The dynamic transcriptome of waxy maize (Zea mays L. sinensis Kulesh) during seed development

다국어 초록 (Multilingual Abstract)

Background Waxy maize (Zea mays L. sinensis Kulesh) is a mutant of maize (Zea mays L.) with a mutation at Waxy1 (Wx1) gene locus. The seed of waxy maize has higher viscosity compared to regular maize. By now, we know little about the expression patterns of genes that involved in the seed development of waxy maize. Objective By analyzing the transcriptome data during waxy maize seed development, we attempt to dig out the genes that may infuence the seed development of waxy maize. Methods The seeds of waxy maize inbred line SWL01 from six phases after pollination were used to do RNA-seq. Bioinformatics methods were used to analyze the expression patterns of the expressed genes, to identify the genes involved in waxy maize seed development. Results A total of 24,546 genes including 1611 transcription factors (TFs) were detected during waxy maize seed development. Coexpression analysis of expressed genes revealed the dynamic processes of waxy maize seed development. Particularly, 2457 genes including 177 TFs were specially expressed in waxy maize seed, some of which mainly involved in the process of seed dormancy and maturation. In addition, 2681, 5686, 4491, 4386, 3669 and 4624 genes were identifed to be diferential expressed genes (DEGs) at six phases compared to regular maize B73, and 113 DEGs among them may be key genes that lead the diference of seed development between waxy and regular maizes in milk stage. Conclusion In summary, we elucidated the expression patterns of expressed genes during waxy maize seed development globally. A series of genes that associated with seed development were identifed in our research, which may provide an important resource for functional study of waxy maize seed development to help molecular assisted breeding.

참고문헌 (Reference)

1 Gutierrez-Marcos JF, "maternally expressed gene1 Is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression" 16 : 1288-1301, 2004

2 Tian T, "agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017update" 45 : W122-W129, 2017

3 Chen J, "Zygotic genome activation occurs shortly after fertilization in maize" 29 : 2106-2125, 2017

4 Yeung KY, "Validating clustering for gene expression data" 17 : 309-318, 2001

5 Davidson RM, "Utility of RNA sequencing for analysis of maize reproductive transcriptomes" 4 : 191-203, 2011

6 Jones SI, "Using RNA-Seq to profile soybean seed development from fertilization to maturity" 8 : e59270-, 2013

7 Ni J, "Updating and interaction of polycomb repressive complex 2 components in maize(Zea mays)" 250 : 573-588, 2019

8 Bolduc N, "Unraveling the KNOTTED1 regulatory network in maize meristems" 26 : 1685-1690, 2012

9 Gao Y, "Transcriptomic analysis of rice(Oryza sativa)endosperm using the RNA-Seq technique" 81 : 363-378, 2013

10 Kramer V, "The sh2-R allele of the maize shrunken-2 locus was caused by a complex chromosomal rearrangement" 128 : 445-452, 2015

11 Cheng WH, "The miniature1 seed locus of maize encodes a cell wall invertase required for normal development of endosperm and maternal cells in the pedicel" 8 : 971-983, 1996

12 Dworkin-Rastl E, "The maternal histone H1 variant, H1M(B4 protein), is the predominant H1 histone in Xenopus pregastrula embryos" 161 : 425-439, 1994

13 Evans MM, "The indeterminate gametophyte1 gene of maize encodes a LOB domain protein required for embryo Sac and leaf development" 19 : 46-62, 2007

14 Scippa GS, "The histone-like protein H1-S and the response of tomato leaves to water deficit" 55 : 99-109, 2004

15 Domaschenz R, "The histone variant H2A. Z is a master regulator of the epithelial-mesenchymal transition" 21 : 943-952, 2017

16 Trivedi I, "The histone H1 variant accumulates in response to water stress in the drought tolerant genotype of Gossypium herbaceum L" 31 : 477-486, 2012

17 Zeng M, "The genetic relationship of waxy maize in China" 3 : 8-10, 1987

18 Nelson OE, "The enzymatic deficiency in the waxy mutant of maize" 9 : 297-300, 1962

19 Perez-Montero S, "The embryonic linker histone H1 variant of Drosophila, dBigH1, regulates zygotic genome activation" 26 : 578-590, 2013

20 Li P, "The developmental dynamics of the maize leaf transcriptome" 42 : 1060-1067, 2010

21 Scippa GS, "The H1 histone variant of tomato, H1-S, is targeted to the nucleus and accumulates in chromatin in response to water-deficit stress" 211 : 173-181, 2000

22 Chourey PS, "Sugar-hormone cross-talk in seed development : two redundant pathways of IAA biosynthesis are regulated differentially in the invertase-deficient miniature1(mn1)seed mutant in maize" 3 : 1026-1036, 2010

23 Luk E, "Stepwise histone replacement by SWR1 requires dual activation with histone H2A. Z and canonical nucleosome" 143 : 725-736, 2010

24 Sprague GF, "Some effects of the waxy gene in corn on properties of the endosperm starch" 35 : 817-822, 1943

25 Cox MP, "SolexaQA : At-a-glance quality assessment of Illumina second-generation sequencing data" 11 : 485-, 2010

26 Li XJ, "Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize(Zea mays)and rice(Oryza sativa)" 79 : 797-809, 2014

27 Shewry PR, "Seed storage proteins : structures and biosynthesis" 7 : 945-956, 1995

28 Zhan J, "RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation" 27 : 513-531, 2015

29 Collins NE, "Performance of broilers fed normal and waxy corn diets formulated with chick and rooster derived apparent metabolizable energy values for the grains" 12 : 196-206, 2003

30 Over RS, "Open and closed : the roles of linker histones in plants and animals" 7 : 481-491, 2014

31 Zhan J, "Opaque-2 regulates a complex gene network associated with cell differentiation and storage functions of maize endosperm" 30 : 2425-2446, 2018

32 Kelliher T, "One-step genome editing of elite crop germplasm during haploid induction" 37 : 287-292, 2019

33 Love MI, "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2" 15 : 550-, 2014

34 Gutierrez-Marcos JF, "Maternal gametophytic baseless1 is required for development of the central cell and early endosperm patterning in maize(Zea mays)" 174 : 317-329, 2006

35 Leroux BM, "Maize early endosperm growth and development : from fertilization through cell type differentiation" 101 : 1259-1274, 2014

36 Huang Y, "Maize VKS1 regulates mitosis and cytokinesis during early endosperm development" 31 : 1238-1256, 2019

37 Thimm O, "MAPMAN : a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes" 37 : 914-939, 2004

38 Jia Y, "Loss of RNA-dependent RNA polymerase 2(RDR2)function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs" 5 : e1000737-, 2009

39 Fedoroff N, "Isolation of the transposable maize controlling elements Ac and Ds" 35 : 235-242, 1983

40 Havel L, "In vitro pollination of maize(Zea mays L. )—proof of double fertilization" 1 : 26-28, 1981

41 Jiao Y, "Improved maize reference genome with single-molecule technologies" 546 : 524-527, 2017

42 Bernardi J, "Impaired auxin biosynthesis in the defective endosperm18 mutant is due to mutational loss of expression in the ZmYuc1 gene encoding endosperm-specific YUCCA1 protein in maize" 160 : 1318-1328, 2012

43 Wang G, "Identification and characterization of Maize floury4 as a novel semidominant opaque mutant that disrupts protein body assembly" 165 : 582-594, 2014

44 Ingouff M, "Histone3 variants in plants" 119 : 27-33, 2010

45 Jiang D, "Histone variants in plant transcriptional regulation" 1860 : 123-130, 2017

46 Deal RB, "Histone variants and modifications in plant gene regulation" 14 : 116-122, 2011

47 Yi F, "High temporal-resolution transcriptome landscape of early maize seed development" 31 : 974-992, 2019

48 Bennetzen JL, "Handbook of maize: its biology" Springer 2009

49 Kim D, "HISAT : a fast spliced aligner with low memory requirements" 12 : 357-360, 2015

50 Zlatanova J, "H2A.Z: view from the top" 16 : 166-179, 2008

51 Kumar SV, "H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis" 140 : 136-147, 2010

52 Asakura T, "Global gene expression profiles in developing soybean seeds" 52 : 147-153, 2012

53 Le BH, "Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors" 107 : 8063-8070, 2010

54 Wang X, "Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize" 21 : 1053-1069, 2009

55 Dumas C, "Gametes and fertilization : maize as a model system for experimental embryogenesis in flowering plants" 5 : 1337-1348, 1993

56 Godfray HC, "Food security : the challenge of feeding 9 billion people" 327 : 812-818, 2010

57 Coleman CE, "Expression of a mutant alpha-zein creates the floury2 phenotype in transgenic maize" 94 : 7094-7097, 1997

58 Sharma R, "Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice" 12 : 229-248, 2012

59 Young TE, "Ethylene-mediated programmed cell death during maize endosperm development of wild-type and shrunken2 genotypes" 115 : 737-751, 1997

60 Liu YJ, "Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize" 25 : 868-883, 2013

61 Lu DL, "Effects of protein removal on the physicochemical properties of waxy maize flours" 64 : 874-881, 2012

62 Schweizer L, "Dynamics of maize endosperm development and DNA endoreduplication" 92 : 7070-7074, 1995

63 Shindo Y, "Dynamics of free and chromatinbound histone H3 during early embryogenesis" 29 : 359-366, 2019

64 Chen J, "Dynamic transcriptome landscape of maize embryo and endosperm development" 166 : 252-264, 2014

65 Wang B, "Development of a haploid-inducer mediated genome editing system for accelerating maize breeding" 12 : 597-602, 2019

66 Cui B, "Deposition and function of histone H3 variants in Tetrahymena thermophila" 26 : 7719-7730, 2006

67 Chen X, "Dek35encodes a PPR protein that affects cis-splicing of mitochondrial nad4 Intron 1 and seed development in maize" 10 : 427-441, 2017

68 Luger K, "Crystal structure of the nucleosome core particle at 2. 8 A resolution" 389 : 251-260, 1997

69 Belmonte MF, "Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed" 110 : E435-444, 2013

70 Locatelli S, "Chromatin and DNA modifications in the Opaque2-mediated regulation of gene transcription during maize endosperm development" 21 : 1410-1427, 2009

71 Lai J, "Characterization of the maize endosperm transcriptome and its comparison to the rice genome" 14 : 1932-1937, 2004

72 Kriz AL, "Characterization of embryo globulins encoded by the maize Glb genes" 27 : 239-251, 1989

73 Shannon JC, "Brittle-1, an adenylate translocator, facilitates transfer of extraplastidial synthesized ADP–glucose into amyloplasts of maize endosperms" 117 : 1235-1252, 1998

74 Ghosh S, "Analysis of RNA-Seq data using TopHat and Cufflinks" 1374 : 339-361, 2016

75 Xu JH, "Amplification of prolamin storage protein genes in different subfamilies of the Poaceae" 119 : 1397-1412, 2009

76 Giroux MJ, "ADP-glucose pyrophosphorylase in shrunken-2 and brittle-2 mutants of maize" 243 : 400-408, 1994

77 Collins GN, "A new type of Indian corn from China. US Department of Agriculture" Bureau of Plant Industry 1909

78 Vicente-Carbajosa J, "A maize zinc-finger protein binds the prolamin box in zein gene promoters and interacts with the basic leucine zipper transcriptional activator Opaque2" 94 : 7685-7690, 1997

79 Coleman CE, "A defective signal peptide in the maize high-lysine mutant floury 2" 92 : 6828-6831, 1995