果树学报2026，Vol.43Issue(3)：505-520,16.DOI:10.13925/j.cnki.gsxb.20250324
李AP2亚家族转录因子的全基因组鉴定与表达分析
Genome-wide identification and expression patterns of AP2 subfamily transcription factor in plums
摘要
Abstract
[Objective]The AP2 subfamily transcription factor represents one of the most important transcription factor families in plants,playing pivotal roles in regulating various biological processes in-cluding floral organ morphogenesis,embryogenesis,meristem differentiation,leaf morphology estab-lishment,and biotic and abiotic stress responses.Despite their well-characterised functions in model plants,systematic investigation of AP2 family in economically important fruit crops like Chinese plum(Prunus salicina Lindl.)remains limited.This study presented the first comprehensive genome-wide identification of AP2 transcription factors in three major Chinese plum cultivars Sanyueli,Zhongli No.6,and Wushancuili.[Methods]Using high-quality genome assemblies of the three plum cultivars,we sys-tematically identified AP2 family members through comprehensive bioinformatics approaches.Multiple sequence alignment and phylogenetic analysis were conducted using MEGA 11 with AP2 proteins from Arabidopsis thaliana,Malus domestica,and other related species.Gene structure and conserved motifs were analyzed using SMART and MEME suites.Chromosomal locations and synteny relationships were determined using MCScanX.Cis-acting regulatory elements in promoter regions were predicted using PlantCARE.Expression patterns were investigated through qRT-PCR analysis of six selected AP2 genes(SYPsAP2-5/7,ZLPsAP2-15/16,and WSPsAP2-9/11)across eight fruit developmental stages in Shibanwannai plum.[Results]We identified 20,22,and 18 AP2 genes in Sanyueli,Zhongli No.6,and Wushancuili genomes,respectively.The expansion and contraction of the AP2 gene family were likely closely associated with species'evolutionary history and ecological adaptation.The size of the plum AP2 gene family not only reflected shared characteristics within Rosaceae plants,but also demonstrated genus-specific adaptations in Prunus species.The relatively conserved number of AP2 genes in stone fruits may be related to their specific developmental regulatory requirements.The subcellular localiza-tion prediction results indicated that the AP2 family members in the three plum varieties were predomi-nantly localized in the nucleus(48 out of 60,80％;16 in Sanyueli,17 in Zhongli No.6,and 15 in Wushancuili).A small number of AP2 family members were distributed in organelles such as chloro-plasts and peroxisomes.This distribution pattern was consistent with the typical subcellular localization pattern of transcription factors.Referring to the classification criteria of the Arabidopsis thaliana AP2 transcription factor family,the plum AP2 transcription factor family was divided into 13 subfamilies,in-cluding the AP2-type,RAP2-7-type,T11A7.19-type,WRIl-type,ADAP-type,ANT-type,AIL5-type,AIL6-type,AIL 1-type,BBM-type,PLTl-type,PLT2-type,and TOE-type.From the perspective of spe-cies phylogenetic relationships,the AP2 gene members of the three plum varieties clustered together and exhibited closer phylogenetic relationships compared to those of Rosaceae species like apple and pear.This finding is consistent with their systematic taxonomic status.Chromosomal distribution re-vealed uneven gene dispersion,with Chrl being a hotspot in Sanyueli(35％).This distribution pattern indicated a clear chromosomal preference.The intraspecies synteny analysis revealed that the genome of Sanyueli contained 3 pairs of SYPsAP2 syntenic genes,while Wushancuili harbored 4 pairs of WSP-sAP2 syntenic genes.Among the three plum varieties,Zhongli No.6 exhibited the most extensive syn-tenic relationships within the ZLPsAP2 family,with a total of 7 pairs of ZLPsAP2 syntenic genes identi-fied.Motif 2 was conserved across all 60 PsAP2 members and served as the core motif.Motifs 2,4,1,and 5 were most frequent,typically arranged orderly and biased toward the 5'end.Protein domain anal-ysis showed that all PsAP2 members possessed the canonical double AP2 domain.Notably,WSPsAP2-3 contained additional Amb all and Pec_lyase_N domains,while SYPsAP2-19 harbored a dermokine su-perfamily domain at its C-terminus.These unique domains suggested potential evolutionary divergence and novel functions for these genes.Cis-acting element analysis of the AP2 gene family promoters in plums revealed significant enrichment of diverse response elements.The three plum varieties shared several core response elements:light-responsive elements(282 in SYPsAP2,307 in ZLPsAP2,and 226 in WSPsAP2),abscisic acid-responsive elements(66 in SYPsAP2,62 in ZLPsAP2,and 52 in WSP-sAP2),MeJA-responsive elements(40 in SYPsAP2,48 in ZLPsAP2,and 32 in WSPsAP2),gibberellin-responsive elements(25 in SYPsAP2,28 in ZLPsAP2,and 23 in WSPsAP2),and anaerobic induction el-ements(52 in SYPsAP2,57 in ZLPsAP2,and 49 in WSPsAP2).Each variety had distinct regulatory fea-tures.For example,Sanyueli(SYPsAP2)had a higher number of MYBHv1 binding sites(20)compared to Zhongli No.6(6)and Wushancuili(8),indicating a potential role in MYBHv1-mediated regulation.Zhongli No.6(ZLPsAP2)had the most diverse and abundant ciss-acting elements,suggesting a complex regulatory network for its AP2 genes.Wushancuili(WSPsAP2)contained unique wound-responsive ele-ments,likely involved in plant wound response mechanisms.Specific AP2 gene family members may be involved in seed development and light signal transduction.SYPsAP2-7/11,ZLPsAP2-3/16,and WSPsAP2-1/11 contained seed-specific regulatory elements.SYPsAP2-2,ZLPsAP2-18,and WSPsAP2-6 contained phytochrome regulatory elements.Six representative genes from the AP2 and BBM clades were selected based on phylogenetic and promoter analyses.Their expression patterns were analyzed across eight developmental stages of Shibanwannai,revealing significant tissue-specific profiles.The gene expression profiling demonstrated that AP2 clade genes(SYPsAP2-5,ZLPsAP2-15,and WSSPsAP2-9)showed peak expression during early fruit development and the BBM clade genes(SYPsAP2-7,ZLP-sAP2-16,and WSPsAP2-11)exhibited seed-specific expression,with dramatic upregulation during T4-T8(from 88 to 148 days after full bloom)stages coinciding with seed abortion events.[Conclusion]The PsAP2 subfamily genes of Chinese plum were identified and analyzed in detail at the genome-wide level.The temporal-spatial expression characteristic of this subfamily genes was studied,which would establish a foundation for future functional studies and molecular breeding applications targeting fruit quality and seed development traits in plum.The identification of seed-specific PsAP2 regulators offers promising targets for addressing seed abortion issues in plum production.关键词
李/AP2转录因子/基因家族/果实发育/基因表达Key words
Plums/AP2 transcription factor/Gene family/Fruit development/Gene expression分类
农业科技引用本文复制引用
刘俊伟,林圣城,陈发炘,龙振烨,公俊凝,王佳颖,陈发兴,邓红红,张芊芊,罗诗诗,王源源,张子扬,梁茜,薛傲琪,谢婷婷,李斌奇..李AP2亚家族转录因子的全基因组鉴定与表达分析[J].果树学报,2026,43(3):505-520,16.基金项目
福建省科技厅高校产学合作项目(2025N5004) （2025N5004）
永泰县"李梅基因库"建设暨'皇冠李'新品种引种与示范推广项目(KH240149A) （KH240149A）
福建农林大学青年教师赴海峡联合院访学研修专项计划(KFXH23029) （KFXH23029）
福建省林业科技推广项目(2023TG18) （2023TG18）
福建农林大学大学生创新创业训练项目(FAFUXMPC20250429001-00021、FAFUXMPC20250429001-00356) （FAFUXMPC20250429001-00021、FAFUXMPC20250429001-00356）
