Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Almond Reveal Its Expression Features in Different Flowering Periods

Abstract

The MADS-box gene family is an important family of transcription factors involved in multiple processes, such as plant growth and development, stress, and in particular, flowering time and floral organ development. Almonds are the best-selling nuts in the international fruit trade, accounting for more than 50% of the world’s dried fruit trade, and one of the main economic fruit trees in Kashgar, Xinjiang. In addition, almonds contain a variety of nutrients, such as protein and dietary fiber, which can supplement nutrients for people. They also have the functions of nourishing the yin and kidneys, improving eyesight, and strengthening the brain, and they can be applied to various diseases. However, there is no report on the MADS-box gene family in almond (Prunus dulcis). In this study, a total of 67 PdMADS genes distributed across 8 chromosomes were identified from the genome of almond ‘Wanfeng’. The PdMADS members were divided into five subgroups—Mα, Mβ, Mγ, Mδ, and MIKC—and the members in each subgroup had conserved motif types and exon and intron numbers. The number of exons of PdMADS members ranged from 1 to 20, and the number of introns ranged from 0 to 19. The number of exons and introns of different subfamily members varied greatly. The results of gene duplication analysis showed that the PdMADS members had 16 pairs of segmental duplications and 9 pairs of tandem duplications, so we further explored the relationship between the MADS-box gene members in almond and those in Arabidopsis thaliana, Oryza sativa, Malus domestica, and Prunus persica based on colinear genes and evolutionary selection pressure. The results of the cis-acting elements showed that the PdMADS members were extensively involved in a variety of processes, such as almond growth and development, hormone regulation, and stress response. In addition, the expression patterns of PdMADS members across six floral transcriptome samples from two almond cultivars, ‘Wanfeng’ and ‘Nonpareil’, had significant expression differences. Subsequently, the fluorescence quantitative expression levels of the 15 PdMADS genes were highly similar to the transcriptome expression patterns, and the gene expression levels increased in the samples at different flowering stages, indicating that the two almond cultivars expressed different PdMADS genes during the flowering process. It is worth noting that the difference in flowering time between ‘Wanfeng’ and ‘Nonpareil’ may be caused by the different expression activities of PdMADS47 and PdMADS16 during the dormancy period, resulting in different processes of vernalization. We identified a total of 13,515 target genes in the genome based on the MIKC DNA-binding sites. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on the PdMADS gene family and investigated six flowering samples from two almond cultivars, the early-flowering ‘Wanfeng’ and late-flowering ‘Nonpareil’, for quantitative expression level identification. These findings lay a foundation for future in-depth studies on the mechanism of PdMADS gene regulation during flowering in different almond cultivars.