DOI: 10.5061/dryad.rfj6q57g6
title: Data for: Defective kernel 66 encodes a GTPase essential for kernel development in maize

description: Mitochondria is a semi-autonomous organelle that provides energy for cell
 activities through oxidative phosphorylation. In this study, we identified
 a defective kernel 66 (dek66)-mutant maize with defective kernels. We
 characterized the candidate gene DEK66, encoding a ribosomal
 assembly factor, located in mitochondria, and possessing GTPase activity
 (the GTPase belonged to ribosome biogenesis GTPase A family). In the dek66
 mutant, abolishment of mitochondrial structure and function led to the
 accumulation of reactive oxygen species and promoted programmed cell death
 in endosperm cells. Furthermore, transcript levels of most of the key
 genes associated with nutrient storage, mitochondrial respiratory chain
 complex, and mitochondrial ribosomes in the dek66 mutant were
 significantly altered. Collectively, the results suggested that DEK66 is
 essential for the development of maize kernels via affecting mitochondrial
 function. This study provided a reference to understand the impact of
 mitochondrial ribosomal assembly factors in maize kernel development.
description: # Data for: Defective kernel 66 encodes a GTPase essential for kernel
 development in maize Primary data in experimental procedures and
 results.This file is intended to provide key information for understanding
 and reuse of the dataset “Defective kernel 66 encodes a GTPase essential
 for kernel development in maize”. ## Description of the data and file
 structure Each figure plate corresponds to a sheet in the excel file. The
 content marked in bright yellow and bright blue in each datasheet
 represent the Figure number and line headers, respectively. The contents
 in parentheses in the line headers is the unit of each parameter. 1. Fig.
 1G The statistical data of the length of per kernel of WT and dek66 2.
 Fig. 1H The statistical data of the width of per kernel of WT and dek66 3.
 Fig. 1I The statistical data of hundered-grain weight of WT and dek66 4.
 Fig.2D Quantification of zein, non-zein, and total protein contents in WT
 and dek66 mature endosperm <br> repeat 1, repeat 2, repeat 3
 technical replicates A595 absorbance value at 595nm 1/2 total The total
 protein diluted by twice 1/2 ZEIN The zein protein diluted by twice 1/2
 Non-ZEIN The Non-zein protein diluted by twice 5. Fig.2I, J The raw data
 of starch content per kernel <br> WT1, WT2, WT3 biological
 replicates dek66-1, dek66-2, dek66-3 biological replicates A510 absorbance
 value of sample at 510nm ODck absorbance value of the control at 510nm
 ODstandard absorbance value of the standard solution at 510nm 6. Fig. 2K
 The raw data of the soluble sugars content in WT and dek66 endosperm
 <br> A620 absorbance value at 620nm Ack absorbance value of the
 control at 620nm WT1, WT2...WT6 biological replicates dek66-1,
 dek66-2...dek66-6 biological replicates g edosperm weight in gram (g) 7.
 Fig. 2L The raw data of carbon/nitrogen (C/N) ratio in mature WT and dek66
 endosperm 8. Fig. 4B Expression pattern analysis of DEK66 <br> Ratio
 expression level of DEK66 Ratio Error Standard deviation (SD) of three
 biological replicates YL young leaves OL old leaves 5 DAP, 10 DAP, 15 DAP,
 20 DAP the seeds of 5, 10, 15, and 20 days after pollination 9. Fig. 4D
 Kinetic analysis of GTP hydrolysis rates of DEK66 proteins <br> GTP
 (mM) the concentration of GTP standard solution concentration of Pi (μM)
 the concentration of Pi in three technical replicates 10. Fig. 5A, S8
 Mitochondrial gene expression analysis WT1, WT2...WT6 biological
 replicates dek66-1, dek66-2...dek66-6 biological replicates n/a invalid
 data 11. Fig. 6C Alternate oxidase gene (ZmAOX1, ZmAOX2, ZmAOX3)
 expression analysis Mean the average value of three/six biological
 replicates SD Standard deviation (SD) of three/six biological replicates N
 the numbers of biological replicates 12. Fig. 7C Concentration of H2O2 in
 15 DAP endosperm of WT and dek66 standard solution (μM) the concentration
 of GTP standard solution A560 absorbance value at 560nm WT1, WT2...WT6
 biological replicates dek66-1, dek66-2...dek66-6 biological replicates
 repeat 1, repeat 2, repeat 3 absorbance value at 560nm of three technical
 replicates 13. Fig. 7D Expression analysis of NADPH oxidase family genes
 in 15 DAP endosperm of WT and dek66 WT1, WT2, WT3 biological replicates
 dek66-1, dek66-2, dek66-3 biological replicates Ratio expression level of
 DEK66 Ratio Error Standard deviation (SD) of three biological replicates
 14. Fig. 7E Expression analysis of antioxidant-related genes in 15 DAP
 endosperm of WT and dek66 AOX2 alternative oxidase 2 APX4 ascorbate
 peroxidase 4 CAT1 catalase 1 GST4 glutathione-S-transferase 4 POX1
 guaiacol peroxidase 1 POX3 guaiacol peroxidase 3 SOD3 superoxide dismutase
 3 SOD4A superoxide dismutase 4A Ratio expression level of DEK66 Ratio
 Error Standard deviation (SD) of three biological replicates 15. Fig. S6B
 qPCR assay of DEK66 mRNA level of transgenic lines CK non-transgenic
 control OE-1, OE-2, OE-3 three independent overexpression transgenic lines
 Ratio expression level of DEK66 Ratio Error Standard deviation (SD) of
 three biological replicates 16. Fig. S6K The statistical data of the
 length of per kernel CK non-transgenic control OE-1, OE-2, OE-3 three
 independent overexpression transgenic lines 17. Fig. S6L The statistical
 data of the width of per kernel CK non-transgenic control OE-1, OE-2, OE-3
 three independent overexpression transgenic lines 18. Fig. S6M The
 statistical data of hundered-grain weight CK non-transgenic control OE-1,
 OE-2, OE-3 three independent overexpression transgenic lines 19. Fig. S9
 raw data of RNAseq for differentially expressed genes <br> MT\_1,
 MT\_2, MT\_3 Three biological repeats of dek66 WT\_1, WT\_2, WT\_3 Three
 biological repeats of WT log2FoldChange It represents the log2-transformed
 fold change, indicating the difference in gene expression levels lfcSE
 Log2 Fold Change Standard Error stat Statistic pvalue a statistical test
 that represents the probability of observing a difference under the
 assumption of no difference padj Adjusted P-Value baseMean It serves as
 the foundation for calculating differential expression 20. Fig. S10 raw
 data of RNAseq for genes of interest (DEGs related to mitochondria)
 <br> MT\_1, MT\_2, MT\_3 Three biological repeats of dek66 WT\_1,
 WT\_2, WT\_3 Three biological repeats of WT log2FoldChange It represents
 the log2-transformed fold change, indicating the difference in gene
 expression levels lfcSE Log2 Fold Change Standard Error stat Statistic
 pvalue a statistical test that represents the probability of observing a
 difference under the assumption of no difference padj Adjusted P-Value
 baseMean It serves as the foundation for calculating differential
 expression 21. Fig. S11 Polysome profiling assay with sucrose density
 gradient <br> A254 absorbance value at 254nm 10-1, 10-2, 10-3, 10-4,
 10-5 The sample from 10% sucrose solution 15-1, 15-2, 15-3, 15-4, 15-5 The
 sample from 15% sucrose solution 20-1, 20-2, 20-3, 20-4, 20-5 The sample
 from 20% sucrose solution 25-1, 25-2, 25-3, 25-4, 25-5 The sample from 25%
 sucrose solution 30-1, 30-2, 30-3, 30-4, 30-5 The sample from 30% sucrose
 solution 35-1, 35-2, 35-3, 35-4, 35-5 The sample from 35% sucrose solution
 40-1, 40-2, 40-3, 40-4, 40-5 The sample from 40% sucrose solution 45-1,
 45-2, 45-3, 45-4, 45-5 The sample from 45% sucrose solution