1 OECD/FAO: OECD-FAO Agricultural Outlook 2011-2020, OECD Publishing and FOA,
2011. http://dx.doi.org/10.1787/agr_outlook-2011-en.
2 Jacks TJ, Hensarling TP, Yatsu LY: Cucurbit seeds: I. Characterizations and uses of oils
and proteins. A Review. Econ Bot 1972, 26: 135-141.
3 Derbyshire E, Wright DJ, Boulter D: Legumin and vicilin, storage proteins of legume seeds.
Phytochemistry 1976, 15: 3-24.
4 Shewry PR, Halford NG: Cereal seed storage proteins: structures, properties and role in
grain utilization. J Exp Bot 2002, 53: 947-958.
5 Baud S, Dubreucq B, Miquel M, Rochat C, Lepiniec L: Storage reserve accumulation in
Arabidopsis: metabolic and developmental control of seed filling. The Arabidopsis Book
2008, 6: e0113.
6 Larré C, Penninck S, Bouchet B, Lollier V, Tranquet O, Denery-Papini S, Guillon F,
Rogniaux H: Brachypodium distachyon grain: identification and subcellular localization
of storage proteins. J Exp Bot 2010, 61: 1771-1783.
7 Chileh T, Esteban-García B, Alonso DL, García-Maroto F: Characterization of the 11S
globulin gene family in the castor plant Ricinus communis L. J Agric Food Chem 2010, 58:
272-281.
8 Osborne TB: The Vegetable Proteins. Monographs in Biochemistry. London: Longmans,
Green and Co. 1924, pp xiii+154.
9 Shewry PR, Napier JA, Tatham AS: Seed storage proteins: structures and biosynthesis.
Plant Cell 1995, 7: 945-956.
10 Mandal S, Mandal RK: Seed storage proteins and approaches for improvement of their
nutritional quality by genetic engineering. Curr Sci 2000, 79: 576-589.
11 Dunwell JM, Purvis A, Khuri S: Cupins: The most functionally diverse protein
superfamily? Phytochemistry 2004, 65: 7-17.
12 Krebbers E, Herdies L, De Clercq A, Seurinck J, Leemans J, Van Damme J, Segura M,
Gheysen G, Van Montagu M, Vandekerckhove J: Determination of the processing sites of an
Arabidopsis 2S albumin and characterization of the complete gene family. Plant Physiol
1988, 87: 859-866.
13 Boutilier K, Hattori J, Baum BR, Miki BL: Evolution of 2S albumin seed storage protein
genes in the Brassicaceae. Biochem Syst Ecol 1999, 27: 223-234.
14 Xu JH, Messing J: Organization of the prolamin gene family provides insight into the
evolution of the maize genome and gene duplications in grass species. Proc Natl Acad Sci
USA 2008, 105: 14330-14335.
15 Xu JH, Bennetzen JL, Messing J: Dynamic gene copy number variation in collinear
regions of grass genomes. Mol Biol Evol, in press.
16 Nielsen NC, Dickinson CD, Cho TJ, Thanh VH, Scallon BJ, Fischer RL, Sims TL, Drews GN,
Goldberg RB: Characterization of the glycinin gene family in soybean. Plant Cell 1989, 1:
313-328.
17 Beilinson V, Chen Z, Shoemaker RC, Fischer RL, Goldberg RB, Nielsen NC: Genomic
organization of glycinin genes in soybean. Theor Appl Genet 2002, 104: 1132-1140.
18 Li C, Zhang YM: Molecular evolution of glycinin and β-conglycinin gene families in
soybean (Glycine max L. Merr.). Heredity 2011, 106: 633-641.
19 Pang PP, Pruitt RE, Meyerowitz EM: Molecular cloning, genome organization, expression
and evolution of 12S seed storage protein genes of Arabidopsis thaliana. Plant Mol Biol
1988, 11: 805-820.
20 Fujiwara T, Nambara E, Yamagishi K, Goto DB, Naito S: Storage proteins. The Arabidopsis
Book 2002, 1: e0020.
21 Higuchi W, Fukazawa C: A rice glutelin and a soybean glycinin have evolved from a
common ancestral gene. Gene 1987, 55: 245-253.
22 Takaiwa F, Kikuchi S, Oono K: A rice glutelin gene family: a major type of glutelin
mRNAs can be divided into 2 classes. Mol Gen Genet 1987, 208: 15-22.
23 Takaiwa F, Oono K, Wing D, Kato A: Sequence of three members and expression of a new
major subfamily of glutelin genes from rice. Plant Mol Biol 1991, 17: 875-885.
24 Kawakatsu T, Yamamoto MP, Hirose S, Yano M, Takaiwa F: Characterization of a new
rice glutelin gene GluD-1 expressed in the starchy endosperm. J Exp Bot 2008, 59: 4233-
4245.
25 Hardison R, Slightom JL, Gumucio DL, Goodman M, Stojanovic N, Miller W: Locus control
regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and
experimental results to gain functional insights. Gene 1997, 205: 73-94.
26 Zhang JZ: Evolution by gene duplication: an update. Trends Ecol Evol 2003, 18: 292–298.
27 Clancy S, Shaw K: DNA deletion and duplication and the associated genetic disorders.
Nature Education 1(1) 2008. http://www.nature.com/scitable/topicpage/DNA-Deletion-and-
Duplication-and-the-Associated-331.
28 Hunt BG, Ometto L, Wurm Y, Shoemaker D, Yi SV, Keller L, Goodisman MA: Relaxed
selection is a precursor to the evolution of phenotypic plasticity. Proc Natl Acad Sci USA
2011, 108: 15936-15941.
29 Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for
genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28:
33-36.
30 Soltis PS, Soltis DE: The origin and diversification of angiosperms. Am J Bot 2004, 91:
1614-1626.
31 Sabelli PA, Larkins BA: The development of endosperm in grasses. Plant Physiol 2009,
149: 14-26.
32 The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering
plant Arabidopsis thaliana. Nature 2000, 408: 796-815.
33 Shoemaker RC, Schlueter J, Doyle JJ: Paleopolyploidy and genome duplication in soybean
and other legumes. Curr Opin Plant Biol 2006, 9: 104-109.
34 Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ,
Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK,
Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K,
Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, et al.: Genome sequence of the
palaeopolyploid soybean. Nature 2010, 463: 178-183.
35 Swigonová Z, Lai J, Ma J, Ramakrishna W, Llaca V, Bennetzen JL, Messing J: Close split of
sorghum and maize genome progenitors. Genome Res 2004, 14:1916-1923.
36 Tang H, Bowers JE, Wang X, Paterson AH: Angiosperm genome comparisons reveal early
polyploidy in the monocot lineage. Proc Natl Acad Sci USA 2010, 107: 472-477.
37 Youle RJ, Huang AH: Protein bodies from the endosperm of castor bean:
Subfractionation, protein components, lectins, and changes during germination. Plant
Physiol 1976, 58: 703-709.
38 Hara I, Ohmiya M, Matsubara H: Pumpkin (Cucurbita sp) seed globulins III. Comparison
of subunit structures among seed globulins of various Cucurbita species and
characterization of peptide components. Plant Cell Physiol 1978, 19: 237–243.
39 Hara-Nishimura I, Nishimura M, Matsubara H, Akazawa T: Suborganellar localization of
proteinase catalyzing the limited hydrolysis of pumpkin globulin. Plant Physiol 1982, 70:
699-703.
40 Utsumi S: Plant food protein engineering. In: Kinsella JE Ed. Advances in food and nutrition
research. 1992, vol. 36. San Diego: Academic Press. pp 89-208.
41 Krishnan HB: Biochemistry and molecular biology of soybean seed storage proteins. J
New Seeds 2000, 2: 1-25.
42 Yamagata H, Sugimoto T, Tanaka K, Kasai Z: Biosynthesis of storage proteins in
developing rice seeds. Plant Physiol 1982, 70: 1094-1100.
43 Furuta M, Yamagata H, Tanaka K, Kasai Z, Fujii S: Cell-free synthesis of the rice glutelin
precursor. Plant Cell Physiol 1986, 27: 1201-1204.
44 Laudencia-Chingcuanco DL, Vensel WH: Globulins are the main seed storage proteins in
Brachypodium distachyon. Theor Appl Genet 2008, 117: 555-563.
45 Krishnan HB, Natarajan SS, Mahmoud AA, Nelson RL: Identification of glycinin and
β-conglycinin subunits that contribute to the increased protein content of high-protein
soybean lines. J Agric Food Chem 2007, 55: 1839-1845.
46 Narikawa T, Tamura T, Yagasaki K, Terauchi K, Sanmiya K, Ishimaru Y, Abe K, Asakura T:
Expression of the stress-related genes for glutathione S-transferase and ascorbate
peroxidase in the most-glycinin-deficient soybean cultivar Tousan205 during seed
maturation. Biosci Biotechnol Biochem 2010, 74: 1976-1979.
47 Yagasaki K, Takagi T, Sakai M, Kitamura K: Biochemical characterization of soybean
protein consisting of different subunits of glycinin. J Agric Food Chem 1997, 45: 656-660.
48 Takahashi M, Uematsu Y, Kashiwaba K, Yagasaki K, Hajika M, Matsunaga R, Komatsu K,
Ishimoto M: Accumulation of high levels of free amino acids in soybean seeds through
integration of mutations conferring seed protein deficiency. Planta 2003, 217: 577-586.
49 Guerche P, Tire C, De Sa FG, De Clercq A, Van Montagu M, Krebbers E: Differential
expression of the Arabidopsis 2S albumin genes and the effect of increasing gene family
size. Plant Cell 1990, 2: 469-478.
50 Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP,
Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H,
Leebens-Mack J, dePamphilis CW: Ancestral polyploidy in seed plants and angiosperms.
Nature 2011, 473: 97-100.
51 Ridley M: Evolution. 3th. Blackwell Science Ltd: Blackwell. 2004, pp 1-91.
52 Löytynoja A, Goldman N: An algorithm for progressive multiple alignment of sequences
with insertions. Proc Natl Acad Sci USA 2005, 102: 10557-10562.
53 Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular
evolutionary genetics analysis using maximum likelihood, evolutionary distance, and
maximum parsimony methods. Mol Biol Evol, in press.
54 Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from
protein sequences. Comput Appl Bio Sci 1992, 8: 275-282.
55 Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed
models. Bioinformatics 2003, 19: 1572-1574.
56 Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24:
1586-1591.
57 Ramsay H, Rieseberg LH, Ritland K: The correlation of evolutionary rate with pathway
position in plant terpenoid biosynthesis. Mol Biol Evol 2009, 26: 1045-1053.
58 Yang Z: Likelihood ratio tests for detecting positive selection and application to primate
lysozyme evolution. Mol Biol Evol 1998, 15: 568-573.
59 Yang Z, Nielsen R: Codon-substitution models for detecting molecular adaptation at
individual sites along specific lineages. Mol Biol Evol 2002, 19: 908-917.
60 Zhang J, Nielsen R, Yang Z: Evaluation of an improved branch-site likelihood method for
detecting positive selection at the molecular level. Mol Biol Evol 2005, 22: 2472-2479.
61 Yang Z, Wong WSW, Nielsen R: Bayes empirical Bayes inference of amino acid sites
under positive selection. Mol Biol Evol 2005, 22: 1107-1118.
62 The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering
plant Arabidopsis thaliana. Nature 2000, 408: 796-815.
63 Huang S, Li R, Zhang Z, Gu X, Fan W, Lucas W, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J,
Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EAG, Wu Y, Guo J, He J, Jia Z,
Ren Y, Tian G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, et al.: The genome of the
cucumber, Cucumis sativus L. Nat Genet 2009, 41: 1275-1281.
64 Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S,
Rombauts S, Salamov, A Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D,
Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J,
Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, et al.: The genome of
black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313: 1596-1604.
65 Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM,
Redman J, Chen G, Cahoon EB, Gedil M, Stanke M, Haas BJ, Wortman JR, Fraser-Liggett CM, Ravel J, Rabinowicz PD, et al.: Draft genome sequence of the oilseed species Ricinus
communis. Nat Biotechnol 2010, 28: 951-956.
66 The International Brachypodium Initiative: Genome sequencing and analysis of the model
grass Brachypodium distachyon. Nature 2010, 463: 763-768.
67 Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL,
Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR: The TIGR Rice Genome
Annotation Resource: improvements and new features. Nucleic Acids Res 2007, 35
(Database issue): D883-887.
68 Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L,
Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C,
Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton
M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, et al.: The B73 maize genome:
complexity, diversity, and dynamics. Science 2009, 326:1112-1115.
69 Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G,
Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti
AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M,
Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, et al.:
The Sorghum bicolor genome and the diversification of grasses. Nature 2009, 457:
551-556.