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Development of a target capture sequencing SNP genotyping platform for genetic analysis and genomic breeding in rapeseed

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The Crop Journal 2023年第2期11卷 499-510页

作者： Xiaodong Li Xumei Liu Yonghai Fan Shengting Li Mengna Yu Mingchao Qian Yuling Chen Hongqiao Chen Xinchun Li Bei Liu Xinfu Xu Cunmin Qu Jiana Li Kun Lu Integrative Science Center of Germplasm Creation in Western China(CHONGQING)Science City and Southwest University College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqing 400715China Engineering Research Center of South Upland Agriculture Ministry of EducationChongqing 400715China Academy of Agricultural Sciences Southwest UniversityBeibeiChongqing 400715China China Golden Marker(Beijing)Biotech Co. Ltd.Beijing 102206China

Rapeseed(Brassica napus)is an oil crop grown worldwide,making it a key plant species in molecular breeding ***,the complexity of its polyploid genome increases sequencing costs and reduces sequencing *** capture coupled with high-throughput sequencing is an efficient approach for detecting genetic variation at genomic regions or loci of *** this study,588 resequenced accessions of rapeseed were used to develop a target capture sequencing SNP genotyping platform named *** platform comprised 54,765,with 54,058 resequenced markers from the pan-genome,and 855 variant trait-associated markers for 12 agronomic *** capture quality of BnaPan50T was demonstrated well in 12 typical *** with a conventional genotyping array,BnaPan50T has a high SNP density and a high proportion of SNPs in unique physical positions and in annotated functional genes,promising wide *** capture sequencing and wholegenome resequencing in 90 doubled-haploid lines yielded 60%specificity,78%uniformity within tenfold coverage range,and 93%genotyping accuracy for the ***50T was used to construct a genetic map for quantitative trait loci(QTL)mapping,identify 21 unique QTL,and predict several candidate genes for yield-related traits in multiple environments.A set of 132 core SNP loci was selected from BnaPan50T to construct DNA fingerprints and germplasm identification *** study provides genomics resources to support target capture sequencing,genetic analysis and genomic breeding of rapeseed.

关键词： Rapeseed Target capture SNP genotyping platform genomic breeding

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Recent progression and future perspectives in cotton genomic breeding

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Journal of Integrative Plant Biology 2023年第2期65卷 548-569页

作者： Zhaoen Yang Chenxu Gao Yihao Zhang Qingdi Yan Wei Hu Lan Yang Zhi Wang Fuguang Li Zhengzhou Research Base State Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhou 450000China State Key Laboratory of Cotton Biology Institute of Cotton Research of the Chinese Academy of Agricultural SciencesAnyang 455000China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572000China Sanya Institute Zhengzhou UniversitySanya 572000China

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein *** in cotton genomics promotes the advancement of cotton genetics,evolutionary studies,functional genetics,and breeding,and has ushered cotton research and breeding into a new ***,we summarize high-impact genomics studies for cotton from the last 10 *** diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic *** next review recent progress in cotton molecular biology and genetics,which builds on cotton genome sequencing efforts,population studies,and functional genomics,to provide insights into the mechanisms shaping abiotic and biotic stress tolerance,plant architecture,seed oil content,and fiber *** also suggest the application of novel technologies and strategies to facilitate genome-based crop *** growth in the amount of novel genomic data,identified genes,gene modules,and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate"super cotton",synergistically improving multiple *** strategies must rise to meet urgent demands for a sustainable cotton industry.

关键词： functional genomics genomic breeding germplasm resource Gossypium integrated breeding strategy major locus multi-omics

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Develop genotyping tools for rice genomic breeding

Develop genotyping tools for rice genomic breeding

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第十四届全国植物基因组学大会

作者： Fasong Zhou Haodong Chen Weibo Xie Huihui Yu Hang He Jing Li Yuqing He Qifa Zhang Life Science and Technology Center China National Seed Group Co.Ltd. Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology State Key Laboratory of Protein and Plant Gene ResearchCollege of Life SciencesPeking University National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Huazhong Agricultural University

The completed gnome sequences of rice subspecies,indica and japonica,as well as the characterization of a large number of important trait-related genes,laid a sound foundation for genomics-based breeding in ***-sequen... 详细信息

关键词： rice high throughput genotyping genomic breeding

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Improving the resistance of the rice PTGMS line Feng39S by pyramiding blast,bacterial blight,and brown planthopper resistance genes

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The Crop Journal 2022年第4期10卷 1187-1197页

作者： Dabing Yang Lizhong Xiong Tongmin Mou Jiaming Mi National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070HubeiChina

Knowledge of rice(Oryza sativa L.)genes and various DNA markers can be used in genomic breeding programs aimed at developing improved elite rice *** used an efficient genomic breeding approach to pyramid four resistance genes(Pi2,Xa23,Bph14,and Bph15)in the popular photoperiod-and thermosensitive genic male sterile(PTGMS)rice line *** performed foreground selection for the target genes,followed by recombinant selection and background *** process reduced the sizes of the genomic segments harboring the target genes(566.8 kb for Pi2,1143.9 kb for Xa23,774.7 kb for Bph14,and 1574.9 kb for Bph15)and accelerated the recovery of the recurrent parent genome to proportions ranging from 98.77%to 99.16%,thus resulting in four near-isogenic *** assemble the four resistance genes in Feng39S,we performed a double-way cross combined with foreground and background selection to generate two improved lines of Feng39S(Pi2+Xa23+Bph14+Bph15)with a recurrent parent genome recovery of 98.98%.The two lines showed agronomic performance,grain quality,and fertility–sterility transition characteristics similar to those of the original Feng39S *** newly developed PTGMS lines and corresponding hybrid combinations were resistant to various field blast isolates and seven representative isolates of bacterial *** the seedling stage,the lines also showed resistance against brown *** study provides an efficient and accurate genomic breeding approach for introducing desirable traits into PTGMS lines.

关键词： Bacterial blight resistance Blast resistance Brown planthopper resistance genomic breeding PTGMS line Two-line hybrid rice

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Decoding the fish genome opens a new era in important trait research and molecular breeding in China

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Science China(Life Sciences) 2024年第10期67卷 2064-2083页

作者： Qian Zhou Jialin Wang Jiongtang Li Zhangfan Chen Na Wang Ming Li Lei Wang Yufeng Si Sheng Lu Zhongkai Cui Xuhui Liu Songlin Chen State Key Laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China Laboratory for Marine Fisheries Science and Food Production Processes Qingdao Marine Science and Technology CenterQingdaoShandong 266237China Key Laboratory of Aquatic genomics Ministry of Agriculture and Rural AffairsBeijing Key Laboratory of Fishery BiotechnologyChinese Academy of Fishery SciencesBeijing 100041China

Aquaculture represents the fastest-growing global food production sector,as it has become an essential component of the global food *** has the world's largest aquaculture industry in terms of production ***,the sustainable development of fish culture is hindered by several concerns,including germplasm degradation and disease *** practice of genomic breeding,which relies heavily on genome information and genotypephenotype relationships,has significant potential for increasing the efficiency of aquaculture *** 2014,the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in *** then,domestic researchers have made dramatic progress in functional genomic *** date,the genomes of more than 60 species of fish in China have been assembled and *** on these reference genomes,evolutionary,comparative,and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes,including growth and development,sex determination,disease resistance,metamorphosis,and ***,genomic tools and breeding techniques such as SNP arrays,genomic selection,and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding *** review aims to summarize the current status,advances,and perspectives of the genome resources,genomic study of important traits,and genomic breeding techniques of fish in *** review will provide aquaculture researchers,fish breeders,and farmers with updated information concerning fish genomic research and breeding *** summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

关键词： fish genomics economic traits genomic selection genome editing genomic breeding

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From Green Super Rice to green agriculture:Reaping the promise of functional genomics research

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Molecular Plant 2022年第1期15卷 9-26页

作者： Sibin Yu Jauhar Ali Shaochuan Zhou Guangjun Ren Huaan Xie Jianlong Xu Xinqiao Yu Fasong Zhou Shaobing Peng Liangyong Ma Dingyang Yuan Zefu Li Dazhou Chen Ruifeng Zheng Zhigang Zhao Chengcai Chu Aiqing You Yu Wei Susong Zhu Qiongyao Gu Guangcun He Shigui Li Guifu Liu Changhua Liu Chaopu Zhang Jinghua Xiao Lijun Luo Zhikang Li Qifa Zhang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China International Rice Research Institute DAPO Box 7777Metro ManilaPhilippines Guangdong Academy of Agricultural Sciences GuangzhouChina Sichuan Academy of Agricultural Sciences ChengduChina Fujian Academy of Agricultural Sciences FuzhouChina Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijingChina Shanghai Agrobiological Gene Center ShanghaiChina China National Seed Group Co. LtdBeijingChina China National Rice Research Institute HangzhouChina Hunan National Hybrid Rice Center ChangshaChina Anhui Academy of Agricultural Sciences HefeiChina Jiangxi Academy of Agricultural Sciences NanchangChina Nanjing Agricultural University NanjingChina State Key Laboratory of Plant genomics Institute of Genetics and Developmental BiologyThe Innovative Academy for Seed DesignChinese Academy of SciencesBeijingChina Hubei Academy of Agricultural Sciences WuhanChina Guangxi Academy of Agricultural Sciences NanningChina Guizhou Academy of Agricultural Sciences GuiyangChina Yunnan Academy of Agricultural Sciences KunmingChina Wuhan University WuhanChina Sichuan Agricultural University ChengduChina Heilongjiang Academy of Agricultural Sciences HarbinChina College of Agronomy Anhui Agricultural UniversityHefeiChina Wuhan Greenfafa Institute of Novel Genechip R&D China

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great ***,we review the concept and practices of Green Super Rice(GSR)that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable *** momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources,functional gene discoveries,and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving,environmentally friendly crop production *** also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agricul-ture and better nourish the world population.

关键词： rice functional genomics Green Super Rice genomic breeding nutritious crops sustainable agriculture

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