qSTA2-2, a novel QTL that contributes to seed starch synthesis in Zea mays L.

Abstract

The seed storage materials accumulate during seed development, and are essential for seed germination and seedling establishment. Here we employed two bi-parental populations of an F2:3 population developed from a cross of improved 220 (I220, small seeds with low starch) and PH4CV (large seeds with high starch), as well as recombinant-inbred lines (RILs) of X178 (high starch) and its improved introgression line I178 (low starch), to identify the genes that control seed storage materials. We identified a total of 12 QTLs for starch, protein and oil, which explained 3.44–10.79% of the phenotypic variances. Among them, qSTA2-1 identified in F2:3 and qSTA2-2 identified in the RILs partially overlapped at an interval of 7.314–9.554 Mb, and they explained 3.44–10.21% of the starch content variation, so they were selected for further study. Fine mapping of qSTA2-2 with the backcrossed populations of I220/PH4CV in each generation narrowed it down to a 199.7 kb interval that contains 14 open reading frames (ORFs). Transcriptomic analysis of developing seeds from the near-isogenic lines (NILs) of I220/PH4CV (BC5F2) showed that only 11 ORFs were expressed in 20 days after pollination (DAP) seeds. Five of them were upregulated and six of them were downregulated in NILI220, and the differentially expressed genes (DEGs) between NILI220 and NILPH4CV were enriched in starch metabolism, hormone signal transduction and glycosaminoglycan degradation. Of the eleven NILI220 differential expressed ORFs, ORF4 (Zm00001d002260) and ORF5 (Zm00001d002261) carry 75% protein sequence similarity, both encodes an glycolate oxidase, were the possible candidates of qSTA2-2. Further analysis and validation indicated that mutation of the qSTA2-2 locus resulted in the dysfunction of ABA accumulation, the embryo/endosperm ratio and the starch and hormone levels.

Keywords

• QTL mapping
• seed starch
• transcriptomic analysis
• hormone