Selecting SNP markers reflecting population origin for cacao(Theobroma cacao L.)germplasm identification  

作　　者：Osman A.Gutiérrez Kathleen Martinez Dapeng Zhang Donald S.Livingstone Chris J.Turnbull Juan Carlos Motamayor 

机构地区：[1]USDA-ARS Subtropical Horticulture Research Station,13601 Old Cutler Road,Miami,FL 33158,USA [2]USDA-ARS,Beltsville Agricultural Research Center,SPCL,10300 Baltimore Avenue,Bldg.001,Rm.223,BARC-W,Beltsville,MD 20705,USA [3]Mars Wrigley Plant Science Laboratory,Davis,CA 95616,USA [4]School of Agriculture,Policy and Development,University of Reading,RG66AR,UK [5]Universal GeneticSolutions,LLC,Orlando,FL,USA

出　　处：《Beverage Plant Research》2021年第1期133-141,共9页饮料植物研究（英文）

基　　金：the USDA-ARSSHRS Development and Application of Genomic-assisted Breeding Strategies to Produce Disease-resistant Cacao Genetic Resources(Project No.6038-21000-025-000-D);Also funding for this projectwas provided by MARS,Inc.;Trust Agreement No.6038-21000-025-12-T:Genomic Enhancement of Theobroma cacao.

摘　　要：Cacao is one of the most economically important agricultural commodities in the world,providing the principal ingredient for the global chocolate industry.Accurate genotype identification is essential for effective conservation and utilization of cacao germplasm.Here,we report the screening of 956 candidate SNPs,pre-selected from the 6 and 15K Theobroma cacao SNP Arrays using targeted Genotyping-by-Sequencing on 451 cacao germplasm accessions,representing ten known genetic groups from the tropical Americas.Based on call rate(No call rate<5%),Minor Allele Frequency(MAF>0.15)and Linkage Disequilibrium(LD≤0.5),a total of 219 SNPs were selected.The efficacy of these SNP markers for population classification was compared with the previous SSR-based analysis in cacao.The population assignment results of the retained 420 cacao accessions was highly comparable with the SSR study.The matrix of genetic distance between SSR and SNP markers is highly correlated(r=0.718;P<0.001).These results demonstrated the consistency in using the present SNP markers for cacao germplasm identification.This is our pilot project for the development of SNP markers reflecting population origin for cacao germplasm identification.These SNP markers and the selected reference germplasm for different populations are suitable for use in cacao germplasm management and crop improvement,including genotype identification,seed gardens and nursery accreditation,and cocoa authentication.Effort is being continued with the emphasis on selecting SNP markers for the detection of sub-population structures in the primary gene pool of T.cacao.

关 键 词：GERMPLASM ORIGIN continued 

分 类 号：F75[经济管理—国际贸易]