Xia Zhang, Karl J. Haro von Mogel, Vai S. Lor, Candice N. Hirsch, Brian De Vries, Heidi F. Kaeppler, William F. Tracy, and Shawn M. Kaeppler

PNAS October 8, 2019 116 (41) 20776-20785

Significance

Maize sugary enhancer1 (se1) is a genetic modifier of su1 expression and is a commercially important allele that modifies kernel carbohydrate metabolism and improves fresh market quality. Carbohydrates, and primarily starch, are a major globally important product of cereal grains, but mechanisms affecting grain composition and genetic networks are not fully understood. In this study, we identify a gene that affects endosperm carbohydrate composition by modifying metabolism in a sugary1 background. This discovery provides another entry point to understand metabolism and genetic background effects in cereal grains.

Abstract

sugary enhancer1 (se1) is a naturally occurring mutant allele involved in starch metabolism in maize endosperm. It is a recessive modifier of sugary1 (su1) and commercially important in modern sweet corn breeding, but its molecular identity and mode of action remain unknown. Here, we developed a pair of near-isogenic lines, W822Gse (su1-ref/su1-ref se1/se1) and W822GSe (su1-ref/su1-ref Se1/Se1), that Mendelize the se1 phenotype in an su1-ref background. W822Gse kernels have lower starch and higher water soluble polysaccharide and sugars than W822GSe kernels. Using high-resolution genetic mapping, we found that wild-type Se1 is a gene Zm00001d007657 on chromosome 2 and a deletion of this gene causes the se1 phenotype. Comparative metabolic profiling of seed tissue between these 2 isolines revealed the remarkable difference in carbohydrate metabolism, with sucrose and maltose highly accumulated in the mutant. Se1 is predominantly expressed in the endosperm, with low expression in leaf and root tissues. Differential expression analysis identified genes enriched in both starch biosynthesis and degradation processes, indicating a pleiotropic regulatory effect of se1. Repressed expression of Se1 and Su1 in RNA interference-mediated transgenic maize validates that deletion of the gene identified as Se1 is a true causal gene responsible for the se1 phenotype. The findings contribute to our understanding of starch metabolism in cereal crops.

See https://www.pnas.org/content/116/41/20776

Figure 2:

Genetic mapping of Se1. (A) Location of Se1 region on chromosome 2 indicated by the red box near the distal end. (B) Locus zoom of the Se1 region in B73 showing the 1.26 Mb between the markers Agt1 and UMC1736. Mapping markers and the number of recombinant plants with the Se1 genotype from the mapping population are indicated by the vertical lines and associated numbers. (C) Locus zoom of the 24-kb region surrounding Se1 in B73, with gene models indicated by the blue and yellow bars. AC217415.3_FG004 (Se1) is renamed Zm00001d007657 in gene model set Zm00001d.2 for assembly version Zm-B73-REFERENCE-GRAMENE-4.0. (D) Mapping data from 3 proximal and 3 distal recombinants (identified on the left). Vertical lines indicate marker locations. The purple bar represents regions Se1/se1 genotypes, teal indicates se1/se1 genotype, and gray indicates unknown genotype between markers. The genotypes of recombinants at the Se1 locus were determined by sequencing. All recombinants shown and homozygous se1/se1 controls possessed the deletion indicated by the light blue box and dotted lines, and all other gene models were excluded by the markers used for fine mapping.