View Full Table | Close Full ViewTable 1.

Descriptions of maize tissues used in this study.

 
Tissue name Tissue description Time of harvest
Leaves
Leaves (V2) Pooled leaves 20 d after sowing
Female
Preemergence cob (V15) Immature cob 10 d before cob emergence
Postemergence cob (VT) Whole cob Silk emergence
Silk (R1) Mature silk Anthesis
Ovule (R1) Mature ovule with stigma and style removed Anthesis
Male
Preemergence tassel (V18) Post meiotic whole tassel including anthers 10 d before tassel emergence
Postemergence tassel (VT) Post meiotic whole tassel including anthers Tassel emergence from whorl
Whole Anthers (VT) Whole anther including pollen dissected from tassel structural tissue Anthesis
Pollen (VT) Mature pollen Anthesis
Seed
Seed 5 DAP (R1) Whole seed 5 DAP
Seed 10 DAP (R2) Whole seed 10 DAP
Embryo 25 DAP (R4) Developing embryo 25 DAP
Endosperm 25 DAP (R4) Developing endosperm 25 DAP
Vegetative (V) and reproductive (R) growth development stages defined in the Iowa State University Extension Corn Field Guide (Abendroth et al., 2011).
DAP, days after pollination.



View Full Table | Close Full ViewTable 2.

Read mapping and expression summary for 13 maize tissues. Fragments per kilobase pair of exon model per million fragments mapped (FPKM) values were calculated using Cufflinks version 0.9.3 (Trapnell et al., 2010), the version 2 (v2) pseudomolecules, and the v2 annotation.

 
Tissue Number of purity filtered reads Number of mapped reads Maximum FPKM Number of expressed genes Number of tissue restricted genes
Leaves 17.1 million 14.5 million 128,735 21,956 492
Preemergence cob 18.3 million 16.0 million 17,256 23,338 70
Postemergence cob 18.3 million 15.8 million 17,784 23,948 44
Silk 18.9 million 16.8 million 257,614 23,015 138
Ovule 29.9 million 26.3 million 33,621 25,003 108
Preemergence tassel 19.8 million 17.0 million 24,576 25,165 88
Postemergence tassel 18.6 million 16.1 million 35,766 24,984 42
Whole anthers 27.0 million 24.0 million 127,465 22,178 96
Pollen 27.9 million 25.3 million 1,004,070 13,418 206
Seed 5 DAP 19.2 million 16.5 million 22,966 24,390 37
Seed 10 DAP 26.4 million 22.9 million 26,927 24,486 105
Embryo 25 DAP 19.9 million 17.0 million 36,127 22,493 188
Endosperm 25 DAP 23.6 million 20.3 million 283,698 22,887 251
Genes with a 95% confidence interval lower boundary FPKM value greater than zero were considered expressed.
Genes were considered tissue restricted when only one tissue within this study had a 95% confidence interval lower boundary FPKM value greater than zero.
§DAP, days after pollination.



View Full Table | Close Full ViewTable 3.

Spearman rank correlations of log2 expression values between ribonucleic acid sequencing (RNA-seq) and microarray based expression profiles. Eleven RNA-seq libraries generated in this study were compared to the most similar corresponding tissues in a maize microarray study (Sekhon et al., 2011). Three comparisons of dissimilar tissues were included as negative controls. Log2 expression values for a subset of 17,573 maize genes from the v1 annotation without multiple predicted isoforms and present in both data sets were correlated with the nonparametric Spearman rank correlation statistic (SAS Institute, 2003).

 
RNA-seq library Microarray experiment SCC Tissues types
Leaves (V2) First leaf (V3) 0.76 Similar
Preemergence cob (V15) Immature cob (V18) 0.82 Similar
Postemergence cob (VT) Prepollination cob (R1) 0.81 Similar
Silk (R1) Silks (R1) 0.78 Similar
Ovule (R1) Whole seed 2 DAP (R1) 0.79 Similar
Preemergence tassel (V18) Meiotic tassel (V18) 0.68 Similar
Whole anthers (VT) Anthers (R1) 0.74 Similar
Whole seed 5 DAP (R1) Whole seed 4 DAP (R1) 0.80 Similar
Whole seed 10 DAP (R2) Whole seed 10 DAP (R2) 0.81 Similar
Embryo 25 DAP (R4) Embryo 24 DAP (R4) 0.82 Similar
Endosperm 25 DAP (R4) Endosperm 24 DAP (R4) 0.74 Similar
Pollen (VT) Silks (R1) 0.30 Dissimilar
Leaves (V2) Endosperm 24 DAP (R4) 0.51 Dissimilar
Embryo 25 DAP (R4) Anthers (R1) 0.56 Dissimilar
Vegetative (V) and reproductive (R) growth development stages defined in the Iowa State University Extension Corn Field Guide (Abendroth et al., 2011).
SCC, Spearman correlation coefficient.
§DAP, days after pollination.



View Full Table | Close Full ViewTable 4.

Number of differentially expressed genes between each set of tissues. Differential expression analysis was conducted using the cuffdiff program in Cufflinks version 0.9.3 (Trapnell et al., 2010), the version 2 (v2) pseudomolecules, the v2 annotation, and false discovery rate of 0.01.

 
Preemergence cob Postemergence cob Silk Ovule Preemergence tassel Postemergence tassel Whole anthers Pollen Seed 5 DAP Seed 10 DAP Embryo 25 DAP Endosperm 25 DAP
Leaves 14,541 (75%) 14,195 (73%) 12,547 (69%) 14,930 (70%) 13,361 (70%) 12,795 (70%) 13,510 (83%) 13,578 (90%) 13,294 (69%) 14,022 (70%) 14,551 (77%) 13,793 (76%)
Preemergence cob 2653 (15%) 12,202 (63%) 8393 (41%) 13,677 (67%) 14,184 (70%) 15,664 (80%) 16,942 (90%) 10,869 (56%) 11,365 (57%) 9186 (50%) 12,527 (66%)
Postemergence cob 11,543 (60%) 6493 (32%) 12,869 (63%) 13,460 (67%) 15,494 (79%) 16,972 (90%) 9496 (50%) 10,519 (53%) 8689 (47%) 11,953 (63%)
Silk 11,049 (53%) 10,809 (56%) 11,123 (58%) 14,145 (76%) 15,966 (89%) 8781 (47%) 8694 (45%) 13,123 (69%) 12,623 (68%)
Ovule 12,263 (57%) 12,961 (60%) 16,316 (76%) 18,962 (90%) 8296 (40%) 10,472 (50%) 11,189 (54%) 12,649 (61%)
Preemergence tassel 3522 (19%) 12,514 (68%) 16,117 (88%) 10,160 (51%) 11,425 (56%) 13,691 (68%) 12,444 (64%)
Postemergence tassel 11,301 (66%) 14,942 (87%) 10,743 (55%) 11,972 (58%) 14,059 (71%) 12,891 (68%)
Whole anthers 9386 (83%) 14,811 (76%) 15,470 (76%) 15,161 (81%) 14,293 (80%)
Pollen 17,029 (90%) 17,886 (90%) 15,841 (90%) 15,275 (90%)
Seed 5 DAP 4810 (25%) 12,169 (63%) 12,083 (64%)
Seed 10 DAP 12,930 (65%) 12,533 (64%)
Embryo 25 DAP 11,088 (62%)
DAP, days after pollination.
Numbers in parenthesis indicate the percent of significantly different tests out of the total number of tests that could be performed for each pairwise comparison.