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Seeking Diversity in Ag Genomics

  • Title: Postdoctoral Research Associate, University of Florida
  • Education: PhD, Indian Council for Forestry Research and Education, 2004
  • Recommended by: Chittaranjan Kole

Madhugiri Rao traces his longstanding interest in agriculture to his childhood, when he was continually impressed by the diversity surrounding him. That fascination stayed with him through school, where he studied genetic and population diversity, and still plays a role today in his work with plants of agricultural importance.

As a postdoc at the Citrus Research and Education Center at the University of Florida, Rao has been involved in a number of programs centering on citrus, a major crop — and therefore a critical part of the economy — in the state. As a participant in the International Citrus Genomics Consortium, which is working to obtain a complete genome sequence of the fruit, Rao helped develop and work with the BAC library of Citrus sinensis, the sweet orange, in a project to look for particular markers. “Our team wanted to work on the whole genome sequencing of citrus, so our lab has been involved in that,” he says. That work is being done with standard Sanger sequencing as well as a collaboration to use 454’s next-gen sequencing platform.

He also works extensively on rootstocks, which contribute to life span, size, and other characteristics of citrus trees. Traditional methods to screen for these rootstocks are time-consuming and tedious, limited significantly by the long growing time — up to seven years after planting — of these trees. Rao’s research in this field has focused on using molecular marker approaches to allow for rapid screening of the key characteristics breeders are looking for in the citrus they’ll plant. “Genomics tools have given us much more opportunity to achieve our goals very fast,” Rao says.

When he’s not working on citrus, Rao can be found conducting research on Coreopsis, the Florida state wildflower. Relying on data from proxy genomes, since no sequence data is available for the flower, Rao is working to understand and analyze the genetic diversity of the genus.

Rao headed to the University of Florida from India, where he was previously a research associate at the University of Agricultural Sciences in Bangalore. The work there continued Rao’s theme of genetic diversity, and he focused in particular on identifying hotspots of genetic variability as well as on population genetics of forest plants. That work may one day become a model to promote effective conservation of endangered plant species, according to Rao.

Publications of note

Rao and his colleagues published a paper in June of this year in the journal Tree Genetics & Genomes. Entitled “Characterization of zygotic and nucellar seedlings from sour orange-like citrus rootstock candidates using RAPD and EST-SSR markers,” the paper described how the team worked to develop an alternative rootstock. The group used randomly amplified polymorphic DNA along with fluorescently labeled molecular markers known as EST simple sequence repeats. They then created hybrid plants and selected from that group using the EST-SSR primer pairs; they eventually emerged with two superior candidates that appear well-suited to breeding programs for mandarin and pummelo.

Rao, lead author, and his co-authors wrote in the abstract, “Our results indicate that either RAPD or EST-SSR analyses could be equally successful in identifying true nucellars among the progenies obtained from introgression crosses of mandarin and pummelo, thus improving the accuracy of early selection in a citrus rootstock breeding program.”

For another paper published earlier in the year in the same journal, Rao was part of a team that developed the EST-SSR markers and made them freely available to the community. The group built EST maps for sweet orange as well as for the Poncirus genomes.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.