Table2_Genome-wide identification and expression analysis of the ZF-HD gene family in pea (Pisum sativum L.).DOCX

Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ–III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ–V). The PsZF-HD members were named PsMIF1–PsMIF4 and PsZHD1–PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.豌豆是西藏地区常规的粮饲兼用作物，亦是该区域唯一的高蛋白豆科植物，因此在西藏粮草安全保障中发挥着关键作用。锌指同源域（Zinc finger-homeodomain, ZF-HD）属于一类纯合异型盒基因家族，在植物生长发育与逆境胁迫响应过程中具有重要调控功能。本研究通过生物信息学方法，共鉴定得到18个PsZF-HD家族成员。这些基因分布于7条染色体与2个支架片段，进化分析将其划分为MIF与ZHD两个亚家族：其中MIF亚家族可细分为3个亚类（PsMIFⅠ~Ⅲ），ZHD亚家族则分为5个亚类（ZHDⅠ~Ⅴ）；研究人员将PsZF-HD家族成员命名为PsMIF1~PsMIF4以及PsZHD1~PsZHD14。在PsZF-HD家族中共鉴定到12个保守基序与4个保守结构域，其中MIF亚家族仅含1种结构域，而ZHD亚家族包含2种结构域。此外，两个亚家族的蛋白成员三维结构存在显著差异。多数PsZF-HD基因不含内含子（13/18），仅5个基因各含1个内含子。本研究共预测并筛选得到45个顺式作用元件，可分为光响应、胁迫、激素以及生长发育四大类别。对豌豆不同生长发育阶段的组织进行转录组分析结果显示，PsZHD11、8、13、14及MIF4在各组织中均不表达或仅呈低水平表达；其余13个PsZF-HD基因则呈现差异表达且具有组织偏好性：在地上生殖器官中，PsZHD6、2、10以及MIF1（未成熟种子除外）呈现高表达；在地上营养器官中，PsZHD6、1、10显著高表达；而在地下根系中，PsMIF3呈现特异性高表达。低氮环境下的叶片转录组分析表明，地上器官中17个PsZF-HD家族成员的表达量均显著上调。低温环境下的叶片转录组分析则显示，PsZHD10等基因受胁迫诱导上调表达，而PsZHD6基因表达量下调。本研究结果为深入解析PsZF-HD家族基因的功能奠定了基础，同时也为豌豆抗逆分子育种提供了参考依据。