Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize
P1B-type ATPases, known as heavy metal ATPases (HMAs), play an important role in the control of cadmium (Cd) accumulation in plants. In this study, a total of 12 ZmHMA genes were identified in the maize genome and particularly classified into six clusters based on their phylogenetic relationship and...
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PeerJ Inc.
2019-10-01
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| author | Yanhua Cao Xiongwei Zhao Yajuan Liu Yalong Wang Wenmei Wu Yiwei Jiang Changjian Liao Xiaoxun Xu Shibin Gao Yaou Shen Hai Lan Chaoying Zou Guangtang Pan Haijian Lin |
| author_facet | Yanhua Cao Xiongwei Zhao Yajuan Liu Yalong Wang Wenmei Wu Yiwei Jiang Changjian Liao Xiaoxun Xu Shibin Gao Yaou Shen Hai Lan Chaoying Zou Guangtang Pan Haijian Lin |
| author_sort | Yanhua Cao |
| collection | DOAJ |
| description | P1B-type ATPases, known as heavy metal ATPases (HMAs), play an important role in the control of cadmium (Cd) accumulation in plants. In this study, a total of 12 ZmHMA genes were identified in the maize genome and particularly classified into six clusters based on their phylogenetic relationship and motif compositions. Furthermore, the expression patterns of different ZmHMA genes varied with developmental stages, and were tissue specific under normal conditions. ZmHMA2 and ZmHMA3 genes exhibited significant up-regulation under Cd treatment. Eventually, the association analysis between 103 inbred lines and alleles in ZmHMA2 and ZmHMA3 revealed that one insertion–deletion (InDel) in the intron from ZmHMA2 was associated with leaf Cd concentration under low Cd condition at the seedling stage. Twenty polymorphisms in ZmHMA3 were significantly associated with leaf Cd concentration under various Cd levels at seedling and maturing stages. Five single nucleotide polymorphisms (SNPs) and two InDels of these significantly associated polymorphic loci from ZmHMA3 caused the amino acid substitutions and insertion or deletion events. Importantly, the proteins encoded by ZmHMA2 and ZmHMA3 genes were located in the plasma membrane. This comprehensive analysis will provide an important theoretical basis for future functional verification of ZmHMA genes to unravel the mechanisms of Cd accumulation in leaves of maize. Additionally, the favorable alleles in ZmHMA3 will lay a foundation for the marker-assisted selection of low Cd accumulation in maize. |
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| language | English |
| last_indexed | 2024-03-09T06:23:46Z |
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| spelling | doaj.art-57d26b4bc3b64618829e343193eb444a2023-12-03T11:30:29ZengPeerJ Inc.PeerJ2167-83592019-10-017e787710.7717/peerj.7877Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maizeYanhua Cao0Xiongwei Zhao1Yajuan Liu2Yalong Wang3Wenmei Wu4Yiwei Jiang5Changjian Liao6Xiaoxun Xu7Shibin Gao8Yaou Shen9Hai Lan10Chaoying Zou11Guangtang Pan12Haijian Lin13Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaCollege of Life Sciences, Shanxi Agricultural University, Jinzhong, Shanxi, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaDepartment of Agronomy, Purdue University, West Lafayette, IN, USACrop Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, ChinaCollege of Environment Sciences, Sichuan Agricultural University, Chengdu, Sichuan, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaMaize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, ChinaP1B-type ATPases, known as heavy metal ATPases (HMAs), play an important role in the control of cadmium (Cd) accumulation in plants. In this study, a total of 12 ZmHMA genes were identified in the maize genome and particularly classified into six clusters based on their phylogenetic relationship and motif compositions. Furthermore, the expression patterns of different ZmHMA genes varied with developmental stages, and were tissue specific under normal conditions. ZmHMA2 and ZmHMA3 genes exhibited significant up-regulation under Cd treatment. Eventually, the association analysis between 103 inbred lines and alleles in ZmHMA2 and ZmHMA3 revealed that one insertion–deletion (InDel) in the intron from ZmHMA2 was associated with leaf Cd concentration under low Cd condition at the seedling stage. Twenty polymorphisms in ZmHMA3 were significantly associated with leaf Cd concentration under various Cd levels at seedling and maturing stages. Five single nucleotide polymorphisms (SNPs) and two InDels of these significantly associated polymorphic loci from ZmHMA3 caused the amino acid substitutions and insertion or deletion events. Importantly, the proteins encoded by ZmHMA2 and ZmHMA3 genes were located in the plasma membrane. This comprehensive analysis will provide an important theoretical basis for future functional verification of ZmHMA genes to unravel the mechanisms of Cd accumulation in leaves of maize. Additionally, the favorable alleles in ZmHMA3 will lay a foundation for the marker-assisted selection of low Cd accumulation in maize.https://peerj.com/articles/7877.pdfMaizeZmHMA2ZmHMA3Cadmium accumulationNatural variationAssociation analysis |
| spellingShingle | Yanhua Cao Xiongwei Zhao Yajuan Liu Yalong Wang Wenmei Wu Yiwei Jiang Changjian Liao Xiaoxun Xu Shibin Gao Yaou Shen Hai Lan Chaoying Zou Guangtang Pan Haijian Lin Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize PeerJ Maize ZmHMA2 ZmHMA3 Cadmium accumulation Natural variation Association analysis |
| title | Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize |
| title_full | Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize |
| title_fullStr | Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize |
| title_full_unstemmed | Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize |
| title_short | Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize |
| title_sort | genome wide identification of zmhmas and association of natural variation in zmhma2 and zmhma3 with leaf cadmium accumulation in maize |
| topic | Maize ZmHMA2 ZmHMA3 Cadmium accumulation Natural variation Association analysis |
| url | https://peerj.com/articles/7877.pdf |
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