Genes deregulated during maize haploid induction.

This is mRNA-seq data from maize pollen. There are four biological replicates for each of four genotypes, totaling sixteen samples. The four genotypes are two pairs of near isogenic lines, with each pair consisting of one haploid inducer line and one non-inducer near-isogenic line. The haploid inducer and non-inducer line in each pair differ from each other genetically by the chromosome 1 QTL in bin 1.04 (a.k.a. qhir11) that has been associated with the haploid inducer trait. The inducer line in each pair has a haploid induction rate over 10%, while the non-inducer near-isogenic line in each pair has a haploid induction rate of less than 0.2% (wild-type levels). The trait is associated with the male gametophyte of maize (pollen), which is why pollen was sampled for this study.The haploid inducer and non-inducer line in each pair are compared to each other to identify differentially expressed genes that are associated with the haploid induction trait, in the context of a (mostly) fixed genetic background. Because the genetic backgrounds are not perfectly fixed (as they are near-isogenic), we expect that many of the DEGs found in a given comparison would reflect differences from other genetic differences between the parent lines, rather than specifically being due to the haploid inducer trait. Therefore wanted to include two different germplasm backgrounds and examine the overlap between them.Those two backgrounds are “RWK” (in which there are RWK-HI (haploid inducer) and RWK-NIL (non-inducer) genotypes) and “NP2222” (in which there are NP2222-HI (haploid inducer) and NP2222 (non-inducer) genotypes. By examining the DEG lists from both of these pairs of comparisons, and specifically looking at the overlap between them, one can more accurately derive a list of DEGs consistently associated with the haploid inducer trait in both of the genetic backgrounds.

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