Twentieth century marks the beginning of genomic era. The first plant sequenced was Arabidopsis thaliana (published in 2000) and then a major important crop, rice was published in 2005. From then the sequencing of many model species have been sequenced and assembled. To date about 150 species of plants are sequenced, assembled and annotated. Having a single high-quality reference genome for each of the species was an important goal, since that provided a starting point for many genetic analyses, be it identification of QTL (Quantitative Trait Loci; regions of genome that are responsible for trait variation) or candidate genes (genes that are associated with phenotype), synteny (conservation of gene order between two species or samples) and inter species variation that helps us understand the evolutionary aspects of the genome.
With decrease sequencing costs, and better understanding of various aspects of genomics, it made us realize that a single reference genome is inadequate for many purposes. By sampling a diverse set of samples, sequencing and assembling independently provides a large collection of DNA elements (genes, repeats etc.) that constitute the pan genome. With this pan-genome, we can capture the variation missed in the single reference genome. These additional genomes enable further studies on genomic diversity, genome evolution and adaptation for the basis of trait variation.
Maize (aka corn) is an important crop since the dawn of plant domestication, and is an important source of human nutrition and animal feed. There are many classification systems for corn, and one of them classifies corn into five different types based on usage – Popcorn, Flint, Flour, Dent and sweet which vary a lot in seed characteristics. Dent corn makes up the majority of commercially raised corn in the US. This is primarily used for animal feed, processed foods, industrial products and ethanol. Flint corn (aka field corn or Indian corn) is grown mostly in Europe, Central and South America, because it is early maturing and cold-tolerant. The present-day dent corns grown in US are inbreds of crosses between southern dents and northern flints.
European varieties are mostly made up of flint and US varieties are made of dent genomes. It is estimated that about 25% flint genome blend with the current dent types.
Worldwide, hybrid breeding programs are mostly focused on dent germplasm, and breeding programs in cooler regions of Central Europe exploit heterotic effects between the two major types, dent and flint. The first maize genome of a dent line (B73) was published in 2009. Later four other dent lines were sequenced. There exists no complete reference genome for flint line so far. Now, four flint lines of European origin are assembled into a reference quality genome and compared with two dent lines1. It should be noted that the assembly of maize is difficult to assemble given the repeat content in the genome (about 80%). The number of genes varied between 43,700-45,900. Of these 34,352 are syntelogs (genes that are conserved in order, i.e. present in the same order in all 6 genomes).
The differences in genes support that flint and dent are separate groups. This is also supported by the expression patterns of genes, core genes (genes present in all samples) have high expression patterns compared to shell genes (present in only few samples). However, only 3% full length long terminal repeats (fl-LTR) are shared among the 6 genomes. Overall, the comparative analysis of gene and repeat content, whole genome alignments and SNPs confirm the differences between the two groups. Each group shares larger number of syntenic genes, repeats, aligned regions and haplotypes with members of same group compared to members of other group. One major difference for the 2 groups included shared haplotypes within each of the group, indicative of a common ancestry. The genes in these haplotype blocks were observed for gene expression differences and the genes that have higher expression differences include genes involved in starch metabolism like the sugar transporters, limiting gene for starch biosynthesis among others. This work has a huge impact on understanding maize genetics given that corn is one of the most important grain in the world.