Genetic Relationships and Population Structure among Maize (Zea mays L.) Landraces as Revealed by Simple Sequence Repeat Markers

Abstract

A set of 48 maize (Zea mays L.) genotypes, including landraces, some hybrids and inbreds, was characterized using 34 simple sequence repeat markers distributed throughout the genome. The 34 SSR primers produced bands in the range of 2 to 6 with an average of 3.2 bands per primer. The size range of these bands varied from 90 to 310 bp. Genetic similarity calculated using Jaccard’s coefficient varied from 0.122 to 0.750 with a mean of 0.475. Gene diversity or expected heterozygosity varied from 0.208 to 0.805, averaging 0.502. The average PIC was 0.433, with a range of 0.078 to 0.776. The range of resolving power was from 0.17 to 2.15 and marker index ranged from 0.16 to 4.83. Cluster analysis using the unweighted pair group method with arithmetic mean showed two major clusters with minor sub-clusters. The first three principal coordinates accounted for 26.7% of the total variation. Principal coordinates analysis and population structure aided in further elucidation of the genetic relationships as well as differentiation of genotypes. Analysis of variance revealed 81.7% within population variation and 18.3% between population variation. The analysis also led to the identification of specific and highly informative SSR markers, namely BNLG 1182, BNLG 1175, UMC 1353, BNLG 1159, BNLG 1272 and BNLG 1045, which significantly contributed to the differentiation of the material.