A High-Density Genetic Map Constructed for Maize (Zea mays L.) Based on Large-Scale SNP Discovery Using Whole-Genome Resequencing and Specific-Locus Amplified Fragments Sequencing (SLAF-Seq)

Maize is an important food and industrial material resource. We constructed a high-density genetic map using the whole-genome resequencing and specific-locus amplified fragments sequencing (SLAF-seq) techniques for the "HZS" and "X224M" elite maize inbred lines, and 196 F-2 individuals from a cross between "HZS" and "X224M." In our study, the average resequencing depth of the maternal and paternal parents was 13.30-fold and 11.94-fold, respectively. In the F-2 population, the sequencing depth ranged from 9.64-fold to 45.16-fold with an average of 23.18-fold. In total, 12, 354, 021 SNPs were detected in the F-2 population, and 87.78% of which were polymorphic. Among these SNPs, 2, 843, 917 (53.96%) were included in the segregation pattern aa x bb. Finally, 6, 186 SNPs were used to construct a high-density genetic map. The length of this map included all 10 chromosomes in maize and was 1, 667.36 cM, with an average distance of 0.318 cM between markers. The number of mapped SNPs in different linkage groups (LGs) ranged from 254 to 960, and the genetic distance of each LGs ranged from 157.22 to 192.72 cM. Based on the evaluation of haplotype and heat maps, the results indicated that our genetic map is of high quality, and we now have more detailed information for gene mapping and marker-assisted breeding.