Genome-wide SNP discovery, identification of QTLs and candidate genes associated with morpho-physiological and yield related traits for drought tolerance in maize

Abstract Drought is one of most important abiotic stresses affecting maize yield. The present study was aimed to map genomic regions associated with the morpho-physiological and yield related traits in maize under well-watered and water-deficit stress conditions using recombinant inbred population (RILs) derived from the cross HKI161 × SNJ201126 by genome-wide SNP discovery using genotyping-by-sequencing approach. Phenotyping of RILs showed normal frequency distribution for most of the traits indicating their polygenic nature. The SNP linkage map was generated using 1241 SNP markers which were distributed over 10 linkage groups and covered a total genetic distance of 5471.55cM. A total of 40 QTLs were identified for the various morpho-physiological and yield related traits under well-watered (26) and water-deficit stress conditions (14). Of these 14 were major QTLs, 26 were minor QTLs and two QTLs (qCW2-1, qCH1-1) were detected under both conditions. Three QTL hotspots regions were identified, one for net CO2 assimilation rate (AN) and transpiration rate (TR) (qAN3-1, qTR3-1 and qAN3-2) on chromosome (chr) 3, cob height (CH) and plant height (PH) (qCH8-1 and qPH8-1) on chr 8 and cob weight (CW), total biomass (TB) and grain yield (GY) (qCW2-1, qTB2-1, qTB2-2 and qGY2-1) on chr 2 capturing phenotypic variability ranging between 10.10–22.33%. The QTL hotspot region for AN & TR encoded for genes involved in signal transduction pathway under water-deficit stress tolerance, maintenance of plant membrane and cell wall integrity and cross membrane transport. While QTL hotspot for PH and CH encoded genes involved in carbon utilization in plant growth and development, directed movement of proteins in the cell and transmembrane transporter activity. The QTL hotspot for yield encoded genes involved in signal transduction and plant development. These regions can be further fine mapped and used for marker assisted breeding in maize.