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Comparative Gene Expression Analysis of Seed Development in Waxy and Dent Corn (Zea mays L.)
Plant Breed. Biotech. 2018;6:337-353
Published online December 1, 2018
© 2018 Korean Society of Breeding Science.

Kyu Jin Sa1, Ik-Young Choi2, Dae Hyun Park1, Ju Kyong Lee1*

1Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
2Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
Correspondence to: Ju Kyong Lee,, Tel: +82-33-250-6415, Fax: +82-33-255-5558
Received August 19, 2018; Revised October 9, 2018; Accepted October 10, 2018.
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
We used Illumina/HiSeq sequencing for analysis of gene expression profiling among four maize seed types (dent, CM3 and CM6; waxy, CM5 and CM19) at 10 DAP (days after pollination). A total of 88,993,000 (CM3), 103,817,340 (CM6), 103,139,640 (CM5), and 66,978,958 (CM19) sequence reads were generated with read lengths of about 0.9, 1.0, 1.0, and 0.7 billion bp, respectively. We obtained 69.1 (CM3), 71.0 (CM6), 71.2 (CM5), and 71.8% (CM19) high quality reads from the raw data and compared them with reference RNA sequences in a public DB (NCBI). It was revealed that mapped reads were 58%, 63%, 62%, and 62% of the EST reference in CM3, CM6, CM5 and CM19, respectively; and more than 51,000 genes were expressed based on RPKM criteria (over 0.25 value) in each CM3, CM6, CM5, and CM19 inbred line. In differentially expressed gene (DEG) analysis, we found that 3,527 genes were differentially expressed by at least two-fold with 1,709 upregulated in the two waxy inbred lines and 1,818 upregulated in the two dent inbred lines. We also detected genes for the sucrose and starch biosynthesis pathways based on BINs, and different expression patterns between waxy and dent inbred lines were shown for the gene set for starch synthesis, such as sh2, bt2, du1, wx1, and ae1. Although some genes were more expressed in dent lines, most genes for starch synthesis were much expressed in waxy lines. Especially, there was greater expression of the sus2 gene in both waxy lines compared with the dent lines.
Keywords : Maize, Waxy and dent corn, RNA sequence, Seed, Gene expression

December 2018, 6 (4)
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