolism, strengths and milk production.

关键词： Bubalus bubalis genome buffalo domestication re-sequencing traits

Genetic Dissection of Quantitative Trait Loci for Panicle traits and Heat Tolerance by High-Density Bin Map in Rice

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Rice science 2022年第6期29卷 507-511,I0007-I0020页

作者： LIU Hongyan MA Xiaosong LI Enxi ZENG Xianjun LUO Lijun Shanghai Agrobiological Gene Center Shanghai 201106China Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization Ministry of Agriculture and Rural AffairsShanghai 201106China Hainan University Haikou 570228China Huazhong Agricultural University Wuhan 430070China

A recombinant inbred line(RIL)with 179 lines derived from a cross between a heat tolerant line Huhan 1B and a heat sensitive line Hanhui 3 was used for QTL mapping for panicle traits and heat tolerance.A total of 52 QTLs were identified with LOD scores from 3.85 to 54.93,each explaining 0.70%to 21.48%of the phenotypic variances,including 11 for panicle length(PL),11 for seed number per panicle(SN),14 for spikelet number per panicle(SNPP),6 for seed-setting rate(SSR)under normal conditions,and 5 for seed-setting rate(SSR_HT)and 5 for relative seed-setting rate(RSSR)under heat stress,respectively.

关键词： panicle traits Map

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