Convergently selected NPF2.12 coordinates root growth and nitrogen use efficiency in wheat and barley

center dot Understanding the genetic and molecular function of nitrate sensing and acquisition across crop species will accelerate breeding of cultivars with improved nitrogen use efficiency (NUE). center dot Here, we performed a genome-wide scan using wheat and barley accessions characterized under low and high N inputs that uncovered the NPF2.12 gene, encoding a homolog of the Arabidopsis nitrate transceptor NRT1.6 and other low-affinity nitrate transporters that belong to the MAJOR FACILITATOR SUPERFAMILY. center dot Next, it is shown that variations in the NPF2.12 promoter correlated with altered NPF2.12 transcript levels where decreased gene expression was measured under low nitrate availability. Multiple field trials revealed a significantly enhanced N content in leaves and grains and NUE in the presence of the elite allele TaNPF2.12(TT) grown under low N conditions. Furthermore, the nitrate reductase encoding gene NIA1 was up-regulated in npf2.12 mutant upon low nitrate concentrations, thereby resulting in elevated levels of nitric oxide (NO) production. This increase in NO correlated with the higher root growth, nitrate uptake, and N translocation observed in the mutant when compared to wild-type. center dot The presented data indicate that the elite haplotype alleles of NPF2.12 are convergently selected in wheat and barley that by inactivation indirectly contribute to root growth and NUE by activating NO signaling under low nitrate conditions.

Automated summary

Understanding how crops sense and acquire nitrate is crucial for improving nitrogen use efficiency (NUE) in breeding. This study identified the NPF2.12 gene in wheat and barley, which is associated with low-affinity nitrate transporters. The expression of NPF2.12 decreases under low nitrate conditions. Field trials showed that crops with the elite allele TaNPF2.12(TT) had higher nitrogen content and NUE in leaves and grains under low nitrate conditions.