Expressional proﬁling study revealed unique expressional patterns
and dramatic expressional divergence of maize a-zein super
Lingna Feng Æ Jia Zhu Æ Gang Wang Æ Yuanping Tang Æ
Hanjun Chen Æ Weibo Jin Æ Fei Wang Æ Bing Mei Æ
Zhengkai Xu Æ Rentao Song
Received: 12 February 2008 / Accepted: 5 December 2008 / Published online: 28 December 2008
Ó Springer Science+Business Media B.V. 2008
Abstract The a-zein super gene family encodes the most
predominant storage protein in maize (Zea mays) endo-
sperm. In maize inbred line B73, it consists of four gene
families with 41 member genes. In this study, we combined
quantitative real-time PCR and random clone sequencing
to successfully proﬁle the expression of a-zein super gene
family during endosperm development. We found that only
18 of the 41 member genes were expressed, and their
expression levels diverge greatly. At the gene family level,
all families had characteristic ‘‘up-and-down’’ oscillating
expressional patterns that diverged into two major groups.
At the individual gene level, member genes showed dra-
matic divergence of expression patterns, indicating fast
differentiation of their expression regulation. A comparison
study among different inbred lines revealed signiﬁcantly
different expressed gene sets, indicating the existence of
highly diverged haplotypes. Large gene families containing
long gene clusters, e.g. z1A or z1C, mainly contributed the
highly divergent haplotypes. In addition, allelic genes also
showed signiﬁcant divergence in their expressional levels.
These results indicated a highly dynamic and fast evolving
nature to the maize a-zein super gene family, which might
be a common feature for other large gene families.
Keywords Zea mays Á a-zein Á Expression proﬁle Á
Super gene family Á Endosperm development
DAP Days after pollination
O2 Opaque2, transcriptional factor for z1C gene family
A gene family is a group of genes that has descended from
a common ancestral gene and therefore inherits similar
DNA sequences and similar functions. In Escherichia coli,
[50% of the genes are members of identiﬁed gene families
(Koonin et al. 1998), and the proportion of gene family
members in eukaryotes may be in the same range or even
higher (Chervitz et al. 1998; Semple and Wolfe 1999).
Multi-gene families are a distinctive feature of plant gen-
omes. For instance, 65% of Arabidopsis thaliana genes
belong to families, with half of them containing at least ﬁve
members (see The Arabidopsis Genome Initiative 2000). In
the rice genome, about 29% of the genes belong to gene
families (International Rice Genome Sequencing Project,
2005), and in maize, it was estimated that 1/3 of the genes
were members of gene families (Messing et al. 2004). The
evolution of gene families has been the subject of contro-
versy for many years (Nei and Rooney 2005). Therefore,
expression divergence between member genes may be
useful evidence in determining how gene families evolved.
Such evidence requires extensive expressional analysis of
large gene families.
The relative expression and amino acid composition of
seed storage proteins signiﬁcantly impact the nutritional
value of maize as animal feed (Ueda and Messing 1993).
Lingna Feng and Jia Zhu contributed equally to this work.
Electronic supplementary material The online version of this
article (doi:10.1007/s11103-008-9444-z) contains supplementary
material, which is available to authorized users.
L. Feng Á J. Zhu Á G. Wang Á Y. Tang Á H. Chen Á W. Jin Á
F. Wang Á B. Mei Á Z. Xu Á R. Song (&)
Shanghai Key Laboratory of Bio-energy Crop, School of Life
Sciences, Shanghai University, 99 Shangda Road,
Shanghai 200444, People’s Republic of China
Plant Mol Biol (2009) 69:649–659