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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #320887

Research Project: Genetic Enhancement of Dry Bean Nutritional and Processing Qualities

Location: Sugarbeet and Bean Research

Title: Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation

Author
item KAMFWA, KELVIN - Michigan State University
item ZHAO, DONGYAN - Michigan State University
item KELLY, JAMES - Michigan State University
item Cichy, Karen

Submitted to: PLoS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/3/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: Common bean (Phaseolus vulgaris L.) is able to fix atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF) with Rhizobia, a soil bacteria. In common bean there is genetic variability for SNF ability. Effective utilization of existing variability for genetic improvement would be increased by an understanding of underlying genes and molecular mechanisms. The utility of transcriptome profiling using RNA-sequencing was explored to identify genes and molecular mechanisms underlying contrasting SNF phenotypes of two recombinant inbred lines, SP36 and SP118, of common bean. A total of 30 RNA samples were collected from leaves, nodules and roots of SP36 and SP118 grown under N fixing and non-fixing condition, and sequenced using Illumina technology. Genes encoding receptor kinases, transmembrane transporters, and transcription factors (TFs) were among differentially expressed genes (DEGs) between SP36 and SP118 under N-fixing condition but not under non-fixing condition. TFs identified in this study are strong candidates for future studies to support the development of gene-based markers to accelerate genetic improvement of common bean for SNF.

Technical Abstract: Common bean (Phaseolus vulgaris L.) is able to fix atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF). Effective utilization of existing variability for SNF in common bean for genetic improvement requires an understanding of underlying genes and molecular mechanisms. The utility of transcriptome profiling using RNA-sequencing was explored to identify genes and molecular mechanisms underlying contrasting SNF phenotypes of two recombinant inbred lines SP36 and SP118 of common bean. A total of 30 RNA samples were collected from leaves, nodules and roots of SP36 and SP118 grown under N fixing and non-fixing condition, and sequenced using Illumina technology. Genes encoding receptor kinases, transmembrane transporters, and transcription factors (TFs) were among differentially expressed genes (DEGs) between SP36 and SP118 under N-fixing condition but not under non-fixing condition. Enriched molecular functions of DEGs up-regulated in SP36 included purine nucleoside binding, oxidoreductase and transmembrane receptor activities in nodules, and transport activity in roots. TFs identified in this study are strong candidates for future studies aimed at enhancing our understanding of functional roles of these factors in SNF. Information generated in this study could support development of gene-based markers to accelerate genetic improvement of common bean for SNF.