Seed vigor and seed germination are very important traits, determined by several factors including genetic and physical purity, mechanical damage, and physiological condition, characterized by maintaining a high seed vigor and stable content after storage. The search for molecular markers related to improvement in seed vigor under adverse condition is an important issue in maize breeding currently. Higher sowing quality of seeds is necessary for the development of the agriculture production and better ability to resist all kinds of adversity in the seeds’ storage. Condition is a very important factor affecting the yield of plants, thanks to the construction of their vitality. Identification of molecular markers associated with seed germination and seed vigor may prove to be very important in the selection of high-yielding maize varieties. The aim of this study was to identify and select new markers for maize (SNP and SilicoDArT) linked to genes influencing the seed germination and seed vigor in inbred lines of maize (Zea mays L.). The plant material used for the research was 152 inbred maize lines. The seed germination and seed vigor were analyzed. For identification of SNP and SilicoDArT markers related to the seed germination and seed vigor, the SilicoDarT technique developed by Diversity Arrays Technology was used. The analysis of variance indicated a statistically significant differentiation between genotypes for both observed traits. Positive (r = 0.41) correlation (p < 0.001) between seed germination and seed vigor was observed. As a result of next-generation sequencing, the molecular markers SilicoDArT (53,031) and SNP (28,571) were obtained. Out of 81,602 identified SilicoDArT and SNP markers, 15,409 (1559 SilicoDArT and 13,850 SNP) were selected as a result of association mapping, which showed them to be significantly related to the analyzed traits. The 890 molecular markers were associated with seed vigor, and 1323 with seed germination. Fifty-six markers (47 SilicoDArT and nine SNP) were significant for both traits. Of these 56 markers, the 20 most significant were selected (five of these markers were significant at the level of 0.001 for seed vigor and at the level of 0.05 for seed germination, another five markers were significant at the level of 0.001 for seed germination and at the level of 0.05 for seed vigor, five markers significant at the level of 0.001 only for seed vigor and five significant at the level of 0.001 only for seed germination also selected). These markers were used for physical mapping to determine their location on the genetic map. Finally, it was found that six of these markers (five silicoDArT—2,435,784, 4,772,587, 4,776,334, 2,507,310, 25,981,291, and one SNP—2,386,217) are located inside genes, the action of which may affect both seed germination and seed vigor. These markers can be used to select genotypes with high vigor and good seed germination.

Spectacular scientific advances in the area of molecular biology and the development of modern biotechnological tools have had a significant impact on the development of maize heterosis breeding. One technology based on next-generation sequencing is DArTseq. The plant material used for the research consisted of 13 hybrids resulting from the crossing of inbred maize lines. A two-year field experiment was established at two Polish breeding stations: Smolice and Łagiewniki. Nine quantitative traits were observed: cob length, cob diameter, core length, core diameter, number of rows of grain, number of grains in a row, mass of grain from the cob, weight of one thousand grains, and yield. The isolated DNA was subjected to DArTseq genotyping. Association mapping was performed using a method based on the mixed linear model. A total of 81602 molecular markers (28571 SNPs and 53031 SilicoDArTs) were obtained as a result of next-generation sequencing. Out of 81602, 15409 (13850 SNPs and 1559 SilicoDArTs) were selected for association analysis. The 105 molecular markers (8 SNPs and 97 SilicoDArTs) were associated with the heterosis effect of at least one trait in at least one environment. A total of 186 effects were observed. The number of statistically significant relationships between the molecular marker and heterosis effect varied from 8 (for cob length) and 9 (for yield) to 42 (for the number of rows of grain). Of particular note were three markers (2490222, 2548691 and 7058267), which were significant in 17, 8 and 6 cases, respectively. Two of them (2490222 and 7058267) were associated with the heterosis effects of yield in three of the four environments.