DataSheet1_Genome-Wide Identification and Expression Analysis of the MADS-Box Gene Family in Sweet Potato [Ipomoea batatas (L.) Lam].docx

MADS-box gene, one of the largest transcription factor families in plants, is a class of transcription factors widely present in eukaryotes. It plays an important role in plant growth and development and participates in the growth and development of flowers and fruits. Sweet potato is the seventh most important food crop in the world. Its tuberous roots, stems, and leaves contain a large number of proteins, lipids, carotenoids, anthocyanins, conjugated phenolic acids, and minerals, which have high edible, forage, and medicinal value, and is also an important energy crop. At present, MADS-box genes in sweet potato have rarely been reported, and there has been no study on the genome-wide identification and classification of MADS-box genes in Ipomoea batatas. This study provided the first comprehensive analysis of sweet potato MADS-box genes. We identified 95 MADS-box genes, analyzed the structure and protein of sweet potato MADS-box genes, and categorized them based on phylogenetic analysis with Arabidopsis MADS-box proteins. Chromosomal localization indicated an unequal number of MADS-box genes in all 14 chromosomes except LG3, with more than 10 MADS-box genes located on chromosomes LG7, LG11, and LG15. The MADS domain and core motifs of the sweet potato MADS-box genes were identified by motif analysis. We identified 19 MADS-box genes with collinear relationships and analyzed duplication events. Cis-acting elements, such as light-responsive, auxin-responsive, drought-inducible, and MeJA-responsive elements, were found in the promoter region of the MADS-box genes in sweet potato, which further indicates the basis of MADS-box gene regulation in response to environmental changes and hormones. RNA-seq suggested that sweet potato MADS-box genes exhibit tissue-specific expression patterns, with 34 genes highly expressed in sweet potato flowers and fruits, and 19 genes highly expressed in the tuberous root, pencil root, or fibrous root. qRT-PCR again validated the expression levels of the 10 genes and found that IbMADS1, IbMADS18, IbMADS19, IbMADS79, and IbMADS90 were highly expressed in the tuberous root or fibrous root, and IbMADS18, IbMADS31, and IbMADS83 were highly expressed in the fruit. In this study, the molecular basis of MADS-box genes of sweet potato was analyzed from various angles. The effects of MADS-box genes on the growth and development of sweet potato were investigated, which may provide a certain theoretical basis for molecular breeding of sweet potato.

MADS-box基因（MADS-box gene）是植物中最大的转录因子家族之一，属于广泛分布于真核生物中的转录因子类群。该类基因在植物生长发育过程中发挥重要作用，并参与花与果实的生长发育进程。
甘薯（Ipomoea batatas）是全球第七大重要粮食作物，其块根、茎秆与叶片富含大量蛋白质、脂质、类胡萝卜素、花青素、结合型酚酸及矿物质，兼具极高的食用、饲用与药用价值，同时也是一类重要的能源作物。
目前，关于甘薯MADS-box基因的研究报道较为匮乏，且尚未有针对番薯（Ipomoea batatas）全基因组范围MADS-box基因鉴定与分类的相关研究。
本研究首次对甘薯MADS-box基因开展了系统性分析：共鉴定得到95个MADS-box基因，解析了甘薯MADS-box基因的结构与蛋白特征，并通过与拟南芥MADS-box蛋白的系统发育分析对其进行了分类。
染色体定位分析显示，除LG3外，其余14条染色体上的MADS-box基因数量不均等，其中LG7、LG11与LG15染色体上的MADS-box基因数量均超过10个。
通过基序分析，我们鉴定得到了甘薯MADS-box基因的MADS结构域与核心基序。
共鉴定得到19个存在共线性关系的MADS-box基因，并对其复制事件进行了分析。
在甘薯MADS-box基因的启动子区域，我们发现了光响应、生长素响应、干旱诱导及茉莉酸甲酯（MeJA）响应等顺式作用元件，这进一步揭示了MADS-box基因响应环境变化与激素调控的分子基础。
RNA测序（RNA-seq）结果显示，甘薯MADS-box基因呈现组织特异性表达模式：其中34个基因在花与果实中高表达，19个基因在块根、铅笔根或须根中高表达。
实时荧光定量PCR（qRT-PCR）进一步验证了10个基因的表达水平，结果显示IbMADS1、IbMADS18、IbMADS19、IbMADS79及IbMADS90在块根或须根中高表达，而IbMADS18、IbMADS31与IbMADS83在果实中高表达。
本研究从多个维度解析了甘薯MADS-box基因的分子基础，探讨了该类基因对甘薯生长发育的调控作用，可为甘薯的分子育种工作提供一定的理论依据。