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A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing

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Journal of Integrative Plant Biology 2023年第3期65卷 633-645页

作者： Sheng Zhao Cuicui Zhang Liqun Wang Minxuan Luo Peng Zhang Yue Wang Waqar Afzal Malik Yue Wang Peng Chen Xianjin Qiu Chongrong Wang Hong Lu Yong Xiang Yuwen Liu Jue Ruan Qian Qian Haijian Zhi Yuxiao Chang National Key Laboratory for Crop Genetics and Germplasm Enhancement National Center for Soybean ImprovementNanjing Agricultural UniversityNanjing 210095China Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China College of Agriculture Yangtze UniversityJingzhou 434023China Guangdong Provincial Key Laboratory of New Technology in Rice breeding Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China

Whole-genome genotyping methods are important for breeding.However,it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species.In our study,we accidently discovered that in adapter ligation-mediated PCR,the amplification by primertemplate mismatched annealing(PTMA)along the genome could generate thousands of stable PCR products.Based on this observation,we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing(FBI-seq)using one specific primer,in which foreground genotyping is performed by primer-template perfect annealing(PTPA),while background genotyping employs PTMA.Unlike DNA arrays,multiple PCR,or genome target enrichments,FBI-seq requires little preliminary work for primer design and synthesis,and it is easily adaptable to different foreground genes and species.FBI-seq therefore provides a prolific,robust,and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the postgenomics era.

关键词： background selection foreground genotyping primer-template mismatched annealing marker-assisted breeding whole-genome genotyping

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Strategy for marker-assisted breeding,status of genetic linkage maps,and QTL for aquaculture species

Strategy for marker-assisted breeding,status of genetic link...

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2005水产科技论坛

作者： Nobuaki OKAMOTO Kanako FUJI Eriko OHARA Takuya HARA Cecilia Castano SANCHEZ Takashi SAKAMOTO Akiyuki OZAKI M.R.M.COIMBRA Sok Kean KHOO Osamu HASEGAWA Faculty of Marine Science Tokyo University of Marine Science and TechnologyTokyoJapan Faculty of Marine Science Tokyo University of Marine Science and TechnologyTokyoJapan Faculty of Marine Science Tokyo University of Marine Science and TechnologyTokyoJapan Faculty of Marine Science Tokyo University of Marine Science and TechnologyTokyoJapan Faculty of Marine Science Tokyo University of Marine Science and TechnologyTokyoJapan Faculty of Marine Science Tokyo University of Marine Science and TechnologyTokyoJapan National Research Institute of Aquaculture Fisheries Research AgencyMieJapan Universidade Federal Rural de Pernambuco Recife-PEBrazil Laboratory of Cancer Genetics Van Andel Institute Michigan USA Kanagawa Prefectural Fisheries Research Institute KanagawaJapan

＜正＞Recent advanced techniques in molecular biology have facilitated the dissection of many genetic traits in animals. One of the most important tools of these techniques is genetic linkage maps based on DNA markers such as microsatellite markers. The genetic markers mapped on a linkage map can be used to analyze the quantitative trait loci （QTL） responsible for economically important traits such as disease resistance, growth, and fecundity. In addition, genetic linkage maps also facilitate the positional cloning of functional genes contributing to the quantitative traits. Mapping and identifying the genetic markers linked to economically important traits is critical for marker-assisted breeding. marker-assisted breeding such as marker-assisted selection （MAS） and marker-assisted gene introgression （MAI） are highly expected to improve the selective breeding programs of aquaculture species. In this paper, we introduce a comprehensive strategy for selective breeding by integrating molecular markers, genetic linkage maps, and QTL data that have been reported in aquaculture species.

关键词： DNA marker genetic linkage map QTL marker-assisted breeding MAS MAI

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Genetic Improvement of Rice for Bacterial Blight Resistance:Present Status and Future Prospects

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Rice science 2022年第2期29卷 118-132页

作者： R.ABDUL FIYAZ D.SHIVANI K.CHAITHANYA K.MOUNIKA M.CHIRANJEEVI G.S.LAHA B.C.VIRAKTAMATH L.V.SUBBA RAO R.M.SUNDARAM ICAR-Indian Institute of Rice Research RajendranagarHyderabad 500030India Professor Jayashankar Telangana State Agricultural University RajendranagarHyderabad 500030India

The production and productivity of rice has been challenged due to biotic and abiotic factors.Bacterial blight(BB)disease,caused by Xanthomonas oryzae pv.oryzae,is one of the important biotic stress factors,which reduces rice production by 20%-50%.The deployment of host plant resistance is the most preferred strategy for management of BB disease,and breeding disease resistant varieties remains a very economical and effective option.However,it is difficult to develop rice varieties with durable broad-spectrum resistance against BB using conventional approaches alone.Modern biotechnological tools,particularly the deployment of molecular markers,have facilitated the cloning,characterization and introgression of BB resistance genes into elite varieties.At least 46 BB resistance genes have been identified and mapped from diverse sources till date.Among these,11 genes have been cloned and characterized.marker-assisted breeding remains the most efficient approach to improve BB resistance by introducing two or more resistance genes into target varieties.Among the identified genes,xa5,xa13 and Xa21 are being widely used in marker-assisted breeding and more than 70 rice varieties or hybrid rice parental lines have been improved for their BB resistance alone or in combination with genes/QTLs conferring tolerance to other stress.We review the developments related to identification and utilization of various resistance genes to develop BB resistant rice varieties through marker-assisted breeding.

关键词： rice bacterial blight resistance gene marker-assisted breeding gene pyramiding

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A novel mutation in ACS11 leads to androecy in cucumber

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Journal of Integrative Agriculture 2023年第11期22卷 3312-3320页

作者： WANG Jie LI Shuai CHEN Chen ZHANG Qi-qi ZHANG Hui-min CUI Qing-zhi CAI Guang-hua ZHANG Xiao-peng CHAI Sen WAN Li YANG Xue-yong ZHANG Zhong-hua HUANG San-wen CHEN Hui-ming SUN Jin-jing College of Horticulture Qingdao Agricultural UniversityQingdao 266109P.R.China State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081P.R.China Hunan Vegetable Research Institute Hunan Academy of Agricultural SciencesChangsha 410125P.R.China Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124P.R.China Chinese Academy of Tropical Agriculture Sciences Haikou 571101P.R.China College of Horticulture Hunan Agricultural UniversityChangsha 410128P.R.China

Sex determination in plants gives rise to unisexual flowers. A better understanding of the regulatory mechanism underlying the production of unisexual flowers will help to clarify the process of sex determination in plants and allow researchers and farmers to harness heterosis. Androecious cucumber(Cucumis sativus L.) plants can be used as the male parent when planted alongside a gynoecious line to produce heterozygous seeds, thus reducing the cost of seed production. The isolation and characterization of additional androecious genotypes in varied backgrounds will increase the pool of available germplasm for breeding. Here, we discovered an androecious mutant in a previously generated ethyl methanesulfonate(EMS)-mutagenized library of the cucumber inbred line ‘406’. Genetic analysis, whole-genome resequencing, and molecular marker-assisted verification demonstrated that a nonsynonymous mutation in the ethylene biosynthetic gene 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 11(ACS11) conferred androecy. The mutation caused an amino acid change from serine(Ser) to phenylalanine(Phe) at position 301(S301F). In vitro enzyme activity assays revealed that this S301F mutation leads to a complete loss of enzymatic activity. This study provides a new germplasm for use in cucumber breeding as the androecious male parent, and it offers new insights into the catalytic mechanism of ACS enzymes.

关键词： cucumber androecy ethylene marker-assisted breeding

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breeding Novel Short Grain Rice for Tropical Region to Combine Important Agronomical Traits, Biotic Stress Resistance and Cooking Quality in Koshihikari Background

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Rice science 2021年第5期28卷 479-492,I0029-I0032页

作者： Uthomphon Saichompoo Possawat Narumol Pawat Nakwilai Peeranut Thongyos Aekchupong Nanta Patompong Tippunya Siriphat Ruengphayak Teerarat Itthisoponkul Niranee Bueraheng Sulaiman Cheabu Chanate Malumpong Department of Agronomy Faculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon Pathom 73140Thailand Tana Group International Co. Ltd.PhanChiang Rai 57120Thailand Rice Science Center&Rice Gene Discovery Unit Kasetsart UniversityKamphaeng Sean CampusNakhon Pathom 73140Thailand Faculty of Agricultural Product Innovation and Technology Srinakharinwirot UniversityBangkok 10110Thailand Faculty of Science Technology and Agriculture Yala Rajabhat UniversityMueangYala 95000Thailand Faculty cf Agriculture Princess ofNaradhiwas UniversityNarathiwat 96000Thailand

breeding program strategies to develop novel short grain white rice varieties such as japonica(short grain)that introgress biotic stress resistance and high grain quality have been developed usingindica rice(Pin Kaset+4 and Riceberry)for applications in japonica rice(Kashihikari)improvement.Fourbreeding lines showing promising agronomic performance with short grain and low amylose content(breeding lines showed high scores thatsimilar to Kashihikari.Two promising lines,KP48-1-5and KP48-1-9,which possessed a combination offour genes resistance to different biotic stresses(Bph3+TPS+Xa21+Pi-ta)and four genes for grainquality(G83+SSlla+w+badh2),were deveiaped using marker-assisted selection(MAS)with thepedigree method.The current study clearly illustrated the successful use of MAS in combining resistanceto multiple biotic stresses while maintaining a high yield potential and preferred grain quality.Moreover,the results indicated that this breeding program,which includes crossing temperate japonica with indica,can create novel short grain rice varieties adapted to a trapical environment like the japonica type.

关键词： marker-assisted breeding short grain rice grain quality biotic resistance

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marker-assisted pyramiding of soybean resistance genes R_(SC4),R_(SC8),and R_(SC14Q) to soybean mosaic virus

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Journal of Integrative Agriculture 2017年第11期16卷 2413-2420页

作者： WANG Da-gang ZHAO Lin LI Kai MA Ying WANG Li-qun YANG Yong-qing YANG Yun-hua ZHI Hai-jian College of Agriculture Nanjing Agricultural University/National Center for Soybean Improvement/National Key Laboratory for Crop Genetics and Germplasm Enhancement Crop Institute Anhui Academy of Agricultural Sciences/Anhui Key Laboratory of Crops Quality Improving

Soybean mosaic virus （SMV） is one of the major viral pathogens affecting soybean crops worldwide. Three SMV resistance genes, Rsc4, Rsc8, and Rsc14Q, have been identified and mapped on soybean chromosomes 14, 2, and 13 from Dabaima, Kefeng 1, and Qihuang 1 cultivars, respectively. Soybean cultivar Nannong 1138-2 is widely grown in the Yangtze River Valley of China. In this study, crosses were made between Qihuang l^Kefeng 1 and DabaimaxNannong 1138-2. Ten simple sequence repeat （SSR） markers linked to three resistance loci （Rsc4, Rsc8, and Rsc^4Q） were used to assist pyramided breeding. Pyramided families containing three resistance loci （Rsc4, Rsc8, and Rsc14Q） were evaluated by inoculating them with 21 SMV strains from China. Results indicated that the 10 markers can be used effectively to assist the selection of resistant individuals containing Rsc4, Rsc8, and Rsc14Q. A total of 53 F6 plants were confirmed to contain three homozygous alleles conferring resistance to SMV. Five F7 homozygous pyramided families exhibited resistance to 21 strains of SMV and showed desirable agronomic traits using dual selection. The strategy of pyramiding resistance gene derived from different varieties has practical breeding value in providing broad-spectrum resistance against the existing strains of SMV in China.

关键词： soybean soybean mosaic virus resistance genes pyramiding marker-assisted breeding

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