Bowie State University
Modern day genomics holds the promise of helping scientists to answer very complex questions in basic plant science, and of catalyzing practical advances in plant breeding. Recent advances in next generation sequence technologies offer great opportunities for the dissection and understanding of genome interaction in allopolyploid species like the bananas and plantains. Most cultivated bananas are usually hybrids of two Musa species, M. acuminata Colla (AA) and M. balbisiana Colla (BB). Based on chromosome numbers and morphological determination, Musa cultivars and hybrids derived from these wild species are traditionally divided into seven genomic groups-namely, AA, BB, AAA, AAB, ABB, BBB, ABBB. My undergraduate research program at Bowie State University is using Illumina TrueSeq RNA-Seq data to understand differential gene expression between three major flower and fruit types found in the genomic groups of the genus Musa. These three major inflorescence types are the French, False horn and horn and it is to these inflorescence types that most of the consumer desirable traits like fruit bunch weight, number of hands, number of fingers per hand, size of fingers and other agronomic characteristics are tied. Unfortunately, plant breeders working on crop improvement have to wait until plant maturity to determine the inflorescence phenotypes, leading to delay in the release of improved varieties. The goal of this RNA Seq project is to identify gene transcripts involved in the floral developmental signaling pathways of the different Musa flower types and to screen them for usefulness as potential molecular markers for early identification of the floral types by breeders and farmers involved in crop improvement. We also aim to use the RNA seq data set to understand the interaction of the Musa acuminata (A) and Musa balbisiana (B) genomes in the complex polyploids of Musa, especially the plantains (AAB) and the East African bananas (AAB).
RNA will be extracted from floral parts collected from three banana and plantain inflorescence types (French, False horn and Horn) and gene libraries made using standard NGS protocols. RNA will be extracted from the collected floral parts, sequenced and analyzed for differential gene expression between the flower types. Sequences of differentially expressed transcripts will be verified and then used as molecular markers (tags) for flower and fruit bunch characteristics in bananas and plantains.
I will release SRA data from three types of plantain inflorescences:
The RNA seq data will be used by researchers and my undergraduate students to identify genes affecting the developmental stages of banana inflorescences, allowing follow-up experiments that explore their functions. Unique and distinguishing transcripts will be used as diagnostic markers for early detection of the floral and bunch types in the cultivated varieties by breeders. The RNA seq data set will also allow us to study the interaction of the Musa acuminata (A) and Musa balbisiana (B) genomes in the complex allopolyploids of Musa, especially the plantains (AAB) and the East African bananas (AAB).
The data set from this project will be applied to hands-on undergraduate research experience for students taking Molecular Biology (Biol 303) and Applied Biotechnology (Biol 423) courses at Bowie State University. Students will extract RNA and participate in sequence data analysis using NGS technologies in the study of gene expression and regulation.
Materials are under development.