title: Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines.
abstract: BACKGROUND
  Genetic diversity provides the capacity for plants to meet changing environments. It is fundamentally important in crop improvement. Fifty-nine local maize lines developed at INERA and 41 exotic (temperate and tropical) inbred lines were characterized using 1057 SNP markers to (1) analyse the genetic diversity in a diverse set of maize inbred lines; (2) determine the level of genetic diversity in INERA inbred lines and patterns of relationships of these inbred lines developed from two sources; and (3) examine the genetic differences between local and exotic germplasms.
  
  
  RESULTS
  Roger's genetic distance for about 64% of the pairs of lines fell between 0.300 and 0.400. Sixty one per cent of the pairs of lines also showed relative kinship values of zero. Model-based population structure analysis and principal component analysis revealed the presence of 5 groups that agree, to some extent, with the origin of the germplasm. There was genetic diversity among INERA inbred lines, which were genetically less closely related and showed a low level of heterozygosity. These lines could be divided into 3 major distinct groups and a mixed group consistent with the source population of the lines. Pairwise comparisons between local and exotic germplasms showed that the temperate and some IITA lines were differentiated from INERA lines. There appeared to be substantial levels of genetic variation between local and exotic germplasms as revealed by missing and unique alleles.
  
  
  CONCLUSIONS
  Allelic frequency differences observed between the germplasms, together with unique alleles identified within each germplasm, shows the potential for a mutual improvement between the sets of germplasm. The results from this study will be useful to breeders in designing inbred-hybrid breeding programs, association mapping population studies and marker assisted breeding.
authors.affiliation: Institute of Environment and Agricultural Research (INERA), BP 910, Bobo-Dioulasso, Burkina Faso. adao@wacci.edu.gh.
authors.forename: Abdalla
authors.initials: A
authors.lastname: Dao
authors.affiliation: Institute of Environment and Agricultural Research (INERA), BP 910, Bobo-Dioulasso, Burkina Faso. jsanou24@yahoo.fr.
authors.forename: Jacob
authors.initials: J
authors.lastname: Sanou
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA. sem30@cornell.edu.
authors.forename: Sharon E
authors.initials: SE
authors.lastname: Mitchell
authors.affiliation: Department of Plant Breeding and Genetics, 520 Bradfield Hall, Cornell University, Ithaca, NY, 14850, USA. vg45@cornell.edu.
authors.forename: Vernon
authors.initials: V
authors.lastname: Gracen
authors.affiliation: West Africa Centre for Crop Improvement (WACCI), University of Ghana, BMP 30, Accra, Legon, Ghana. edanquah@wacci.edu.gh.
authors.forename: Eric Y
authors.initials: EY
authors.lastname: Danquah
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D005787:Gene Frequency; D017343:Genes, Plant; D005819:Genetic Markers; D006824:Hybridization, Genetic; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D003313:Zea mays / Q000235:genetics*
chemical_list: D005819:Genetic Markers