Genetic basis of Fusarium ear rot resistance and productivity traits in a heterozygous multi-parent recombinant inbred intercross (RIX) maize population

Abstract

Maize (Zea mays L.) is one of the most productive crops worldwide. As a heterotic crop predominantly grown as F₁ hybrid, maize exhibits challenges for genetic studies of complex traits, since homozygous genotypes, which are largely used in these studies, may not accurately reflect what happens in cultivated conditions. To map Fusarium Ear Rot (FER) resistance to Fusarium verticillioides and traits with potential impact on yield, including phenology, we constructed a recombinant intercross (RIX) population. This was achived by crossing pairs of recombinant inbred lines (RILs) derived from a multi-parent maize population. We characterized the RIX population over two growing seasons, employing artificial F. verticillioides inoculation. The heterozygous background of the material enabled the identification of QTL and candidate genes through in silico reconstruction of RIX genotype probabilities. A total of 37 loci were identified using single-year BLUPs while 29 with joint-year BLUPs. These, included several known QTL associated with days to tasseling, kernel row number and a QTL on the chromosome 9 associated with FER resistance. In this region, we could identify candidates based on their predicted functions and potential roles in plant-pathogen interactions and/or resistance mechanisms. These QTL represent potential breeding targets to FER resistance and yield components in commercial maize varieties.

Keywords: Ear traits; Flowering time; Fusarium ear rot resistance; Maize; Multiparent mapping populations; QTL mapping; Recombinant Inbred Intercross (RIX).

Fig. 1

A) Schematic representation of the chain-crossing scheme used to produce the RIX panel: Each RIL was crossed with its adjacent RIL. Exceptions to this scheme occurred due to differences in flowering times. B) Kinship represented as heatmap of pairwise similarities between the 214 RIX genomes reconstructed starting from MAGIC maize RILs: white and red represent low and high similarities, respectively. On the left and top side, a hierarchical tree represents relationship between RIX. Samples were ordered according to R base function hclust(). The histogram in inset represents the count of occurrences (i.e. similarity, y axis) vs the similarity value subdivided by 1,000 bins

Fig. 2

A) Pairwise complete observation correlations BLUPs of the MAGIC maize RIX population measured in 2018 and 2019. Non-significant coefficients (P < 0.05) are marked with an ‘x’. B) PCA of scaled joint-model BLUPs of 214 MAGIC maize RIX. Individual RIX are depicted as gray dots while the MAGIC founder lines are higligheted with colors. Abbreviations: DT: Days to Tasseling, Krows: n° of kernel rows; EL: Ear length; ED: Ear diameter; CD: Cob diameter; Vweight: Volumetric weight; FER_score: Fusarium Ear Rot severity scores; C) boxplots of joint model BLUPs of Ear Diameter and D) FER score, with color coding according to panel B

Fig. 3

QTL mapping results of the Fusarium Ear Rot (FER) score phenotyping; A) Genome-wide LOD score plot. B) LOD score plot of chromosome 9; in both figures the red and the green dotted lines represents the threshold of significance of the 99^th and 95^th percentiles, respectively, of the permuted LOD distribution, based on 999 permutations. C) Effect, expressed as coefficient, of each founder at the QTL confidence interval