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

Abstract

Common bean (Phaseolus vulgaris L.) fixes atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF) at levels lower than other grain legume crops. An understanding of the genes and molecular mechanisms underlying SNF will enable more effective strategies for the genetic improvement of SNF traits in common bean. In this study, transcriptome profiling was used to identify genes and molecular mechanisms underlying SNF differences between two common bean recombinant inbred lines that differed in their N-fixing abilities. Differential gene expression and functional enrichment analyses were performed on leaves, nodules and roots of the two lines when grown under N-fixing and non-fixing conditions. Receptor kinases, transmembrane transporters, and transcription factors were among the differentially expressed genes identified under N-fixing conditions, but not under non-fixing conditions. Genes up-regulated in the stronger nitrogen fixer, SA36, included those involved in molecular functions such as purine nucleoside binding, oxidoreductase and transmembrane receptor activities in nodules, and transport activity in roots. Transcription factors identified in this study are candidates for future work aimed at understanding the functional role of these genes in SNF. Information generated in this study will support the development of gene-based markers to accelerate genetic improvement of SNF in common bean.

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

“…PKs’ expression quantifications were assessed using RNA-Seq experiments detailed in Supplementary Table S1 and obtained from NCBI’s Sequence Read Archive (SRA) (Leinonen et al, 2010). We selected datasets containing samples from different bean genotypes (Negro Jamapa, SA118, SA36, Black Turtle Soup, G19833, Ispir, DOR364 and IAC-Imperador) and analysed in different tissues (leaves, stems, shoots, flowers, pods, seeds and nodules) (Hiz et al, 2014; Kamfwa et al, 2017; Khankhum et al, 2016; Lu et al, 2019; O’Rourke et al, 2014; Silva et al, 2019). RNA-Seq reads were downloaded and their quality assessed with FastQC software (Andrews, 2010).…”

Mapping additive and epistatic QTLs for forage quality and yield in soybean [Glycine max (L.) Merri.] in two environments

“…The number of polymorphism markers between parents may be limited, leading to low marker density, fewer detected intervals and low efficiency of QTL detection. To overcome this limitation, plant breeders had adopted a multi-population improvement strategy, which has been used in rice, arabidopsis, maize and soybean [31][32][33][34][35][36]. In this study, we used two RIL populations with the same female parent (Dongnong L13) to locate QTLs for forage quality and yield traits (Tables 3 and 5).…”

Genomics, genetics and breeding of common bean in Africa: A review of tropical legume project

“…(2017). Traits such as greater BRWN (Lynch, ), percentage of nitrogen derived from atmosphere ( %Ndfa ) (Mehdi, ; Rao, Miles, & Beebe, ), biological nitrification inhibition (BNI) (Subbarao, Yoshihashi, & Worthington, ), receptor kinases, transmembrane transporters, and transcription factors (Kamfwa, Zhao, Kelly, & Cichy, ) have been employed in selecting for tolerance to specific mineral deficiencies. Lines developed by CIAT for combined drought and low soil fertility tolerance are being evaluated in Ethiopia, Uganda and Tanzania.…”