Transcriptome and genome-wide analysis of the potential role of SKP1 gene family in the development of floral organs of two related species of Allium fistulosum

<i>Allium fistulosum</i> is an important plant germplasm resource, rich in nutrients and possessing unique medicinal value. However, due to its small floral organs, low seed setting rate of a single flower, high cost of artificial emasculation, and artificial pollination, the use of male sterile lines to prepare <i>Allium</i> hybrids has become a common choice. In this study, <i>A. fistulosum</i> var. <i>viviparum</i> Makino and <i>A. galanthum</i> were used as materials to study the regulation mechanism of anther development, aiming to provide a reference for male sterility. Through transcriptome differential gene screening and genome-wide bioinformatics analysis, 34 <i>SKP1</i> (S-phase kinase-associated protein 1) genes (<i>AfSKP1-1</i> to <i>AfSKP1-34</i>) were identified in the whole genome of <i>A. fistulosum.</i> The <i>AfSKP1</i> genes are unevenly distributed on eight chromosomes. Furthermore, two pairs of collinear relationships are evident among family members, and fragment replication events between <i>AfSKP1</i> genes have been identified. The phylogenetic tree analysis demonstrated that the <i>AfSKP1, AtSKP1, OsSKP1</i>, and <i>SlSKP1</i> genes were clustered into six groups, exhibiting a gene structure analogous to that observed in members of an evolutionary classification. A combination of gene structure and phylogenetic analysis revealed the presence of cis-acting elements associated with growth, hormone regulation, and stress response within the <i>AfSKP1</i> genes. Furthermore, expression analysis demonstrated that the <i>AfSKP1</i> genes exhibited differential expression patterns across various tissues of <i>A. fistulosum</i>. The tissue-specific expression of the <i>AfSKP1</i> gene was verified by Real-Time PCR. A comparison of the two materials revealed significant differences in the expression of the <i>AfSKP1-8</i> gene in floral buds, the <i>AfSKP1-11</i> gene in inflorescence meristems, and the <i>AfSKP1-14</i> gene in inflorescence meristems, scapes, and floral buds. The results indicated that the three genes may be involved in anther development, thereby providing a theoretical basis for further study of floral organ development and pollen development in <i>AfSKP1</i> family members.