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

BMC Genomics

Research Article

Temesgen Chibsa¹  Berhanu Tadesse Ertiro¹  Girum Azmach¹  Tolera Keno¹  Beyene Abebe¹  Kassa Semagn²  Maryke Labuschagne³  Abebe Menkir⁴  Biswanath Das⁵  Michael Olsen⁵  Mosisa Worku⁵  Veronica Ogugo⁵  Dagne Wegary⁶ 

[1] Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Bako, West Shoa, Oromia, Ethiopia;Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, T6G 2P5, Edmonton, AB, Canada;Department of Plant Sciences, University of Free State, Bloemfontein, South Africa;International Institute of Tropical Agriculture, Oya road PMB, 5320, Ibadan, Nigeria;International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, 00621, Nairobi, Kenya;International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 5689, Addis Ababa, Ethiopia;

关键词: Distance;    GBS;    Genetic purity;    Heterogeneity;    Heterotic grouping;    Kinship;    Population structure;   

DOI  :  10.1186/s12864-017-4173-9

 received in 2016-11-15, accepted in 2017-10-05,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMolecular 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).ResultsOnly 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2017