Single nucleotide polymorphisms (SNPs) are abundantly and evenly distributed throughout the genomes of most plant species. These markers have become popular for use in genetic research in many crops. SNP markers can be used to screen maize cultivars rapidly during the early growth stages. In this study, to develop additional SNP markers for maize, we chose 20 SNP sites per chromosome from the maizeGDB website (www.maizegdb.org) and designed primers with two base pair mismatches using Primer Designer 4 based on putative SNP sites of the B73 genome sequence. The polymerase chain reaction (PCR) products ranged from 200 to 500 bp in size, whereas no PCR product was detected when the SNP site was present in Korean waxy corn. Using nine Korean commercial F₁ hybrids of waxy corn, including Chalok 1, Chalok 4, Ilmichal, Eolrukchal 1, Heukjinjuchal, Hayanchal 95, Mibaekchal, Mibaek 2, and Miheukchal, we selected 16 primer sets showing clear bands or no bands. Based on cluster analysis, we confirmed that the nine Korean waxy corn hybrids could clearly be distinguished. The SNP marker sets are easy to utilize through simple PCR and agarose gel electrophoresis. These results suggest that analysis using the SNP marker set designed in this study would be faster, cheaper, and more reproducible than that using other genotyping tools, such as cleaved amplified polymorphic sequence markers, which require the use of restriction enzymes.

Bacterial leaf pustule (BLP) caused by Xanthomonas axonopodis pv. glycines (Xag) is a serious disease in soybean. To investigate the role of transcription factors (TFs) in plant defense mechanisms under Xag treatment, soybean near-isogenic lines (NILs) carrying BLP-susceptible and BLP-resistant allele were analyzed by RNA-seq. A total of 2,415 differentially expressed genes were identified at 0, 6, and 12 hr after Xag infection. Using SoyDB and SoybeanTFDB (soybean TF databases), a total of 351 differentially expressed TF genes were identified, of which 80% were top ten major TF families. Among 351 TF genes, 263 and 40 were up-regulated and down-regulated, repectively, in BLP-resistant NIL compared to that in BLP-susceptible NIL at the three time points (0, 6, and 12 hr) after Xag infection. The rest 48 TF genes were either up-regulated or down-regulated at each time period in BLP-resistant NIL. Most TF genes were highly up-regulated in the BLP-resistant NIL at 0 hr. Additionally, cis-regulatory elements (CREs) involving in regulation of stress-responsive transcription, ABRE, G-box, MYBR, MYCR, and W-box were investigated. A total of 1,092 downstream genes were identified. Our results will improve the understanding on how plant immunity occurs via TFs and CREs.

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