Natural Variation in NIN-LIKE PROTEIN 4 Associated With Spike-Response to Nitrogen in Barley.

Abstract

Nitrogen (N) fertilisers increase crop yields; however, excessive application reduces nitrogen use efficiency (NUE) and causes environmental pollution, highlighting the urgent need for sustainable agricultural practices. This study investigated the response of tiller-related traits to nitrogen availability during barley domestication and breeding, aiming to identify genetic resources with high NUE. A total of 305 barley accessions were analyzed under two nitrogen levels, focusing on six tiller-related traits and their relationship with nitrogen supply. Domestication reduced tillers per plant (TPP) and nonproductive tillers per plant (NTPP), while breeding increased spikes per plant (SPP), proportion of productive tillers (PPT), and Spike-response to nitrogen (SRN). SRN was used as a key indicator to evaluate spike development under varying nitrogen conditions. Genome-Wide Association Study (GWAS) and RNA-seq analysis identified HvNLP4 as a key candidate gene regulating SRN, with haplotype analysis revealing that HvNLP4^Hap1, associated with high SRN, underwent strong positive selection during domestication and breeding. Moreover, HvNLP4^Hap1 exhibited weaker induction under low nitrogen conditions, suggesting that avoiding its selection in future breeding programmes may enhance NUE in barley. These findings provide valuable insights for developing sustainable barley cultivars with improved nitrogen efficiency.