DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines

Abstract

Diversity analysis using molecular markers serves as a powerful tool in unravelling the intricacies of inclusivity within various populations and is an initial step in the assessment of populations and the development of inbred lines for host plant resistance in maize. This study was conducted to assess the genetic diversity and population structure of 242 newly developed S3 inbred lines using 3,305 single nucleotide polymorphism (SNP) markers and to also assess the level of homozygosity achieved in each of the inbred lines. A total of 1,184 SNP markers were found highly informative, with a mean polymorphic information content (PIC) of 0.23. Gene diversity was high among the inbred lines, ranging from 0.04 to 0.50, with an average of 0.27. The residual heterozygosity of the 242 S3 inbred lines averaged 8.8%, indicating moderately low heterozygosity levels among the inbred lines. Eighty-four percent of the 58,322 pairwise kinship coefficients among the inbred lines were near zero (0.00-0.05), with only 0.3% of them above 0.50. These results revealed that many of the inbred lines were distantly related, but none were redundant, suggesting each inbred line had a unique genetic makeup with great potential to provide novel alleles for maize improvement. The admixture-based structure analysis, principal coordinate analysis, and neighbour-joining clustering were concordant in dividing the 242 inbred lines into three subgroups based on the pedigree and selection history of the inbred lines. These findings could guide the effective use of the newly developed inbred lines and their evaluation in quantitative genetics and molecular studies to identify candidate lines for breeding locally adapted fall armyworm tolerant varieties in Ghana and other countries in West and Central Africa.

Fig 1. Distribution of informative single nucleotide polymorphism (SNP) marker parameters on the 1,184 SNP markers and heterozygosity of the 242 inbred lines.

Gene diversity (GD), Major allele frequency (MAF), Polymorphic information content (PIC), and Percent residual heterozygosity (%HET).

Fig 2. Structure analysis of the 242 inbred lines as revealed by Evanno’s admixture-based method.

A: Best delta K for the population structure obtained by the Evanno method was employed in STRUCTURE HARVESTER (Earl and vonHoldt, 2012). B: Population parameters for the subpopulations. Expected heterozygosity (He), Fixation index (Fst), Proportion of inbred lines in each subpopulation (PLS). C: Estimate of structure among the inbred lines with red, green, and blue representing subpopulations 1, 2, and 3, respectively.

Fig 3. Distribution of pairwise dissimilarity (A) and pairwise relative kinship (B) among the 242 inbred lines based on 1,184 SNP markers.

Fig 4. Principal coordinate (Right) and Neighbour Joining clustering (Left) view of the structure of the 242 inbred lines revealed by the 1,184 SNP markers.

Colouring of the PCoA and the NJ clustering is based on the grouping of the structure analysis; green represents subpopulation 2, red represents subpopulation 1, and black the admixture group. Names of inbred lines phenotypically classified as highly resistant, moderately resistant, and resistant to FAW are written in black font colour; those classified as tolerant to FAW are written in violet font colour; and those classified as susceptible to FAW are written in brown font colour.