Genome-Wide Association Study and Identification of Candidate Genes for Nitrogen Use Efficiency in Barley (Hordeum vulgare L.)

Abstract

Nitrogen (N) fertilizer is largely responsible for barley grain yield potential and quality, yet excessive application leads to environmental pollution and high production costs. Therefore, efficient use of N is fundamental for sustainable agriculture. In the present study, we investigated the performance of 282 barley accessions through hydroponic screening using optimal and low NH 4 NO 3 treatments. Low-N treatment led to an average shoot dry weight reduction of 50%, but there were significant genotypic differences among the accessions. Approximately 20% of the genotypes showed high (>75%) relative shoot dry weight under low-N treatment and were classified as low-N tolerant, whereas 20% were low-N sensitive (≤55%). Low-N tolerant accessions exhibited well-developed root systems with an average increase of 60% in relative root dry weight to facilitate more N absorption. A genome-wide association study (GWAS) identified 66 significant marker trait associations (MTAs) conferring high nitrogen use efficiency, four of which were stable across experiments. These four MTAs were located on chromosomes 1H(1), 3H(1), and 7H(2) and were associated with relative shoot length, relative shoot and root dry weight. Genes corresponding to the significant MTAs were retrieved as candidate genes, including members of the asparagine synthetase gene family, several transcription factor families, protein kinases, and nitrate transporters. Most importantly, the highaffinity nitrate transporter 2.7 (HvNRT2.7) was identified as a promising candidate on 7H for root and shoot dry weight. The identified candidate genes provide new insights into our understanding of the molecular mechanisms driving nitrogen use efficiency in barley and represent potential targets for genetic improvement.

Quantitative Trait Loci Mapping for Vigour and Survival Traits of Barley Seedlings after Germinating under Salinity Stress

“…Completely randomised design with three replications was used and the experiments were repeated four times. The solution in each tank was replaced after seven days and the pH adjusted to 6.5 through addition of NaOH and/or HCl [31].…”

Genotypic Variation of Nitrogen Use Efficiency and Amino Acid Metabolism in Barley

“…Indeed, at the time of harvest, i.e., 14 days after sowing, most of the metabolic processes may have been adjusted and stabilized under LN and HN. Among the genes found to be commonly up-regulated, the putative nitrate transporter coding gene HvNRT2.10 (HORVUHrG098550) orthologous to the Arabidopsis AtNRT2.7 gene, is of particular interest since it was found in a QTL mapping study as involved in barley tolerance to low N (Karunarathne et al, 2020). This gene is closely related to OsNRT2.4 (Guo et al, 2020) which encodes a dual affinity nitrate transporter and was found to be involved in rice N nutrition although no phenotype was found for the knockout mutant (Wei et al, 2018).…”

“…Importantly, nitrogen fertilization impacts plant tolerance to abiotic and biotic stresses (Fagard et al, 2014;Abid et al, 2016;Mur et al, 2017;Ding et al, 2018;Verly et al, 2020). The genetic diversity in terms of barley tolerance to nitrogen starvation has been explored (Oscarsson et al, 1998;Górny, 2001;Sinebo et al, 2004;Quan et al, 2016Quan et al, , 2019Karunarathne et al, 2020). However few data are available concerning the diversity of molecular responses of barley to nitrogen limitation (Møller et al, 2011;Quan et al, 2016Quan et al, , 2019Karunarathne et al, 2020Karunarathne et al, , 2021.…”

Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants

“…The importance of these studies was demonstrated in a recent study of GWAS developed in wild and domesticated accessions of barley, allowing to identify markers trait associations conferring efficient nitrogen use. HvNRT2.7 was identified as a promising candidate to increase the dry weight of the root and shoot and became a potential target for genetic improvement in this species [ 103 ]. In addition, for the pleiotropic effects of the NRT2 and NRT3 gene families, recent findings indicate that the genetic basis of efficient transport of nitrate involves these transporters among a pyramid of several genes that must be ranked to achieve the most effective approach that allows a satisfactory NUE level in the field [ 104 ] In rice crops, it has been shown that the overexpression of the OsNRT2.3b transporter increases the NUE, but this response improves if this transporter is introduced together with the promoter OsNAR2.1p.…”