Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stresses
Abstract Background Fasciclin-like arabinogalactan proteins (FLAs) are a class of plant-specific proteins that contribute to various aspects of plant growth, development, and adaptation. However, these proteins have not yet been identified or characterized in maize. This study conducted bioinformati...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-07-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-025-06981-1 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849344752641638400 |
|---|---|
| author | Yongyan Cao Xuanxuan Chen Bo Wei Tuo Zeng Hongcheng Wang Bin Zhu Xuye Du Lei Gu |
| author_facet | Yongyan Cao Xuanxuan Chen Bo Wei Tuo Zeng Hongcheng Wang Bin Zhu Xuye Du Lei Gu |
| author_sort | Yongyan Cao |
| collection | DOAJ |
| description | Abstract Background Fasciclin-like arabinogalactan proteins (FLAs) are a class of plant-specific proteins that contribute to various aspects of plant growth, development, and adaptation. However, these proteins have not yet been identified or characterized in maize. This study conducted bioinformatics and expression analyses of the ZmFLA gene family. Results Based on the homologous comparison methods, 27 ZmFLAs were identified in maize. They were unevenly distributed across ten maize chromosomes, forming 14 pairs of fragment replication with no tandem duplication, revealing that segmental duplication might be the main driving force of the family expansion. Ka/ks analysis of duplicated genes indicating ZmFLAs may undergoing both positively selected and purification selection in evolutionary history. Homologous evolutionary analysis classified 109 FLAs from maize (27 ZmFLAs), rice (27 OsFLAs), wheat (34 TaFLAs), and Arabidopsis (21 AtFLAs) into three groups. The gene structure and protein domain of the ZmFLAs in the same subfamily were highly conserved. The promoter regions of many ZmFLA family members comprised light-, plant growth/hormone-, and abiotic stress-responsive elements. RNA-seq data revealed that the expression pattern of ZmFLAs exhibited organizational specificity and could be influenced by heat, cold, drought, UV, and salt stresses. RT-qPCR of ten ZmFLAs (ZmFLA1/4/5/9/11/16/19/23/25/27) showed that they were either positively or negatively regulated by drought and salt stresses. These findings suggested that ZmFLAs might be involved in the maize response to drought and salt stresses. Conclusion Taken together, the comprehensive analysis of ZmFLAs in the whole genome provides a novel perspective on the evolutionary relationship among maize FLA genes and lays a foundation for further analysis of the biological functions of ZmFLAs. |
| format | Article |
| id | doaj-art-b0f24bd9c2594f6293167e904451f913 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-b0f24bd9c2594f6293167e904451f9132025-08-20T03:42:35ZengBMCBMC Plant Biology1471-22292025-07-0125111510.1186/s12870-025-06981-1Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stressesYongyan Cao0Xuanxuan Chen1Bo Wei2Tuo Zeng3Hongcheng Wang4Bin Zhu5Xuye Du6Lei Gu7School of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversitySchool of Life Sciences, Guizhou Normal UniversityAbstract Background Fasciclin-like arabinogalactan proteins (FLAs) are a class of plant-specific proteins that contribute to various aspects of plant growth, development, and adaptation. However, these proteins have not yet been identified or characterized in maize. This study conducted bioinformatics and expression analyses of the ZmFLA gene family. Results Based on the homologous comparison methods, 27 ZmFLAs were identified in maize. They were unevenly distributed across ten maize chromosomes, forming 14 pairs of fragment replication with no tandem duplication, revealing that segmental duplication might be the main driving force of the family expansion. Ka/ks analysis of duplicated genes indicating ZmFLAs may undergoing both positively selected and purification selection in evolutionary history. Homologous evolutionary analysis classified 109 FLAs from maize (27 ZmFLAs), rice (27 OsFLAs), wheat (34 TaFLAs), and Arabidopsis (21 AtFLAs) into three groups. The gene structure and protein domain of the ZmFLAs in the same subfamily were highly conserved. The promoter regions of many ZmFLA family members comprised light-, plant growth/hormone-, and abiotic stress-responsive elements. RNA-seq data revealed that the expression pattern of ZmFLAs exhibited organizational specificity and could be influenced by heat, cold, drought, UV, and salt stresses. RT-qPCR of ten ZmFLAs (ZmFLA1/4/5/9/11/16/19/23/25/27) showed that they were either positively or negatively regulated by drought and salt stresses. These findings suggested that ZmFLAs might be involved in the maize response to drought and salt stresses. Conclusion Taken together, the comprehensive analysis of ZmFLAs in the whole genome provides a novel perspective on the evolutionary relationship among maize FLA genes and lays a foundation for further analysis of the biological functions of ZmFLAs.https://doi.org/10.1186/s12870-025-06981-1MaizeFLA proteinGenome-wideBioinformatics analysisDrought and salt stresses |
| spellingShingle | Yongyan Cao Xuanxuan Chen Bo Wei Tuo Zeng Hongcheng Wang Bin Zhu Xuye Du Lei Gu Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stresses BMC Plant Biology Maize FLA protein Genome-wide Bioinformatics analysis Drought and salt stresses |
| title | Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stresses |
| title_full | Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stresses |
| title_fullStr | Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stresses |
| title_full_unstemmed | Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stresses |
| title_short | Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stresses |
| title_sort | genome wide identification and analysis of the fla gene family in maize zea mays l and its expression in response to abiotic stresses |
| topic | Maize FLA protein Genome-wide Bioinformatics analysis Drought and salt stresses |
| url | https://doi.org/10.1186/s12870-025-06981-1 |
| work_keys_str_mv | AT yongyancao genomewideidentificationandanalysisoftheflagenefamilyinmaizezeamayslanditsexpressioninresponsetoabioticstresses AT xuanxuanchen genomewideidentificationandanalysisoftheflagenefamilyinmaizezeamayslanditsexpressioninresponsetoabioticstresses AT bowei genomewideidentificationandanalysisoftheflagenefamilyinmaizezeamayslanditsexpressioninresponsetoabioticstresses AT tuozeng genomewideidentificationandanalysisoftheflagenefamilyinmaizezeamayslanditsexpressioninresponsetoabioticstresses AT hongchengwang genomewideidentificationandanalysisoftheflagenefamilyinmaizezeamayslanditsexpressioninresponsetoabioticstresses AT binzhu genomewideidentificationandanalysisoftheflagenefamilyinmaizezeamayslanditsexpressioninresponsetoabioticstresses AT xuyedu genomewideidentificationandanalysisoftheflagenefamilyinmaizezeamayslanditsexpressioninresponsetoabioticstresses AT leigu genomewideidentificationandanalysisoftheflagenefamilyinmaizezeamayslanditsexpressioninresponsetoabioticstresses |