Table 1: Transcripts and physiological/biochemical parameters, which showed similar correlative patterns with the change in the amount or rate of accumulation of sugars, amylose, amylopectin, and A- and B-granule. The expression patterns of genes in developing caryopses of spring wheat T. aestivum cv. Bobwhite were examined using RNA from six time-points with 3 biological replicates for each time-point. The gene expression patterns that correlated with the accumulation profiles of the physiological/biochemical parameters were identified using the Pearson Correlation module in GeneSpring GX Software (Santa Clara, CA). Only genes with Pearson’s correlation coefficient (r-value) are shown. The Gene ID and closest BLAST N hit description (cut-off -value 10-10; DNA database release 144) of each transcript are indicated. NA denotes not applicable. Species abbreviations—Os: Orzya sativa, Ta: Triticum aestivum; Tt: Triticum turgidum; Aegilops markgrafii (Am); At: Arabidopsis thaliana; Hv: Hordeum vulgare; Bo: Bambusa oldhamii.

Gene name (Species) GenBank ID (A) Sugars Sucrose (mg/gDW) putative transcription factor BTF3 (Os) BG263006 sucrose:fructan 6-fructosyltransferase (Ta) BQ806964 ATP/ADP carrier protein (Tt) BE426214 putative cytosolic 6-phosphogluconate dehydrogenase (Zm) BE499049 putative transcription factor (Os) BE422879 Fructose (mg/gDW) (top 10 genes) OsCDPK protein (Os) BE424694 Phosphoglucomutase (Ta) BF484585 Vacuolar invertase1 (Ta) BE470578 Putative aldose reductase (Os) BE426211 Putative myb protein (Os) BM134356 0.19 dimeric alpha-amylase inhibitor (Am) BE425004 Kelch repeat-containing F-box family protein-like (Os) BQ805590 Putative DNA methyltransferase DMT106 (Os) BG274989 Putative UDP-glucose dehydrogenase (Os) BQ804766 Transmembrane protein kinase (Os) BG604519 Glucose (mg/gDW) (top 10 genes) Calmodulin (Zm) BE495028 14-3-3 protein homologue (Hv) BE424346 Putative transcription factor (Os) BE404468 Cold shock protein-1 (Ta) BF146102 Phosphoglucomutase (Ta) BF484585 Putative transcription factor PCF3 (Os) BQ838703 Auxin responsive protein-like (Os) BF429053 Putative UDP-glucose dehydrogenase (Os) BQ804766 Putative phosphogluconate dehydrogenase (Os) BQ806618 Putative aldose reductase (Os) BE426211 (A) Amylose and Amylopectin Percentage Amylose Amylose amount (mg/gDW) NA Alpha-gliadin (Ta) BE399594 Fresh weight per caryopsis NA B-granule % volume NA Gamma-gliadin (Ta) BE422921 Amylose rate (mg caryopsis/day) NA Amylose amount (mg/caryopsis) NA Gamma-gliadin (Ta) BE422980 Percentage Amylopectin (top 10 genes) Auxin-induced protein (Saccharum hybrid cultivar) BE444720 Putative zinc finger protein (Os) BG604730 Triose phosphate translocator (Ta) BE488921 Putative OsLRK1(receptor-type protein kinase) (Os) BG607784 Putative pyruvate dehydrogenase E1 beta subunit (Os) BE494481 Putative alkaline/neutral invertase (Os) BQ806650 Putative zinc finger protein (Os) BF201579 MADS box transcription factor (Ta) BF429033 Thioredoxin H (Ta) BE423204 Putative pyruvate dehydrogenase E1 beta subunit (Os) BE399382 Amylose rate (mg/gDW/day) Sucrose synthase (Type I) (Hv) BF474552 Brittle-1 protein; chloroplast precursor BE399058 Sucrose synthase 2 (Bo) BE498731 BRI1-KD interacting protein 103 (Os) BE424602 DnaJ domain family (At) BE497111 Nuclear inhibitor of PP1-like (Os) BE637971 (B) Starch granules A-granule number % (top 10 genes) Putative TATA box-binding protein associated factor 10 (Os) BE399264 Putative DEAD BOX RNA helicase (Os) BE404899 MADS box transcription factor (Ta) BF429033 Adenosine kinase (Zm) BE424366 Glucose-6-phosphate dehydrogenase (Ta) BF291587 Granule-bound starch synthase GBSSII BE497955 MADS-box protein 9 (Hv) BQ804479 TaWIN1 (Ta) BE424197 Putative transcription factor (Os) BE422879 Putative transcription factor (Os) BE423371 B-granule number % (top 10 genes) Gamma-gliadin (Ta) BE423485 B-granule volume % NA Gamma-gliadin (Ta) BE422921 Aldolase (Os) BE488825 B/A-granule number ratio NA Beta-amylase 1 (Hv) BE423462 Water content (mg/caryopsis) NA Low molecular weight glutenin (Ta) BE424477 Gamma-gliadin (Ta) BE422980 Seed storage protein (Ta) BQ805009 A-granule volume % Putative SNF2 domain-containing protein (Os) BE399473 Putative zinc finger protein (Os) BF201579 B-granule volume % (top 10 genes) Gamma-gliadin (Ta) BE423485 B-granule number % NA B/A-granule number ratio NA Gamma-gliadin (Ta) BE422921 Aldolase (Os) BE488825 B/A-granule volume ratio NA Beta-amylase 1 (Hv) BG262481 Triticin precursor (Ta) BF428943 Gamma-gliadin (Ta) BE422980 Globulin (Tt) BE398314