scholarly journals Comparative Genomics of Three-domain Multi-copper Oxidase Gene Family in Foxtail Millet (Setaria italica L.)

2021 ◽  
Author(s):  
Huilong Chen ◽  
Xiyin Wang ◽  
Weina Ge
Keyword(s):  
Comparative Genomics ◽  
Gene Family ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Oxidase Gene ◽  
Copper Oxidase

scholarly journals Genome-wide identification and in silico characterization of chitinase gene family in Foxtail millet (Setaria italica)

2020 ◽  
Author(s):  
Motukuri S. R. Krishna ◽  
Nerella Dheeraj ◽  
Bathuru Jayasree ◽  
Chodisetty Bhavya ◽  
Nallamothu Jaswanthi
Keyword(s):  
Gene Family ◽  
In Silico ◽  
Foxtail Millet ◽  
Chitinase Gene ◽  
Setaria Italica ◽  
Genome Wide ◽  
In Silico Characterization

Genome-wide characterization of the SiDof gene family in foxtail millet (Setaria italica)

Biosystems ◽  
2017 ◽  
Vol 151 ◽  
pp. 27-33 ◽  
Author(s):  
Li Zhang ◽  
Baoling Liu ◽  
Gewen Zheng ◽  
Aiying Zhang ◽  
Runzhi Li
Keyword(s):  
Gene Family ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Genome Wide

scholarly journals 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

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
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.

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

2022 ◽  
Author(s):  
Ashima Nehra ◽  
Punam Kundu ◽  
Kirti Ahlawat ◽  
Ashmita Chhikara ◽  
Niraj Agarwala ◽  
...  
Keyword(s):  
Gene Family ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Ef Hand

scholarly journals Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Hiroshi Shinozuka ◽  
Noel O. I. Cogan ◽  
German C. Spangenberg ◽  
John W. Forster
Keyword(s):  
Gene Expression ◽  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Gene Family ◽  
Perennial Ryegrass ◽  
Plant Architecture ◽  
Foxtail Millet ◽  
Grass Species ◽  
Plant Type ◽  
Bac Clone

Perennial ryegrass is an important pasture grass in temperate regions. As a forage biomass-generating species, plant architecture-related characters provide key objectives for breeding improvement. In silico comparative genomics analysis predicted colocation between a previously identified QTL for plant type (erect versus prostrate growth) and the ortholocus of the rice OsABCG5 gene (LpABCG5), as well as related QTLs in other Poaceae species. Sequencing of an LpABCG5-containing BAC clone identified presence of a paralogue (LpABCG6) in the vicinity of the LpABCG5 locus, in addition to three other gene-like sequences. Comparative genomics involving five other 5 grass species (rice, Brachypodium, sorghum, maize, and foxtail millet) revealed conserved microsynteny in the ABCG5 ortholocus-flanking region. Gene expression profiling and phylogenetic analysis suggested that the two paralogues are functionally distinct. Fourteen additional ABCG5 gene family members, which may interact with the LpABCG5 gene, were identified through sequencing of transcriptomes from perennial ryegrass leaf, anther, and pistils. A larger-scale phylogenetic analysis of the ABCG gene family suggested conservation between major branches of the Poaceae family. This study identified the LpABCG5 gene as a candidate for the plant type determinant, suggesting that manipulation of gene expression may provide valuable phenotypes for perennial ryegrass breeding.

scholarly journals The foxtail millet ( Setaria italica ) terpene synthase gene family

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

scholarly journals 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

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.

scholarly journals 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

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.

scholarly journals 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

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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