Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers 英文参考文献.docVIP
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Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers 英文参考文献
GeneticCharacterizationandLinkageDisequilibrium
EstimationofaGlobalMaizeCollectionUsingSNP
Markers
JianbingYan1,2,TrusharShah3,MarilynL.Warburton4*,EdwardS.Buckler5,6,7,MichaelD.McMullen8,9
,
JonathanCrouch1
1GeneticResourcesProgram,InternationalMaizeandWheatImprovementCenter,MexicoCity,Mexico,2DepartmentofBioinformatics,InternationalCropsResearch
Institute for the Semi-Arid Tropics, Hyderabad, India, 3National Maize Improvement Center of China, China Agriculture University, Beijing, China, 4Corn Host Plant
ResistanceResearchUnit,UnitedStatesDepartmentofAgriculture,AgriculturalResearchService,Starkville,Mississippi,UnitedStatesofAmerica,5InstituteforGenomic
Diversity,CornellUniversity,Ithaca,NewYork,UnitedStatesofAmerica,6Plant,SoilandNutritionResearchUnit,UnitedStatesDepartmentofAgriculture,Agricultural
ResearchService,Ithaca,NewYork,UnitedStatesofAmerica,7DepartmentofPlantBreedingandGenetics,CornellUniversity,Ithaca,NewYork,UnitedStatesofAmerica,
8DivisionofPlantSciences,UniversityofMissouri,Columbia,Missouri,UnitedStatesofAmerica,9PlantGeneticsResearchUnit,UnitedStatesDepartmentofAgriculture,
AgriculturalResearchService,Columbia,Missouri,UnitedStatesofAmerica
Abstract
AnewlydevelopedmaizeIlluminaGoldenGateAssaywith1536SNPsfrom582lociwasusedtogenotypeahighlydiverse
globalmaizecollectionof632inbredlinesfromtemperate,tropical,andsubtropicalpublicbreedingprograms.Atotalof
1229informativeSNPsand1749haplotypeswithin327lociwasusedtoestimatethegeneticdiversity,populationstructure,
and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial
relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within
chromosomes,allelicfrequencygroups,subgroupsrelatedbygeographicorigin,andsubgroupsofdifferentsamplesizes.
TheLDdecaydistancedifferedamongchromosomesandrangedbetween1to10kb.TheLDdistanceincreasedwiththe
increaseofminorallelicfrequency(MAF),andwithsmallersamplesize
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