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    Genetic variation and population structure of maize inbred lines adapted to the midaltitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers

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    U17ArtErtiroGeneticInthomDev.pdf (1.310Mb)
    Date
    2017
    Author
    Ertiro, B.T.
    Semagn, K.
    Das, B.
    Olsen, M.
    Labuschagne, M.T.
    Worku, M.
    Wegary, D.
    Azmach, G.
    Ogugo, V.
    Keno, T.
    Abebe, B.
    Chibsa, T.
    Menkir, A.
    Type
    Journal Article
    Target Audience
    Scientists
    Metadata
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    Abstract/Description
    Background Molecular characterization is important for efficient utilization of germplasm and development of improved varieties. In the present study, we investigated the genetic purity, relatedness and population structure of 265 maize inbred lines from the Ethiopian Institute of Agricultural Research (EIAR), the International Maize and Wheat Improvement Centre (CIMMYT) and the International Institute of Tropical Agriculture (IITA) using 220,878 single nucleotide polymorphic (SNP) markers obtained using genotyping by sequencing (GBS). Results Only 22% of the inbred lines were considered pure with <5% heterogeneity, while the remaining 78% of the inbred lines had a heterogeneity ranging from 5.1 to 31.5%. Pairwise genetic distances among the 265 inbred lines varied from 0.011 to 0.345, with 89% of the pairs falling between 0.301 and 0.345. Only <1% of the pairs had a genetic distance lower than 0.200, which included 14 pairs of sister lines that were nearly identical. Relative kinship analysis showed that the kinship coefficients for 59% of the pairs of lines was close to zero, which agrees with the genetic distance estimates. Principal coordinate analysis, discriminant analysis of principal components (DAPC) and the model-based population structure analysis consistently suggested the presence of three groups, which generally agreed with pedigree information (genetic background). Although not distinct enough, the SNP markers showed some level of separation between the two CIMMYT heterotic groups A and B established based on pedigree and combining ability information. Conclusions The high level of heterogeneity detected in most of the inbred lines suggested the requirement for purification or further inbreeding except those deliberately maintained at early inbreeding level. The genetic distance and relative kinship analysis clearly indicated the uniqueness of most of the inbred lines in the maize germplasm available for breeders in the mid-altitude maize breeding program of Ethiopia. Results from the present study facilitate the maize breeding work in Ethiopia and germplasm exchange among breeding programs in Africa. We suggest the incorporation of high density molecular marker information in future heterotic group assignments.
    http://dx.doi.org/10.1186/s12864-017-4173-9
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/2391
    Digital Object Identifier (DOI)
    http://dx.doi.org/10.1186/s12864-017-4173-9
    IITA Subjects
    Maize
    Agrovoc Terms
    Distance; Maize; Population Structure; Gbs; Genetic Purity; Heterogeneity; Heterotic Grouping; Kinship
    Regions
    Africa; East Africa
    Countries
    Ethiopia
    Journals
    BMC Genomics
    Collections
    • Journal and Journal Articles4835
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