本研究以前期通过全基因组关联分析联合转录组测序挖掘到的玉米萌发期耐低温基因ZmFAH1为研究对象，以耐低温等级不同的116份玉米自交系为材料，对该基因CDS区进行遗传变异分析，挖掘与耐低温显著关联的位点，开发分子标记并验证。结果表明：ZmFAH1基因位于玉米1号染色体负链，为参与编码具有疏水能力的跨膜碱性蛋白，启动子包含多个与非生物胁迫响应相关的元件；在CDS区挖掘到15个SNP和1个InDel，划分为9种单倍型，其中HAP2为优异单倍型，针对表型贡献率最大的非同义突变位点InDel708-710开发了耐低温dCAPs标记DNCAPS708，该标记与萌发期相对发芽指数（RGI）、相对活力指数（RVI）、相对简易活力指数（RSVI）和相对芽长（RGL）等4个耐低温性状显著相关，在玉米自交系及双单倍体群体中基因型与表型分子符合率达到80%以上。

ZmFAH1, a cold tolerance gene during maize germination identified by previous GWAS and transcriptome sequencing, was studied using 116 inbred lines with different cold tolerance levels. Genetic variation analysis of its CDS region identified loci associated with cold tolerance, followed by molecular marker development and validation. ZmFAH1 is on the negative strand of maize chromosome 1, encoding a transmembrane alkaline protein with hydrophobicity, and its promoter harbors multiple abiotic stress-responsive elements. Fifteen SNPs and one InDel in the CDS region formed 9 haplotypes, with HAP2 as the elite one. A dCAPs marker DNCAPS708 was developed for the non-synonymous InDel708-710 (highest phenotypic contribution). It was significantly associated with four cold tolerance traits (RGI, RVI, RSVI, RGL) during germination, showing over 80% genotype-phenotype coincidence rate in inbred lines and double haploid populations.

东北区抗病抗逆高产玉米种质改良（22250230）；黑龙江省自然科学优秀青年基金（YQ2022C009）