Abstract
Key messageMolecular characterization information on genetic diversity, population structure and genetic relationships provided by this research will help maize breeders to better understand how to utilize the current CML collection.CIMMYT maize inbred lines (CMLs) have been widely used all over the world and have contributed greatly to both tropical and temperate maize improvement. Genetic diversity and population structure of the current CML collection and of six temperate inbred lines were assessed and relationships among all lines were determined with genotyping-by-sequencing SNPs. Results indicated that: (1) wider genetic distance and low kinship coefficients among most pairs of lines reflected the uniqueness of most lines in the current CML collection; (2) the population structure and genetic divergence between the Temperate subgroup and Tropical subgroups were clear; three major environmental adaptation groups (Lowland Tropical, Subtropical/Mid-altitude and Highland Tropical subgroups) were clearly present in the current CML collection; (3) the genetic diversity of the three Tropical subgroups was similar and greater than that of the Temperate subgroup; the average genetic distance between the Temperate and Tropical subgroups was greater than among Tropical subgroups; and (4) heterotic patterns in each environmental adaptation group estimated using GBS SNPs were only partially consistent with patterns estimated based on combining ability tests and pedigree information. Combining current heterotic information based on combining ability tests and the genetic relationships inferred from molecular marker analyses may be the best strategy to define heterotic groups for future tropical maize improvement. Information resulting from this research will help breeders to better understand how to utilize all the CMLs to select parental lines, replace testers, assign heterotic groups and create a core set of breeding germplasm.
Highlights
Molecular characterization of genetic diversity, population structure and genetic relationships among elite breeding materials within a given set of maize germplasm is useful for understanding how to use the assembled germplasm for further improvement, such as selecting parental lines, assigning heterotic groups and creating a core set of germplasm
The remaining 570 single nucleotide polymorphisms (SNPs) that could not be mapped to any of the ten maize chromosomes were removed from the genetic characterization analyses performed in this study
GBS is a low coverage sequencing technology which results in a very high missing rate, for example, in both the 955,120 and 362,008 SNP datasets it is above 50 %, and high levels of missing data can be a problem for downstream analysis like association mapping
Summary
Molecular characterization of genetic diversity, population structure and genetic relationships among elite breeding materials within a given set of maize germplasm is useful for understanding how to use the assembled germplasm for further improvement, such as selecting parental lines, assigning heterotic groups and creating a core set of germplasm. Maize germplasm can be divided into two major groups—i.e., temperate and tropical germplasm—based on environmental characteristics, day length. The International Maize and Wheat Improvement Center (CIMMYT) focuses mainly on tropical maize germplasm improvement. CIMMYT maize inbred lines (CMLs) are carefully selected for good general combining ability and. From 1984 to 2003, CIMMYT developed and released 539 CMLs, which may well represent the total genetic diversity of improved tropical maize germplasm due to their wide distribution and great contribution to tropical maize breeding improvement
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