English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Plus monthly

Global: Zendy Tools annual

Global: Zendy Tools monthly

Global: Zendy Free Plan

Background  In the model legume  Medicago truncatula , the near saturation genome-wide  Tnt1  insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified many  Tnt1  mutants defective in nodule development and symbiotic nitrogen fixation (SNF). However, progress toward identifying the causative mutations of these symbiotic mutants has been slow because of the high copy number of  Tnt1  insertions in some mutant plants and inefficient recovery of flanking sequence tags (FSTs) by thermal asymmetric interlaced PCR (TAIL-PCR) and other techniques.    Results  Two  Tnt1  symbiotic mutants, NF11217 and NF10547, with defects in nodulation and SNF were isolated during a forward genetic screen. Both TAIL-PCR and whole genome sequencing (WGS) approaches were used in attempts to find the relevant mutant genes in NF11217 and NF10547. Illumina paired-end WGS generated ~16 Gb of sequence data from a 500 bp insert library for each mutant, yielding ~40X genome coverage. Bioinformatics analysis of the sequence data identified 97 and 65 high confidence independent  Tnt1  insertion loci in NF11217 and NF10547, respectively. In comparison to TAIL-PCR, WGS recovered more  Tnt1  insertions. From the WGS data, we found  Tnt1  insertions in the exons of the previously described  PHOSPHOLIPASE C (PLC)-like  and  NODULE INCEPTION (NIN)  genes in NF11217 and NF10547 mutants, respectively. Co-segregation analyses confirmed that the symbiotic phenotypes of NF11217 and NF10547 are tightly linked to the  Tnt1  insertions in  PLC-like  and  NIN  genes, respectively.    Conclusions  In this work, we demonstrate that WGS is an efficient approach for identification of causative genes underlying SNF defective phenotypes in  M. truncatula Tnt1  insertion mutants obtained via forward genetic screens.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2452-5) contains supplementary material, which is available to authorized users.

bmc genomics

Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing