Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships
The MADS-box gene family is one of the largest families in plants and plays an important roles in floral development. The MADS-box family includes the SRF-like domain and K-box domain. It is considered that the MADS-box gene family encodes a DNA-binding domain that is generally related to transcript...
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MDPI AG
2021-12-01
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| Series: | Genes |
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| author | Da Zhao Zheng Chen Lei Xu Lijun Zhang Quan Zou |
| author_facet | Da Zhao Zheng Chen Lei Xu Lijun Zhang Quan Zou |
| author_sort | Da Zhao |
| collection | DOAJ |
| description | The MADS-box gene family is one of the largest families in plants and plays an important roles in floral development. The MADS-box family includes the SRF-like domain and K-box domain. It is considered that the MADS-box gene family encodes a DNA-binding domain that is generally related to transcription factors, and plays important roles in regulating floral development. Our study identified 211 MADS-box protein sequences in the <i>Zea mays</i> proteome and renamed all the genes based on the gene annotations. All the 211 MADS-box protein sequences were coded by 98 expressed genes. Phylogenetic analysis of the MADS-box genes showed that all the family members were categorized into five subfamilies: MIKC-type, Mα, Mβ, Mγ, and Mδ. Gene duplications are regarded as products of several types of errors during the period of DNA replication and reconstruction; in our study all the 98 MADS-box genes contained 22 pairs of segmentally duplicated events which were distributed on 10 chromosomes. We compared expression data in different tissues from the female spikelet, silk, pericarp aleurone, ear primordium, leaf zone, vegetative meristem, internode, endosperm crown, mature pollen, embryo, root cortex, secondary root, germination kernels, primary root, root elongation zone, and root meristem. According to analysis of gene ontology pathways, we found a total of 41 pathways in which MADS-box genes in maize are involved. All the studies we conducted provided an overview of MADS-box gene family members in maize and showed multiple functions as transcription factors. The related research of MADS-box domains has provided the theoretical basis of MADS-box domains for agricultural applications. |
| first_indexed | 2024-03-10T04:02:53Z |
| format | Article |
| id | doaj.art-e423e44fdcc042379aa6343c66b26e1c |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T04:02:53Z |
| publishDate | 2021-12-01 |
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| series | Genes |
| spelling | doaj.art-e423e44fdcc042379aa6343c66b26e1c2023-11-23T08:30:54ZengMDPI AGGenes2073-44252021-12-011212195610.3390/genes12121956Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and RelationshipsDa Zhao0Zheng Chen1Lei Xu2Lijun Zhang3Quan Zou4School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, ChinaSchool of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, ChinaSchool of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen 518055, ChinaSchool of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, ChinaInstitute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, ChinaThe MADS-box gene family is one of the largest families in plants and plays an important roles in floral development. The MADS-box family includes the SRF-like domain and K-box domain. It is considered that the MADS-box gene family encodes a DNA-binding domain that is generally related to transcription factors, and plays important roles in regulating floral development. Our study identified 211 MADS-box protein sequences in the <i>Zea mays</i> proteome and renamed all the genes based on the gene annotations. All the 211 MADS-box protein sequences were coded by 98 expressed genes. Phylogenetic analysis of the MADS-box genes showed that all the family members were categorized into five subfamilies: MIKC-type, Mα, Mβ, Mγ, and Mδ. Gene duplications are regarded as products of several types of errors during the period of DNA replication and reconstruction; in our study all the 98 MADS-box genes contained 22 pairs of segmentally duplicated events which were distributed on 10 chromosomes. We compared expression data in different tissues from the female spikelet, silk, pericarp aleurone, ear primordium, leaf zone, vegetative meristem, internode, endosperm crown, mature pollen, embryo, root cortex, secondary root, germination kernels, primary root, root elongation zone, and root meristem. According to analysis of gene ontology pathways, we found a total of 41 pathways in which MADS-box genes in maize are involved. All the studies we conducted provided an overview of MADS-box gene family members in maize and showed multiple functions as transcription factors. The related research of MADS-box domains has provided the theoretical basis of MADS-box domains for agricultural applications.https://www.mdpi.com/2073-4425/12/12/1956maizegene familyMADS-boxtranscription factorphylogenetic analysis |
| spellingShingle | Da Zhao Zheng Chen Lei Xu Lijun Zhang Quan Zou Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships Genes maize gene family MADS-box transcription factor phylogenetic analysis |
| title | Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships |
| title_full | Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships |
| title_fullStr | Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships |
| title_full_unstemmed | Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships |
| title_short | Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships |
| title_sort | genome wide analysis of the mads box gene family in maize gene structure evolution and relationships |
| topic | maize gene family MADS-box transcription factor phylogenetic analysis |
| url | https://www.mdpi.com/2073-4425/12/12/1956 |
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