The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome
Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes...
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MDPI AG
2024-03-01
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| author | Liqin Chen Kunxiang Chen Xi Xi Xianghong Du Xinyi Zou Yujia Ma Yingying Song Changquan Luo Song Weining |
| author_facet | Liqin Chen Kunxiang Chen Xi Xi Xianghong Du Xinyi Zou Yujia Ma Yingying Song Changquan Luo Song Weining |
| author_sort | Liqin Chen |
| collection | DOAJ |
| description | Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical–chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of <i>HvMOREXann7</i> under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops. |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-6febfe371ed54727b17b45db1872fca72024-04-12T13:20:01ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-03-01257388310.3390/ijms25073883The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-GenomeLiqin Chen0Kunxiang Chen1Xi Xi2Xianghong Du3Xinyi Zou4Yujia Ma5Yingying Song6Changquan Luo7Song Weining8State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, ChinaCollege of Agronomy, Northwest A&F University, Xianyang 712100, ChinaCollege of Agronomy, Northwest A&F University, Xianyang 712100, ChinaCollege of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, ChinaCollege of Plant Protection, Northwest A&F University, Xianyang 712100, ChinaCollege of Life Sciences, Northwest A&F University, Xianyang 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, ChinaPlant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical–chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of <i>HvMOREXann7</i> under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops.https://www.mdpi.com/1422-0067/25/7/3883barley pan-genomeannexinexpression profilesdomestication selection |
| spellingShingle | Liqin Chen Kunxiang Chen Xi Xi Xianghong Du Xinyi Zou Yujia Ma Yingying Song Changquan Luo Song Weining The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome International Journal of Molecular Sciences barley pan-genome annexin expression profiles domestication selection |
| title | The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome |
| title_full | The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome |
| title_fullStr | The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome |
| title_full_unstemmed | The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome |
| title_short | The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome |
| title_sort | evolution expression patterns and domestication selection analysis of the annexin gene family in the barley pan genome |
| topic | barley pan-genome annexin expression profiles domestication selection |
| url | https://www.mdpi.com/1422-0067/25/7/3883 |
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