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

The seed storage materials are accumulated during seed development, and also essential for seed germination, seedling establishment. Here we employed two bi-parental populations of an F2:3 population developed from a cross of improved 220 (I220, small seed with low starch) and PH4CV (large seed with high starch), as well as RILs of X178 (high starch) and its improved introgression line I178 (low starch), to identify genes that control the seed storage materials. Totally we identified 12 QTLs for starch, protein and oil, which explained the 3.44-10.79% of phenotypic variances. Among that, qSTA2-1 identified in F2:3 and qSTA2-2 identified in RILs are partially overlapped at an interval of 7.314-9.554 Mb, explains 3.44-10.21% of starch content, was selected for further study. Fine mapping of qSTA2-2 with the backcrossed populations of I220/PH4CV in each generation narrow down to a 199.7 Kb interval, contains 14 ORFs. Transcriptomic analysis of the developing seeds from NILs of I220/PH4CV (BC5F2) showed that only 11 ORFs expressed in 20 DAP seeds, and 5 of them upregulated and 6 of them downregulated in NILI220, the DEGs between NILI220 and NILPH4CV were enriched in starch metabolism, hormone signal transduction and glycosaminoglycan degradation. For those 5 NILI220 down-regulated ORFs, ORF4 (Zm00001d002260) that encodes an acetalate dehydrogenase, was possible the candidate of qSTA2-2. Further analysis and validation indicated that the mutation of qSTA2-2 locus resulted in the dysfunction of ABA accumulation, embryo/endosperm ratio besides the starch and hormones.