Dr. Khidir Hilu

(540) 231-5407

hilukw@vt.edu

Research

   

Phylogeny of Flowering Plants

bot

Hilu et al. 2003 - Cover page for December 2003 issue of the American Journal of Botany. (With permission from Botanical Society of America)

Our research has been focusing on the evolution of flowering plants (angiosperms) as well as land plants in general using DNA sequence information. This aspect of our work includes both basal angiosperms as well as eudicots. We are emphasizing the rapidly-evolving plastid gene matK and the trnT-trnF region. Examples of ongoing project are the large data set (over 400 taxa) of matK sequences from across angiosperms; this study is in collaboration with various laboratories from Germany, the U.S., England, and France. Another example is the study of basal angiosperm evolution using non-coding trnT-trnF region. This study is in collaboration with colleagues from the University of Bonn and the Natural History Museum in Frankfurt. We are also involved in collaborative studies on molecular systematics of Magnolides, Piperales, and Nymphaealis.

(Click here to see related publications.)

 

Evolution and Systematics of Grasses

The grass family is the fourth largest flowering plant family and is economically the most important, providing about 80% of global food and containing the top four crops that feed the world and more than 10 of the 30 most important crops. Our work on grasses (Poaceae) has moved from using morphological characters to molecular characters. At this point, we are combining information from prolamin (seed storage protein) proteins, prolamin genes, plastid matK gene and trnT-F non-coding region and, the ITS nuclear region. We have reconstructed with sequence data a phylogeny of the grass family, the subfamily Chloridoideae, and genera like Eleusine, Chloris and Oryza. We have generated the largest single-gene phylogeny for the grass family as a whole and also for the subfamily Chloridoideae. We have also used RFLP and RAPD in systematics at the genus and species levels.

(Click here to see related publications.)

 

Protein Multigene Families in Grasses

Prolamin is a class of seed storage proteins specific to the grass family. Our work on prolamin began with studies at the protein level using SDS-acrylamid gel electrophoresis and immunological methods. These studies established the presence of three major prolamin classes; 10-16 kDa, 18-23 kDa, and 30-100 kDa that define three major lineages in grasses and helped define subfamilies and tribes. Our research took the next logical step of exploring theseproteins at the gene level. As a start, we began studying the molecular diversity and evolution of the genes that encode the 10 kDa prolamins. We have surveyed these genes across the grass family, but established a focus on the rice genus Oryza and related groups such as bambusoid species. The reason for our focus now on the 10 kDa prolamin gene family because it is the simplest, and is found mostly in basal grasses. Our next step is to proceed to the intermediate size classes and next to the most complex one. We believe that this study represents an excellent system to address issues related to the evolution of multigene families, as basic genome syndrome in plant and animal evolution. This research has been funded by the Jeffress Memorial Trust.

(Click here to see related publications.)

 

Evolution of Waterlilies

The research work on waterlilies (Nymphaea) includes genetic diversity in population and speciation studies on North American N. ordorata and N. mexicana as well as an overall study of the systematics and evolution of the whole genus Nymphaea worldwide. We are also studying the systematics of the family Nymphaeaceae and the order Nymphaeales. The work on the North American Nymphaea is conducted by Kristi Niehaus, a graduate student in our laboratory. The rest of the work is an international collaboration with Dr. Thomas Borsch at the University of Bonn, Germany, as well as colleagues in the U.S. Department of Agriculture, the Royal Botanical Garden in Sydney, Australia, among others.

(Click here to see related publications.)

 

Crop Evolution

Studying crop evolution and systematics has been a tradition in our laboratory. Our interest has been in examining genetic diversities and evolution of crops and their related wild species. We employ morphology, scanning electron microscopy, chromosome cytology, flavonoids, and DNA techniques (RAPD, RFLP, and gene sequencing). Millets have been the focus of our work. In addition, we have studied wheat and currently we are examining both rice and peanut crops.

(Click here to see related publications.)

 

MatK Gene Evolution

matK has recently emerged as an invaluable gene in plant systematics due to strong phylogenetic signal compared with other genes used in this field.  The matK gene is approximately 1500 bp in length, nested in the group II intron between the 5’ and 3’ exons of trnK in the large single copy region of the chloroplast genome of most green plants. the molecular information generated from matK has been used to resolve phylogenetic relationships from shallow to deep taxonomic levels.

The matK gene stands out among plastid genes used in plant systematics in its distinct mode and tempo of evolution.  The rate of substitution in matK is three times higher at the nucleotide level and is six times higher at the amino acid level than that of rbcL.  The accelerated rate of amino acid substitution in matK is due to almost even distribution of substitution rates among the three codon positions compared with most protein coding genes where the rates are skewed toward the third codon position.

Our work has gone beyond using the matK gene in systematic studies of the Poaceae, angiosperms and land plants, to attempting to understand the mode of amino acid and protein evolution.  We are also conducting functional and structural studies o n the matK and the trnK intron.

(See: Barthet and Hilu 2007, Barthet and Hilu 2008)

 

Arachis (Fabaceae) Phylogeny and the Evolution of the Peanut Crop

The genus Arachis (Fabaceae) contains approximately 80 wild and crop species native to South America and the peanut crop Arachis hypogaea. Species of Arachis are distributed east of the Andes Mountains and south of the Amazon River, with the most species diversity located in areas around the eastern boarder of Bolivia and western Brazil. The most recent monograph of genus Arachis recognized 69 species, including the crop, dividing them into nine sections based on morphology, geographic distribution and cytogenetics (Krapovickas and Gregory, 1994): Trierectoides, Erectoides, Extranervosae, Triseminatae, Heteranthae, Caulorrhizae, Procumbentes, Rhizomatosae and Arachis. The majority of the Arachis species are diploids, with a basic chromosome number x=10. However, there are five tetraploid species (2n = 4x = 40) including the crop species, and three anueploid species (x=9, 2n = 2x = 18).

The peanut crop, A. hypogaea, is an important economical oil-seed crop that is cultivated in over 100 countries.  Other species of Arachis have also been cultivated as indigenous food crop, A. villosulicarpa, and as forage crops, A. glabrata, A. pintoi, and A. repens. 

Our work is focusing on the systematics of the genus and the evolution of the tetraploid crop usi ng DNA sequences from chloroplast and nuclear genomic regions.

(See Tallury, Hilu, Milla, Friend, Alsaghir, Stalker, and Quandt, 2005.)

 

Phalaris (Canary Grass)

Canary grasses belong to the genus Phalaris (Poaceae) and contains 21 annual and perennial species found on five continents: Mediterranean Europe, western Asia, Mediterranean north Africa and southern Africa, North America, and both sides of South America.  The species are based on basic chromosome numbers of 6 or 7, and diploids, tetraploids and hexaploids, Our preliminary data and current distribution hint to a potential Mediterranean Europe origin followed by dispersal to West Asia and Africa and the Americas. 

Our curresnt research on the genus is in collaboration with Professor Riccardo Baldini of the University of Florence, Italy.  We are focusing on extensive field work and molecular phylogenetic and phylogeographic assessments of the evolution of the genus.

 

Last Updated September 7, 2008