Mapping of QTLs for morphophysiological and yield traits under water-deficit stress and well-watered conditions in maize

Abstract

Maize productivity is significantly impacted by drought; therefore, improvement of drought tolerance is a critical goal in maize breeding. To achieve this, a better understanding of the genetic basis of drought tolerance is necessary. Our study aimed to identify genomic regions associated with drought tolerance-related traits by phenotyping a mapping population of recombinant inbred lines (RILs) for two seasons under well-watered (WW) and water-deficit (WD) conditions. We also used single nucleotide polymorphism (SNP) genotyping through genotyping-by-sequencing to map these regions and attempted to identify candidate genes responsible for the observed phenotypic variation. Phenotyping of the RILs population revealed significant variability in most of the traits, with normal frequency distributions, indicating their polygenic nature. We generated a linkage map using 1,241 polymorphic SNPs distributed over 10 chromosomes (chrs), covering a total genetic distance of 5,471.55 cM. We identified 27 quantitative trait loci (QTLs) associated with various morphophysiological and yield-related traits, with 13 QTLs identified under WW conditions and 12 under WD conditions. We found one common major QTL (qCW2-1) for cob weight and a minor QTL (qCH1-1) for cob height that were consistently identified under both water regimes. We also detected one major and one minor QTL for the Normalized Difference Vegetation Index (NDVI) trait under WD conditions on chr 2, bin 2.10. Furthermore, we identified one major QTL (qCH1-2) and one minor QTL (qCH1-1) on chr 1 that were located at different genomic positions to those identified in earlier studies. We found co-localized QTLs for stomatal conductance and grain yield on chr 6 (qg_s6-2 and qGY6-1), while co-localized QTLs for stomatal conductance and transpiration rate were identified on chr 7 (qg_s7-1 and qTR7-1). We also attempted to identify the candidate genes responsible for the observed phenotypic variation; our analysis revealed that the major candidate genes associated with QTLs detected under water deficit conditions were related to growth and development, senescence, abscisic acid (ABA) signaling, signal transduction, and transporter activity in stress tolerance. The QTL regions identified in this study may be useful in designing markers that can be utilized in marker-assisted selection breeding. In addition, the putative candidate genes can be isolated and functionally characterized so that their role in imparting drought tolerance can be more fully understood.

Keywords: QTLs; SNPs; candidate genes; drought; physiological and yield traits.

Figure 1

Frequency distribution of the phenotypic data of the RILs population of the various morphophysiological and yield related traits. The values of the parents (P₁ - HKII61 and P₂ SNJ201126 are indicated by arrows); NDVI, Normalized difference vegetation index; Anet, Net CO₂ assimilation rate; g_s, Stomatal conductance to water vapor; TR, Transpiration rate; LT, Leaf temperature; CH, Cob height; ASI, Anthesis-silking interval; CW, Cob weight; TB, Total biomass; GY,Grain yield/plant; WW, Well-watered; WD, Water-deficit stress.

Figure 2

Positions of the quantitative trait loci (QTLs) for various morphophysiological and yield-related traits on seven chromosomes in the recombinant inbred line (RIL) population grown under well-watered and water-deficit conditions. The scaled numbers on the left side of the chromosomes indicate genetic length (cM), with the corresponding markers on the right side. The colored bars and triangles represent the QTLs identified for the various traits and the condition, respectively. A_net, net CO₂ assimilation rate; ASI, anthesis-silking interval; CH, cob height; CW, cob weight; g_s, stomatal conductance to water vapor; GY, grain yield; LT, leaf temperature; NDVI, Normalized Difference Vegetation Index; TB, total biomass; TR, transpiration rate; chr, chromosome; WW, well-watered conditions; WD, water-deficit conditions.