Using multi-year field trials and transcriptome-wide allele-specific expression analyses, they showed maternal inbred choice can speed seed dehydration in reciprocal hybrids and identified hundreds of candidate imprinted genes that may help regulate harvest moisture content.
Reducing seed moisture content at harvest is a key goal in maize seed production because it improves drying efficiency, lowers post-harvest losses, and helps maintain high seed vigor. Kernel dehydration is often viewed as a two-stage process: a genetically regulated physiological phase before physiological maturity and a later, environment-driven physical phase. Because hybrids are created by crossing inbred lines, breeders evaluate both additive effects (general combining ability) and non-additive effects (specific combining ability). Genomic imprinting—an epigenetic process causing parent-of-origin–biased gene expression—may represent an overlooked non-additive mechanism, yet its role in maize dehydration and harvest moisture remains unclear.
A study (DOI:10.48130/seedbio-0025-0030) published in Seed Biology on 04 March 2026 by Jie Yang's & Riliang Gu's team, Xinjiang Academy of Agricultural Sciences, reveals that maternal effects and genomic imprinting shape dehydration in hybrid maize seeds, offering new molecular targets to breed low-moisture, high-vigor hybrids at harvest.
Using multi-year field phenotyping, RNA-seq transcriptome profiling, and SNP-based allele-specific expression (ASE) analysis, the researchers first measured seed dehydration and then mapped parent-of-origin regulatory signals in reciprocal hybrids. Four inbred lines with contrasting dehydration rates—slow Zheng58 (Z1) and Dan360 (D) versus fast PH4CV (P) and Zheng30 (Z2)—were grown in 2019–2020 to generate three reciprocal hybrid pairs (Z1P/PZ1, Z1Z2/Z2Z1, DP/PD). Seed moisture content (MC) was tracked from 30–60 days after pollination (DAP), showing a consistent developmental decline but stable parental differences: Z1 and D maintained higher MC than P and Z2, confirming P and Z2 as fast-dehydration parents. Across all reciprocal pairs, hybrids using the fast parent as the maternal line (PZ1, Z2Z1, PD) displayed significantly lower MC and faster dehydration than their reciprocals, indicating a strong maternal effect; notably, P showed the highest daily dehydration rate (1.17% d⁻¹ in 2019; 1.11% d⁻¹ in 2020), whereas Z1 was slowest (0.85% d⁻¹; 0.77% d⁻¹). To link phenotype with transcriptional regulation, 55 DAP seeds (largest MC divergence stage) from Z1, P, Z1P, and PZ1 were sequenced (~21.6–23.4 million reads/sample; high mapping to B73), yielding ~30.6k expressed genes and highly reproducible replicates. Differential expression identified 9,899 DEGs between parents and 1,158 DEGs between reciprocal hybrids; importantly, 68.3% of hybrid DEGs overlapped parental DEGs, and expression clustering grouped P with PZ1 and Z1 with Z1P, consistent with maternal-like transcriptome signatures. Enrichment analyses linked shared DEGs to nutrient reservoir activity and secondary metabolism, while hybrid-specific DEGs were enriched for transmembrane transport, suggesting altered nutrient flow from maternal plant to developing seed. ASE analysis across 117,590 well-covered SNPs yielded an overall maternal allele proportion of 0.524 and enabled imprinting discovery: 727 maternally expressed SNPs and 318 paternally expressed SNPs mapped to 226 MEGs and 112 PEGs, with many showing embryo-preferential expression and functional bias toward carbon metabolism (MEGs) or organelle/protein processing (PEGs). Finally, allele-specific qPCR validated two maternally expressed candidates, Zm00001d040697 and Zm00001d052744, confirming strong maternal-allele bias in reciprocal hybrid seeds.
These findings offer breeders a practical insight: choosing the maternal parent matters for achieving lower seed moisture content at harvest in hybrid maize. The identified MEGs and PEGs provide a molecular shortlist for developing markers, screening parental lines, and designing crosses aimed at faster dehydration—potentially reducing drying costs while protecting seed vigor. More broadly, the work links an economically important trait (harvest moisture) to epigenetic regulation, expanding the toolbox beyond conventional additive genetics.
