Dissection of the Genetic Basis Underlying Wax Biosynthesis in Hexaploid Wheat Using Bi-Parental Linkage Mapping and Genome-wide Association Study

Epicuticular wax acts as a plant’s first line of defense against environmental afflictions. Wax is known to be a factor in stress adaptation and also provides resistance to disease, drought, and heat due to its ability to reduce water loss, increase light reflectance, and reduce fungal infection. The introgression of major wax genes into cultivars and breeding lines will improve wheat breeding. In order to dissect the quantitative trait loci (QTLs) underlying wax biosynthesis, a bi-parental QTL mapping study has been conducted on a RIL population and a genome-wide association study (GWAS) has been carried out on a panel of synthetic-derived wheat lines. QTL analysis was performed using 8,440 single-nucleotide polymorphisms (SNPs) identified from a wheat 90K iSelect SNP array. A QTL on chromosome 2BS controlling wax-related traits was stably detected across different developmental stages. The QTL explained up to 18.6% epicuticular wax load (EWL) variation and 18.9% glaucousness variation in the population. The QTLs for head length and tiller number were co-localized with this wax QTL. The pleotropic QTL on 4B may be a developmental stage-specific region controlling wax biosynthesis in the early reproductive stages, as well as controlling plant height. A novel QTL for plant height on 3B was detected in this study, which provides clues for the dissection of the genetic basis underlying this trait. The association panel of 300 synthetic-derived wheat lines has been genotyped using ddRAD-seq and phenotyped in conditions with different combinations of environments and developmental stages. 137,856 SNPs were identified from ddRAD-seq for further analysis. Epicuticular wax load was measured in the conditions: BD16FL, BI16FL, CH16TD, CS16FL, CS16TD, BD17FL, BI17FL, and CL17FL. Glaucousness was recorded in the conditions: BD16HD, BI16HD, BD16FL, BI16FL, CH16TD, BD17FL and PR17FL. About 200 significant marker-trait associations (MTA) have been identified, with most of the SNPs being associated with glaucousness. A majority of significant SNPs were mapped on the short arm of the chromosome 2D. A QTL associated with glaucousness on 2D can be consistently detected across all the non-optimal conditions we studied. This QTL identified in GWAS analysis flanked by 5293194_2ds_2515 and 5348611_2ds_1248 may contain the locus of INHIBITOR OF WAX2 (Iw2), which is also located on the distal region of 2DS. The major QTLs for wax-related traits and significant marker trait associations identified in this study will lay a foundation for the clarification of the genetic basis underlying the regulation of spatiotemporal expression of wax