Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species

Abstract

Zea mays, commonly known as corn, is perhaps the most greatly produced crop in terms of tonnage and a major food, feed, and biofuel resource. Here we analyzed its prolamin gene family, encoding the major seed storage proteins, as a model for gene evolution by syntenic alignments with sorghum and rice, two genomes that have been sequenced recently. Because a high-density gene map has been constructed for maize inbred B73, all prolamin gene copies can be identified in their chromosomal context. Alignment of respective chromosomal regions of these species via conserved genes allow us to identify the pedigree of prolamin gene copies in space and time. Its youngest and largest gene family, the alpha prolamins, arose about 22-26 million years ago (Mya) after the split of the Panicoideae (including maize, sorghum, and millet) from the Pooideae (including wheat, barley, and oats) and Oryzoideae (rice). The first dispersal of alpha prolamin gene copies occurred before the split of the progenitors of maize and sorghum about 11.9 Mya. One of the two progenitors of maize gained a new alpha zein locus, absent in the other lineage, to form a nonduplicated locus in maize after allotetraplodization about 4.8 Mya. But dispersed copies gave rise to tandem duplications through uneven expansion and gene silencing of this gene family in maize and sorghum, possibly because of maize's greater recombination and mutation rates resulting from its diploidization process. Interestingly, new gene loci in maize represent junctions of ancestral chromosome fragments and sites of new centromeres in sorghum and rice.

Fig. 1.

Phylogenetic analysis of the prolamin genes. Phylogenetic analysis was performed as described in Materials and Methods. The graphic representation shows the results by the unweighted pair-group with arithmetic mean (UPGMA) method. The same analysis also was performed with the neighbor-joining method, which confirmed the results of the UPGMA method (data not shown).

Fig. 2.

New centromere formation. The duplicated regions from maize are aligned at the top and the bottom. Vertical bars connect conserved genes with insert providing a key. Clone numbers represent GenBank entries of overlapping maize BAC clones. In the middle, the sorghum and the rice orthologous regions are aligned. Because of the scale, large insertions are indicated in kb or Mb. The rice region contains the largest insertion, which is the centromere of rice chromosome 6. The key to the color-coding is shown in the Inset.

Fig. 3.

(A) Gene pedigree of alpha prolamins in maize, sorghum, and sugarcane. Alpha prolamins fall into subfamilies, four in maize (A, B, C, and D) and three in sorghum (A, C, and D), based on distance analysis (see Materials and Methods). Increases in copy number and speciation are illustrated in progression from left to right. Vertical lines indicate chromosomal segments containing alpha-prolamin genes. Dotted vertical lines indicate the split of progenitor genomes. The progenitor of maize, sorghum, and sugarcane split about 11.9 Mya. One of the progeny genome then split into the progenitors of sorghum and sugarcane, whereas the two other ones hybridized to form maize by allotetraploidization about 4.8 Mya. The approximate timing and direction of gene copying events is indicated in Mya and by arrows. Genes also are color-coded to indicate orthologous and paralogous gene copying, as well as gene- silencing events. Note that we do not have a map of contiguous polamin genes in sugarcane, but only of EST resources. Their relationships are based solely on their sequence homology to kafirin genes. (B) Orthologous regions of the alpha prolamin C1 and A1 genes. To better follow the first duplication event in (A), the orthologous regions of the prolamin C1 and A1 genes of rice 11, sorghum 5, and maize 4 are shown below the diagram. For an explanation, see the legend of Fig. 2.