德国海因里希·海涅大学Thomas Hartwig研究团队取得一项新突破。他们揭示了转录因子结合位点的遗传变异在很大程度上解释了玉米的表型遗传力。相关论文发表在2025年8月11日出版的《自然—遗传学》杂志上。

小组报道了在水分充足和干旱条件下玉米叶片泛雨的构建。该研究团队在25个玉米杂交品种的泛基因组中量化了单倍型特异性TF足迹，并绘制了超过20万个与顺式元件占用相关的遗传、表观遗传或两者兼有的变异（称为结合定量性状位点（bQTL））。三方面的证据支持bQTL的功能意义：(1)在干旱条件下，bQTL与vgt1、ZmTRE1和ZmNAC111附近的MITE转座子等性状的调节基因位点重合；(2)近亲亲本间存在bQTL等位基因偏倚，且与染色质免疫沉淀测序结果相匹配；(3)跨基因组区域遗传变异的划分表明，bQTL捕获了143种表型中约72%的大部分可遗传性状变异。他们的研究为复杂性状的遗传研究和定向工程提供了一种有效的顺式变异方法。

据悉，转录因子（TF）结合位点（顺式元件）功能变异的综合图谱对于阐明基因型如何塑造表型至关重要。

附：英文原文

Title: Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

Author: Engelhorn, Julia, Snodgrass, Samantha J., Kok, Amelie, Seetharam, Arun S., Schneider, Michael, Kiwit, Tatjana, Singh, Ayush, Banf, Michael, Doan, Duong Thi Hai, Khaipho-Burch, Merritt, Runcie, Daniel E., Snchez-Camargo, Victor A., Bader, Rechien, Vladimir Torres-Rodriguez, J., Sun, Guangchao, Stam, Maike, Fiorani, Fabio, Beier, Sebastian, Schnable, James C., Bass, Hank W., Hufford, Matthew B., Stich, Benjamin, Frommer, Wolf B., Ross-Ibarra, Jeffrey, Hartwig, Thomas

Issue&Volume: 2025-08-11

Abstract: Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to cis-element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, including vgt1, ZmTRE1 and the MITE transposon near ZmNAC111 under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional cis-variation accessible at scale for genetic studies and targeted engineering of complex traits.

DOI: 10.1038/s41588-025-02246-7

Source: https://www.nature.com/articles/s41588-025-02246-7