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

Abstract

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4173-9) contains supplementary material, which is available to authorized users.

Hybrid Breeding for MLN Resistance: Heterosis, Combining Ability, and Hybrid Prediction

“…Average genetic distance reported was 0.37 which is comparable with the earlier findings [26][27][28]. Masuka et al, [26] reported distances ranging from 0.004 to 0.40 with a mean of 0.294 from the analysis of 53 parental lines and two F 2 populations derived from the CIMMYT Africa breeding program.…”

“…Beyene et al, [27] analyzed the genetic distances of 703 doubled haploids and reported distances ranging from 0.070 to 0.457 with an average of 0.355. Ertiro et al, [28] reported genetic distances which ranged from 0.011 to 0.346 with an average of 0.313 across pairwise combinations of 265 inbred lines. For Beyene et al, [27] most of the distances fell between 0.300 to 0.475 with a frequency of 69% and in addition, less than 5% of the distances fell below 0.10.…”

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

“…DAPC analysis divided the BSPG into four subpopulations (Fig 2), and this result was confirmed by the NJ phylogram of the SM distance of the whole population (Fig 3). To obtain the population structure, some studies have reported similar or better results for DAPC analysis than for the Bayesian model-based method [63,85–87] implemented in STRUCTURE software [88–90]. In addition, for complex genomes, several assumptions are not fulfilled with the use of STRUCTURE; therefore, the applicability of this algorithm may be limited in sugarcane [34,37,38,91].…”

Genetic diversity and population structure of Ethiopian Capsicum germplasms

“…It is helpful for genotyping without prior knowledge about the genome of the species and is useful for exploring plant genetic diversity on a genome-wide scale [4]. In the last few years, GBS has been used to investigate the genetic diversity of many crop species, including maize, rice, barley, tomato, wheat, sorghum, soybean, watermelon and Capsicum [21–28].…”