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Research Area 5 - Comparative Genomics Among Select Plant Species

Our objectives under this study are multifold: to familiarize and train REU students in the principles and practice of plant molecular biology; to undertake basic exercises in comparative genomics with a focus on bioinformatics and an emphasis on understanding the elements of gene structure and function; and to develop a long-term cooperation with NFU. As a prelude to this REU, Dr. Govind Sharma, professor emeritus at AAMU, met with the research group of Dr. Tongming Yin, a Long River Scholar ( =35B59949-9112-BCCB-2C848286FF18D0DF ) who holds an eminent scientist chair at NFU. He is one of the One Hundred Scholars that hold an endowed position in China. Prior to this, Dr. Yin has had a distinguished career at the Oak Ridge National Lab where he led a group of scientists and students in deciphering the Poplar genome ( Dr. Kantety is establishing a strong molecular biology program at Alabama A&M University and he has taken a leadership role and responsibility in training underrepresented students both at the undergraduate and graduate levels in genomics. He established the Alabama A&M Genome Institute (AAGI) and successfully participated in three REU programs and serves as the PI of the only NSF-funded Plant Genome Research Program at an HBCU.  The objectives listed above are based on previous contacts and visits that have taken place. In addition, two of the three species selected (poplar and willow) are integral to urban environments and are extensively planted in urbanized areas of eastern and central China. Cotton is a species for which a worldwide genomic collaboration exists and leading cotton producing nations (US, China and several others). 

The international community of scientists has come together under the umbrella of the International Cotton Genome Initiative (ICGI) because the genome of this species has not been sequenced. Salix (willow) and Populus (poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. Populus trichocarpa genome has been recently utilized to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 million years ago (Berlin et al. 2010). They share many characteristics such as dioecy, rapid growth and seed development, and ease with which they can be vegetatively propagated. Species across both genus typically have a haploid chromosome number of 19 and relatively small genomes sizes (~500 Mbp). The large phenotypic variation within and among Salix species facilitates the identification of quantitative trait loci (QTLs) in experimental populations (Azuma et al. 2000). Also, natural populations of Salix typically display high genetic diversity and are likely to contain many low-frequency alleles that underlie outstanding phenotypes useful to breeders. Generally, gene order within syntenic groups is very well conserved in the willow-poplar comparison. Gossypium belonging to Malvaceae has not been fully sequenced and therefore it benefits from more detailed genome sequencing conducted for populus and Salix. Comparative genomics therefore will aid in finding similarities and divergence in genes and genomes. Undergraduates with strong interest in plant molecular biology will be selected to see the interrelationships among genes belonging to these three eurosid species. Students will receive exposure to basic molecular biology protocols and to elements of bioinformatics as applied in comparative genomics in China and the U.S. on species of interest to both programs. In addition to cultural exposure students will visit several active molecular biology laboratories to observe approaches utilized in molecular biology on both sides of the Pacific.​