Mapping and validation of QTLs for nitrogen use efficiency traits in sorghum and identification of candidate genes associated with QTLs

Understanding the genetic variation of sorghum response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen use efficiency (NUE). In this study, two F7 recombinant inbred line populations were developed and used to detect QTLs for multiple agronomic traits. The populations were analyzed under normal N (100 kg.ha-1 fertilizer) and low N (0 kg.ha-1 fertilizer) conditions for two years with two replications each. The linkage maps, spanning a length of 1584 cM and 1527 cM were developed using single nucleotide polymorphisms (SNPs) generated from genotyping-by-sequencing (GBS) technology. Composite interval mapping analysis detected several QTLs for 11 traits tested across two populations. The phenotypic variation explained by individual QTL ranged from 6.2% to 50.8%. Five QTLs were detected consistently across two populations. Co-localized regions affecting multiple traits were detected on chromosomes 1, 3, 6, 7 and 9. These pleiotropic regions were coincident with the genomic regions of cloned QTLs, including Ma3 for flowering time on chromosome 1 and Dw2 for plant height on chromosome 6. In the co-localized regions, Illumina RNA sequencing detected differentially expressed genes related to nitrogen metabolism, glycolysis, seed storage proteins, genes involved in plant hormone metabolism and several membrane transporters. Genes underlying the QTL regions could be potential targets for improving the sorghum performance under limited N fertilizer through marker assisted selection