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 (http://cordis.europa.eu/erawatch/index.cfm?fuseaction=prog.documentAjax&uuid
=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 (http://www.esd.ornl.gov/PGG/yin_bio.htm). 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.