Multi-Environment QTL Analysis Of Grain Morphology Traits And Fine Mapping Of A Kernel-Width QTL In Zheng58 × SK Maize Population

To elucidate the genetic basis of kernel traits, a quantitative trait locus(QTL) analysis was conducted in a maize recombinant inbred line population derived from a cross between Zheng58, a widely used elite line with a regular kernel size and SK, a selected line from a tropical landrace with small kernels, evaluated across eight environments. Analysis of variance and correlation study demonstrated that the main effects of genotype and environment were significant for all traits and all the traits were significantly associated with each other. Construction of a high-density linkage map was based on 13,703 single-nucleotide polymorphism markers covering 1,860.9 c M of the whole genome. In total, 18, 26, 23 and 19 QTLs for kernel length, width, thickness and 100-kernel weight, respectively, were detected on the basis of a single-environment analysis, and each QTL explained 3.2 to 23.7% of the phenotypic variance. A great portion of the identified QTL performed high stability across two years at the same environment or even across unlike environment although the phenotypic variation explained by such stable QTLs diverged in magnitude among the different environments. Sixteen major QTLs, which could explain greater than 10% of the phenotypic variation, were mapped in multiple environments, implying that kernel traits might be controlled by many minor and multiple major QTLs. Furthermore, exploiting the best linear unbiased predictor(BLUP) data altogether 34 QTLs were detected for all the four traits studied and 22 of them were clustered in 8 genomic regions on chromosomes 1, 3, 7, 8, 9 and 10. The major QTL q KW-9.2 with physical confidence interval of 1.68 Mbp, affecting kernel width, was then selected for fine mapping. Consequently, heterogeneous inbred families(HIFs) were developed resulting from self pollination of recombinant inbred lines(RILs) which showed residual heterozygosity in the target interval to fine mapping of q KW-9.2 locus. With eight microsatellites markers, we validated this QTL(P<0.0001) and in one generation of mapping, the location of the underlying gene was narrowed down to 630 Kb, harboring 28 putative candidate gene models. This information will enhance molecular breeding for kernel traits and simultaneously assist the gene cloning underlying this QTL, helping to reveal the genetic basis of kernel development in maize.