Genetic Basis of Nitrogen Use Efficiency and Its Application in Wheat Breeding
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Nitrogen is the major limiting factor in crop production worldwide, and N is now the single largest input cost for many crops including wheat. Nitrogen use efficiency (NUE) is a complex trait, and as many as 25 genes have been estimated to be involved in regulating NUE in the diploid model species Arabidopsis. Numerous quantitative trait loci (QTLs) for agronomic traits associated with N use and yield have been mapped in wheat, but no gene has been characterized in this crop species. The genetic mechanisms controlling NUE in wheat are unknown.In this study, we cloned a major QTL for N-related agronomic traits in winter wheat using map-based cloning approach. Based on the phenotypes and genotypes of critical recombinant lines that were generated from a cross between two winter wheat cultivars,"Jagger" and "2174," we delimited the QTL into a genomic region including three candidate genes. We found that the vernalization gene TaVRN-A1 was tightly linked with TaNUE1, the gene shown to influence NUE in wheat. Because of an Ala180/Val180 substitution, TaVRN-A1a protein encoded by the Jagger allele and TaVRN-A1b protein encoded by the 2174 allele interacted differentially with TaANR1, a protein encoded by a wheat orthologue of Arabidopsis nitrate regulated 1 (ANR1). The transcripts of both TaVRN-A1 and TaANR1 were down-regulated by nitrogen. TaANR1 was functionally characterized in TaANR1::RNAi transgenic wheat and in a natural mutant with a 23-bp deletion including 10-bp at the 5' end of intron 5 and 13-bp of exon 6 in its gDNA sequence, which produced transcript that lacked the full 84-bp of exon 6. Both TaANR1 and TaHOX1 bound to the Ala180/Val180 position of TaVRN-A1. These findings explained why NUE was regulated by TaVRN-A1 gene in wheat.We genotyped TaVRN-A1, TaANR1 and TaHOX1 and characterized grain yields in the Jagger x 2174 recombinant inbred lines in a field for two years. Genetically incorporating favorable alleles from TaVRN-A1, TaANR1 and TaHOX1 increased grain yield by 9.84% to 11.58% in the field. Molecular markers for allelic variation in these three genes can be used in breeding programs aimed an improved NUE and grain yield.
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