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Background Zinc finger homeodomain (ZHD) protein is a plant-specific transcription factor and a potential regulator of phosphoenolpyruvate carboxylase (PEPCase)-coding genes, and it also participates in plant growth regulation and abiotic stress responses. To study the function of  MsZF-HD  genes in the alkaline stress response, this paper assessed biological information and performed transcriptome analysis of the  MsZF-HD  gene family by using the genomes of two different varieties of alfalfa (XinJiangDa Ye and Zhongmu No. 1). Results In total, 49 and 11  MsZF-HD  genes were identified in the two different varieties respectively, including the alleles of XinJiangDa Ye. According to their phylogenetic relationships, the 60  MsZF-HD  genes were divided into 5 ZHD subfamilies and 1 MIF subfamily. A total of 88.3% of  MsZF-HD  genes do not contain introns and are unevenly distributed among the 6 chromosomes of alfalfa. A collinearity analysis indicated that 26 genes of XinJiangDa Ye have no orthologous genes in Zhongmu No. 1, although these genes (such as  ZHD-X1–2 ,  ZHD-X3–2  and  ZHD-X4–2 ) have homologous genes in  Arabidopsis thaliana ,  Medicago truncatula  and  Glycine max . Through RNA-seq and qRT–PCR verification, it was found that  MsZF-HD  genes are downregulated to participate in the alkaline stress response. Conclusion The results of this study may lay the foundation for the cloning and functional study of  MsZF-HD  genes and provide a theoretical basis for revealing the difference between XinJiangDa Ye and Zhongmu No. 1 at the genome level.

Genome-wide investigation of the ZF-HD gene family in two varieties of alfalfa (Medicago sativa L.) and its expression pattern under alkaline stress