Structure and evolution of the d2 dwarfing gene in pearl millet, Pennisetum glaucum

Pearl millet (2n=2x=14) is one of the most important subsistence crops grown in India and sub-Saharan Africa. Reduced height remains a key trait for enhancing yield in many crops and dwarf mutants in cereal crops have been extensively used in breeding to reduce yield loss due to lodging.  In pearl millet, the most widely used height-reducing gene is the recessive d2 dwarfing gene. We recently isolated d2 using a combined map-based cloning and comparative genetics approach.  The d2 gene encodes a P-glycoprotein involved in auxin transport and is orthologous to the sorghum Dw3 dwarfing gene. Sequence analysis of a Tift 23DB BAC clone containing the d2 dwarf allele revealed the presence of an ~15 kb LTR retrotransposon insertion in the first exon. This insertion is absent in the tall pearl millet genotype ICMP 451. Analysis of additional accessions also showed the differential presence of the LTR retrotransposon in the dwarf compared to the tall lines.  Transformation experiments are underway to confirm the identity of the gene. Interestingly, this gene also shows variance in the number of introns across plant families. We charted the intron number of this gene in a number of grass species and other monocots, and in selected dicots to gain insight into the evolution of this gene and enhance our understanding of the factors contributing to intron loss and gain.