Pitz Marion, Baldauf Jutta A, Piepho Hans-Peter, Yu Peng, Schoof Heiko, Mason Annaliese S, Li Guoliang, Hochholdinger Frank
Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, 53113, Germany.
Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Stuttgart, 70599, Germany.
Genome Biol. 2025 Sep 22;26(1):291. doi: 10.1186/s13059-025-03768-3.
Classical genetic concepts to explain heterosis attribute the superiority of F-hybrids over their homozygous parents to the complementation of unfavorable by beneficial alleles (dominance) or to heterozygote advantage (overdominance). Here we analyze 112 intermated B73xMo17 recombinant inbred lines of maize and their backcrosses to their original parents B73 and Mo17 to obtain hybrids with an average heterozygosity of ~ 50%. This genetic architecture allows studying the influence of homozygous and heterozygous genomic regions on gene expression in hybrids.
We demonstrate that single parent expression (SPE) complementation explains between - 8% and 29% of the mid-parent heterotic variance in these hybrids. In this expression pattern, consistent with dominance, genes are active in only one parent and in the hybrid, thus increasing the number of expressed genes in hybrids. Furthermore, we establish that eQTL regulating SPE genes are predominantly located in heterozygous regions of the genome. Finally, we identify an SPE gene that regulates lateral root density in hybrids. Remarkably, the activity of this gene depends on the presence of a Mo17 allele in an eQTL that regulates this gene.
Here we show that dominance of SPE genes influences the number of active genes in hybrids, while heterozygosity is instrumental for the regulation of these genes. This finding supports the notion that the genetic constitution of distant regulatory elements is instrumental for the activity of heterosis-associated genes. In summary, our results connect genetic variation at regulatory loci and the degree of heterozygosity with phenotypic variation of heterosis via SPE complementation.
用于解释杂种优势的经典遗传学概念将F1杂种相对于其纯合亲本的优势归因于有害等位基因与有益等位基因的互补（显性）或杂合子优势（超显性）。在此，我们分析了112个玉米B73×Mo17杂交重组自交系及其与原始亲本B73和Mo17的回交后代，以获得平均杂合度约为50%的杂种。这种遗传结构有助于研究纯合和杂合基因组区域对杂种基因表达的影响。
我们证明单亲表达（SPE）互补解释了这些杂种中-8%至29%的中亲杂种优势变异。在这种与显性一致的表达模式中，基因仅在一个亲本和杂种中活跃，从而增加了杂种中表达基因的数量。此外，我们确定调控SPE基因的eQTL主要位于基因组的杂合区域。最后，我们鉴定出一个调控杂种侧根密度的SPE基因。值得注意的是，该基因的活性取决于调控该基因的eQTL中Mo17等位基因的存在。
我们在此表明，SPE基因的显性影响杂种中活跃基因的数量，而杂合性对这些基因的调控至关重要。这一发现支持了这样一种观点，即远距离调控元件的遗传构成对杂种优势相关基因的活性至关重要。总之，我们的结果通过SPE互补将调控位点的遗传变异和杂合度与杂种优势的表型变异联系起来。
