Comprehensive genomic insight deciphers significance of EF-hand gene family in foxtail millet [Setaria italica (L.) P. Beauv.]

Abstract Background Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria and abiotic stress by modulating the transmembrane transfer of amino acids. In this study, we performed a genome-wide screening to analyze the AAT genes in foxtail millet (Setaria italica L.), especially those associated with quality formation and abiotic stresses response. Results A total number of 94 AAT genes were identified and divided into 12 subfamilies by their sequence characteristics and phylogenetic relationship. A large number (58/94, 62%) of AAT genes in foxtail millet were expanded via gene duplication, involving 13 tandem and 12 segmental duplication events. Tandemly duplicated genes had a significant impact on their functional differentiation via sequence variation, structural variation and expression variation. Further comparison in multiple species showed that in addition to paralogous genes, the expression variations of the orthologous AAT genes also contributed to their functional differentiation. The transcriptomic comparison of two millet cultivars verified the direct contribution of the AAT genes such as SiAAP1, SiAAP8, and SiAUX2 in the formation of grain quality. In addition, the qRT-PCR analysis suggested that several AAT genes continuously responded to diverse abiotic stresses, such as SiATLb1, SiANT1. Finally, combined with the previous studies and analysis on sequence characteristics and expression patterns of AAT genes, the possible functions of the foxtail millet AAT genes were predicted. Conclusion This study for the first time reported the evolutionary features, functional differentiation, roles in the quality formation and response to abiotic stresses of foxtail millet AAT gene family, thus providing a framework for further functional analysis of SiAAT genes, and also contributing to the applications of AAT genes in improving the quality and resistance to abiotic stresses of foxtail millet, and other cereal crops.

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The foxtail millet ( Setaria italica ) terpene synthase gene family

The Plant Journal ◽

10.1111/tpj.14771 ◽

2020 ◽

Vol 103 (2) ◽

pp. 781-800

Author(s):

Prema S. Karunanithi ◽

David I. Berrios ◽

Sadira Wang ◽

John Davis ◽

Tong Shen ◽

...

Keyword(s):

Gene Family ◽

Foxtail Millet ◽

Setaria Italica ◽

Terpene Synthase

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Amino Acid Transporter (AAT) Gene Family in Foxtail Millet (Setaria Italica L.): Widespread Family Expansion, Functional Differentiation, Roles in Quality Formation and Response to Abiotic Stresses

10.21203/rs.3.rs-113517/v1 ◽

2020 ◽

Author(s):

Yang Yang ◽

Yongmao Chai ◽

Jiayi Liu ◽

Jie Zheng ◽

Zhangchen Zhao ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Gene Family ◽

Abiotic Stresses ◽

Foxtail Millet ◽

Functional Differentiation ◽

Setaria Italica ◽

Evolutionary Features ◽

Sequence Characteristics ◽

Quality Formation

Abstract Background: Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria and abiotic stress by modulating the transmembrane transfer of amino acids. In this study, we performed a genome-wide screening to analyze the AAT genes in foxtail millet (Setaria italica L.), especially those associated with quality formation and abiotic stresses response.Results: A total number of 94 AAT genes were identified and divided into 12 subfamilies by their sequence characteristics and phylogenetic relationship. A large number (58/94, 62%) of AAT genes in foxtail millet were expanded via gene duplication, involving 13 tandem and 12 segmental duplication events. Tandemly duplicated genes had a significant impact on their functional differentiation via sequence variation, structural variation and expression variation. Further comparison in multiple species showed that in addition to paralogous genes, the expression variations of the orthologous AAT genes also contributed to their functional differentiation. The transcriptomic comparison of two millet cultivars verified the direct contribution of the AAT genes such as SiAAP1, SiAAP8, and SiAUX2 in the formation of grain quality. In addition, the qRT-PCR analysis suggested that several AAT genes continuously responded to diverse abiotic stresses, such as SiATLb1, SiANT1. Finally, combined with the previous studies and analysis on sequence characteristics and expression patterns of AAT genes, the possible functions of the foxtail millet AAT genes were predicted.Conclusion: This study for the first time reported the evolutionary features, functional differentiation, roles in the quality formation and response to abiotic stresses of foxtail millet AAT gene family, thus providing a framework for further functional analysis of SiAAT genes, and also contributing to the applications of AAT genes in improving the quality and resistance to abiotic stresses of foxtail millet, and other cereal crops.

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Genome-wide analysis and identification of cytokinin oxidase/dehydrogenase (CKX) gene family in foxtail millet (Setaria italica)

The Crop Journal ◽

10.1016/j.cj.2014.05.001 ◽

2014 ◽

Vol 2 (4) ◽

pp. 244-254 ◽

Cited By ~ 8

Author(s):

Yuange Wang ◽

Huaihua Liu ◽

Qingguo Xin

Keyword(s):

Gene Family ◽

Foxtail Millet ◽

Setaria Italica ◽

Cytokinin Oxidase ◽

Genome Wide Analysis ◽

Genome Wide

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Amino Acid Transporter (AAT) Gene Family In Foxtail Millet (Setaria Italica L.): Widespread Family Expansion, Functional Differentiation, Roles In Quality Formation And Response To Abiotic Stresses

10.21203/rs.3.rs-119005/v1 ◽

2020 ◽

Author(s):

Yang Yang ◽

Yongmao Chai ◽

Jiayi Liu ◽

Jie Zheng ◽

Zhangchen Zhao ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Gene Family ◽

Abiotic Stresses ◽

Foxtail Millet ◽

Functional Differentiation ◽

Setaria Italica ◽

Evolutionary Features ◽

Sequence Characteristics ◽

Quality Formation

Abstract Background: Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria and abiotic stress by modulating the transmembrane transfer of amino acids. In this study, we performed a genome-wide screening to analyze the AAT genes in foxtail millet (Setaria italica L.), especially those associated with quality formation and abiotic stresses response.Results: A total number of 94 AAT genes were identified and divided into 12 subfamilies by their sequence characteristics and phylogenetic relationship. A large number (58/94, 62%) of AAT genes in foxtail millet were expanded via gene duplication, involving 13 tandem and 12 segmental duplication events. Tandemly duplicated genes had a significant impact on their functional differentiation via sequence variation, structural variation and expression variation. Further comparison in multiple species showed that in addition to paralogous genes, the expression variations of the orthologous AAT genes also contributed to their functional differentiation. The transcriptomic comparison of two millet cultivars verified the direct contribution of the AAT genes such as SiAAP1, SiAAP8, and SiAUX2 in the formation of grain quality. In addition, the qRT-PCR analysis suggested that several AAT genes continuously responded to diverse abiotic stresses, such as SiATLb1, SiANT1. Finally, combined with the previous studies and analysis on sequence characteristics and expression patterns of AAT genes, the possible functions of the foxtail millet AAT genes were predicted.Conclusion: This study for the first time reported the evolutionary features, functional differentiation, roles in the quality formation and response to abiotic stresses of foxtail millet AAT gene family, thus providing a framework for further functional analysis of SiAAT genes, and also contributing to the applications of AAT genes in improving the quality and resistance to abiotic stresses of foxtail millet, and other cereal crops.

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Genome-Wide Analysis of the MADS-Box Gene Family in Foxtail Millet (Setaria Italica L.) and Expression Analyses to Reveal Their Role During Drought Stress

10.21203/rs.3.rs-1036026/v1 ◽

2021 ◽

Author(s):

Xinlei Ma ◽

Ningwei XU ◽

Pengpeng Gu ◽

Liqiang Du ◽

Zhenqing Guo ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Gene Family ◽

Expression Patterns ◽

Foxtail Millet ◽

Setaria Italica ◽

Pcr Analysis ◽

Induced Response ◽

Mads Box ◽

Element Analysis

Abstract MADS-box gene family is a key regulatory factor family, which controls vegetative growth, reproductive development and can be used to mediate abiotic stresses in many plants. However, Knowledge of this gene family is still limited in Setaria italica. In the present study, a total of 70 SitMADS genes were identified and renamed on the basis of the chromosomal distribution of the SitMADS genes. According to gene structure, conserved motif and phylogenetic feature, the 70 SitMADSs were classified into type-Ⅰ (Mα, Mβ, Mγ) and type-Ⅱ (MIKCC and MIKC*). All of the SitMADS genes were randomly distributed on nine chromosomes, and five tandem duplicated genes and 12 pairs of duplicated gene segments were detected in the SitMADS genes family. Synteny analysis provided a high homology between SitMADS genes and OsMADS genes. A cis-element analysis inferred that SitMADS genes, except for SitMADS23, possessed at least one drought stress response and ABA(Abscisic Acid)-induced response cis-element. Real-time quantitative PCR analysis was used to detect the expression patterns of SitMADS genes in various tissues and demonstrated that the genes responded drought stress and ABA treatments. SitMADS23, SitMADS42, SitMADS51, SitMADS52, SitMADS58 and SitMADS64 were highly expressed in PEG(Polyethylene glycol) and drought stress, which suggested its important role in drought stress response. SitMADS51, SitMADS63 and SitMADS64 seemed to be responsive to ABA hormone signaling, suggesting that they were involved in the ABA signaling pathways. This paper provided a deep insight into the evolutionary characteristics of SitMADS genes. The results provide comprehensive information for further analyses of the molecular functions of the MADS-box gene family in Setaria italica.

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