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Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China,India and the US using simple sequence repeat markers

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Journal of Integrative Plant Biology 2016年第5期58卷 452-465页

作者： Hui Wang Pawan khera Bingyan.Huang Mei Yuan Ramesh katam Weijian Zhuang karen Harris-Shultz kim M.Moore albert k.culbreath Xinyou Zhang Rajeev k.Varshney Lianhui Xie Baozhu Guo Fujian Agricultural and Forestry University College of Plant ProtectionFuzhou 350002China Department of Plant Pathology University of GeorgiaTiftonGA 31794USA USDA-ARS Crop Protection and Management Research UnitTiftonGA 31794USA Shandong Peanut Research Institute qingdao 266100China International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Patancheru 502324India Henan Academy of Agricultural Sciences Cash Crops Research InstituteZhengzhou 450002China Department of Biological Sciences Florida A&M UniversityTallahasseeFL 32307USA Fujian Agricultural and Forestry University College of Crop ScienceFuzhou 350002China USDA-ARS Crop Genetics and Breeding Research UnitTiftonGA 31794USA AgResearch Consultants Shingler Little River RoadSumnerGA 31789USA

Cultivated peanut is grown worldwide as rich- source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat （SSR） markers and to assess the genetic diversity and popuJation structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content （PIC） were 0.480 and o.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, o.489 and 0.47 with an average PIC of 0.323, 0.43 and o.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations （P1, P2）, which was consistent with the dendro- gram based on genetic distance （G1, G2） and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

关键词： Arachis hypogaea breeding genetic diversity populationstructure simple sequence repeat

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Identification of ExpIdentification of Expressed Resistance Gene Analogs from Peanut (Arachis hypogaea L.) Expressed Sequence Tags

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Journal of Integrative Plant Biology 2013年第5期55卷 453-461页

作者： Zhanji Liu Suping Feng Manish k. Pandey Xiaoping Chen albert k. culbreath Rajeev k. Varshney Baozhu Guo University of Georgia Department of Plant Pathology Shandong Academy of Agricultural Sciences High-Tech Research Center Qiongzhou University College of Bioscience and Biotechnology International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Guangdong Academy of Agricultural Sciences Crops Research Institute US Department of Agriculture Agricultural Research ServiceCrop Protection and Management Research Unit

Low genetic diversity makes peanut （Arachis hypogaea L.） very vulnerable to plant pathogens, causing severe yield loss and reduced seed quality. Several hundred partial genomic DNA sequences as nucleotide-binding-site leucine-rich repeat （NBS-LRR） resistance genes （R） have been identified, but a small portion with expressed transcripts has been found. We aimed to identify resistance gene analogs （RGAs） from peanut expressed sequence tags （ESTs） and to develop polymorphic markers. The protein sequences of 54 known R genes were used to identify homologs from peanut ESTs from public databases. A total of 1,053 ESTs corresponding to six different classes of known R genes were recovered, and assembled 156 contigs and 229 singletons as peanut-expressed RGAs. There were 69 that encoded for NBS-LRR proteins, 191 that encoded for protein kinases, 82 that encoded for LRR-Pk/transmembrane proteins, 28 that encoded for Toxin reductases, 11 that encoded for LRR-domain containing proteins and four that encoded for TM-domain containing proteins. Twenty-eight simple sequence repeats （SSRs） were identified from 25 peanut expressed RGAs. One SSR polymorphic marker （RGA121） was identified. Two polymerase chain reaction-based markers （Ahsw-1 and Ahsw-2） developed from RGA013 were homologous to the Tomato Spotted Wilt Virus （TSWV） resistance gene. All three markers were mapped on the same linkage group AhIV. These expressed RGAs are the source for RGA-tagged marker development and identification of peanut resistance genes.

关键词： Arachis hypogaea expressed sequence tags resistance gene analogs Tomato Spotted Wilt Virus.

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