Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat

Prabin Bajgain; Blake Russell; Mohsen Mohammadi

doi:10.1038/s41598-018-25430-8

Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat

Prabin Bajgain, Blake Russell, Mohsen Mohammadi

Agronomy and Plant Genetics

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

Abstract

Plants deploy several ammonium transporter (AMT) and nitrate transporter (NRT) genes to acquire NH₄ ⁺ and NO₃ ^- from the soil into the roots and then transport them to other plant organs. Coding sequences of wheat genes obtained from ENSEMBL were aligned to known AMT and NRT sequences of Arabidopsis, barley, maize, rice, and wheat to retrieve homologous genes. Bayesian phylogenetic relationships among these genes showed distinct classification of sequences with significant homology to NRT1, NRT2, and NRT3 (NAR2). Inter-species gene duplication analysis showed that eight AMT and 77 NRT genes were orthologous to the AMT and NRT genes of aforementioned plant species. Expression patterns of these genes were studied via whole transcriptome sequencing of 21-day old seedlings of five spring wheat lines. Eight AMT and 52 NRT genes were differentially expressed between root and shoot; and 131 genes did not express neither in root nor in shoot of 21-day old seedlings. Homeologous genes in the A, B, and D genomes, characterized by high sequence homology, revealed that their counterparts exhibited different expression patterns. This complement and evolutionary relationship of wheat AMT and NRT genes is expected to help in development of wheat germplasm with increased efficiency in nitrogen uptake and usage.

Original language	English (US)
Article number	7082
Journal	Scientific reports
Volume	8
Issue number	1
DOIs	https://doi.org/10.1038/s41598-018-25430-8
State	Published - Dec 1 2018

Bibliographical note

Funding Information:
We are grateful towards Dr. Harold Bockelman and his team (National Small Grains Collection, Aberdeen, ID) for providing seeds of the wheat lines used in this study. We extend our gratitude towards Dr. Cankui Zhang (Purdue University) for reviewing this manuscript and for laboratory support. We also thank Purdue Genomics Core Facility for sequencing services and Purdue University’s Research Computing (RCAC) for computational support. The PI MM is financially supported by the Hatch Fund IND010810 entitled “Genetics and Breeding for Increased Yield, Disease Resistance, and Abiotic Stress Tolerance in Wheat” through the National Institute of Food and Agriculture (NIFA).

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© 2018 The Author(s).

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abstract = "Plants deploy several ammonium transporter (AMT) and nitrate transporter (NRT) genes to acquire NH4 + and NO3 - from the soil into the roots and then transport them to other plant organs. Coding sequences of wheat genes obtained from ENSEMBL were aligned to known AMT and NRT sequences of Arabidopsis, barley, maize, rice, and wheat to retrieve homologous genes. Bayesian phylogenetic relationships among these genes showed distinct classification of sequences with significant homology to NRT1, NRT2, and NRT3 (NAR2). Inter-species gene duplication analysis showed that eight AMT and 77 NRT genes were orthologous to the AMT and NRT genes of aforementioned plant species. Expression patterns of these genes were studied via whole transcriptome sequencing of 21-day old seedlings of five spring wheat lines. Eight AMT and 52 NRT genes were differentially expressed between root and shoot; and 131 genes did not express neither in root nor in shoot of 21-day old seedlings. Homeologous genes in the A, B, and D genomes, characterized by high sequence homology, revealed that their counterparts exhibited different expression patterns. This complement and evolutionary relationship of wheat AMT and NRT genes is expected to help in development of wheat germplasm with increased efficiency in nitrogen uptake and usage.",

author = "Prabin Bajgain and Blake Russell and Mohsen Mohammadi",

note = "Funding Information: We are grateful towards Dr. Harold Bockelman and his team (National Small Grains Collection, Aberdeen, ID) for providing seeds of the wheat lines used in this study. We extend our gratitude towards Dr. Cankui Zhang (Purdue University) for reviewing this manuscript and for laboratory support. We also thank Purdue Genomics Core Facility for sequencing services and Purdue University{\textquoteright}s Research Computing (RCAC) for computational support. The PI MM is financially supported by the Hatch Fund IND010810 entitled “Genetics and Breeding for Increased Yield, Disease Resistance, and Abiotic Stress Tolerance in Wheat” through the National Institute of Food and Agriculture (NIFA). Publisher Copyright: {\textcopyright} 2018 The Author(s).",

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Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat

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