Diversity and selective sweep in the OsAMT1;1 genomic region of rice.

Zehong Ding,Sheng Chen,Chongrong Wang,Sibin Yu

doi:10.1186/1471-2148-11-61

Zehong Ding, Sheng Chen + Show 2 more

Open Access

https://doi.org/10.1186/1471-2148-11-61

Copy DOI

Abstract

BackgroundAmmonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L.), responsible for ammonium uptake at low nitrogen concentration. The expression pattern of the gene has been reported. However, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. In this study, nucleotide diversity of the gene OsAMT1;1 and the diversity pattern of seven gene fragments spanning a genomic region approximately 150 kb long surrounding the gene were surveyed by sequencing a panel of 216 rice accessions including both cultivated rice and wild relatives.ResultsNucleotide polymorphism (Pi) of OsAMT1;1 was as low as 0.00004 in cultivated rice (Oryza sativa), only 2.3% of that in the common wild rice (O. rufipogon). A single dominant haplotype was fixed at the locus in O. sativa. The test values for neutrality were significantly negative in the entire region stretching 5' upstream and 3' downstream of the gene in all accessions. The value of linkage disequilibrium remained high across a 100 kb genomic region around OsAMT1;1 in O. sativa, but fell rapidly in O. rufipogon on either side of the promoter of OsAMT1;1, demonstrating a strong natural selection within or nearby the ammonium transporter.ConclusionsThe severe reduction in nucleotide variation at OsAMT1;1 in rice was caused by a selective sweep around OsAMT1;1, which may reflect the nitrogen uptake system under strong selection by the paddy soil during the domestication of rice. Purifying selection also occurred before the wild rice diverged into its two subspecies, namely indica and japonica. These findings would provide useful insights into the processes of evolution and domestication of nitrogen uptake genes in rice.

Highlights

Ammonium is one of the major forms in which nitrogen is available for plant growth
The examination yielded 32 single nucleotide polymorphisms (SNP) and 9 insertions or deletions (Indels) in this 2.68-kb region (Figure 1), of which 30 polymorphism sites (25 SNPs and 5 Indels) were observed in the wild rice accessions and most were located in the non-coding region
O.rufipogon O.sativa across the gene in O. sativa (190 accessions) and O. rufipogon (19 accessions) revealed a sharp peak at a point of about 200 bp upstream of the start codon of the gene (Figure 2). These results suggest a strong selection at OsAMT1;1, in the 5’ promoter region

Summary

Introduction

Ammonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L.), responsible for ammonium uptake at low nitrogen concentration. A major gene for grain shattering in rice, shattering 4 (sh4), has been characterized: nucleotide diversity of a ~50 kb region surrounding sh, is nearly one-tenth of the average value across the entire chromosome 4 [8,9]. Wang et al [13] showed that maize has retained only 3% of the diversity found in teosinte in the 5’ non-transcribed region of tb, again as a result of human selection. Because of the effect of selection hitchhiking, nucleotide diversity was lower around the region of Y1 from ~600 kb downstream to ~200 kb upstream [17] These results provide significant insights into the selective sweeps brought about by artificial selection during the process of crop domestication

Objectives

Methods

Results

Discussion

Conclusion