Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes
This study investigated the spectral changes in alfalfa molecular structures induced by silencing of Transparent Testa 8 (TT8) and Homeobox 12 (HB12) genes with univariate and multivariate analyses. TT8-silenced (TT8i), HB12-silenced (HB12i) and wild type (WT) alfalfa were grown in a greenhouse unde...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2018-03-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1422-0067/19/4/1046 |
| _version_ | 1811223580216655872 |
|---|---|
| author | Yaogeng Lei Abdelali Hannoufa David Christensen Haitao Shi Luciana L. Prates Peiqiang Yu |
| author_facet | Yaogeng Lei Abdelali Hannoufa David Christensen Haitao Shi Luciana L. Prates Peiqiang Yu |
| author_sort | Yaogeng Lei |
| collection | DOAJ |
| description | This study investigated the spectral changes in alfalfa molecular structures induced by silencing of Transparent Testa 8 (TT8) and Homeobox 12 (HB12) genes with univariate and multivariate analyses. TT8-silenced (TT8i), HB12-silenced (HB12i) and wild type (WT) alfalfa were grown in a greenhouse under normal conditions and were harvested at early-to-mid vegetative stage. Samples were free-dried and grounded through 0.02 mm sieve for spectra collections with attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Afterwards, both univariate and multivariate analyses were conducted on amide, carbohydrate and lipid regions. Univariate results showed that silencing of TT8 and HB12 genes affected peak heights of most total carbohydrate (TC) and structural carbohydrate (STC), and structural carbohydrate area (STCA) in carbohydrate regions; and β-sheet height, amide areas, and ratios of amide I/II and α-helix/β-sheet in amide region; and symmetric CH2 (SyCH2), asymmetric CH2 (AsCH2) and (a)symmetric CH2 and CH3 area (ASCCA) in the lipid region. Multivariate analysis showed that both hierarchy cluster analysis (HCA) and principal component analysis (PCA) clearly separated WT from transgenic plants in all carbohydrate regions and (a)symmetric CH2 and CH3 (ASCC) lipid region. In the amide region, PCA separated WT, TT8i and HB12i into different groups, while HCA clustered WT into a separate group. In conclusion, silencing of TT8 and HB12 affected intrinsic molecular structures of both amide and carbohydrate profiles in alfalfa, and multivariate analyses successfully distinguished gene-silenced alfalfa from its parental WT control. |
| first_indexed | 2024-04-12T08:36:26Z |
| format | Article |
| id | doaj.art-8cd38d6c898a4278b3e691d1d1b79ab4 |
| institution | Directory Open Access Journal |
| issn | 1422-0067 |
| language | English |
| last_indexed | 2024-04-12T08:36:26Z |
| publishDate | 2018-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-8cd38d6c898a4278b3e691d1d1b79ab42022-12-22T03:40:01ZengMDPI AGInternational Journal of Molecular Sciences1422-00672018-03-01194104610.3390/ijms19041046ijms19041046Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 GenesYaogeng Lei0Abdelali Hannoufa1David Christensen2Haitao Shi3Luciana L. Prates4Peiqiang Yu5Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, CanadaLondon Research and Development Centre, Agriculture and Argi-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, CanadaDepartment of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, CanadaDepartment of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, CanadaDepartment of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, CanadaDepartment of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, CanadaThis study investigated the spectral changes in alfalfa molecular structures induced by silencing of Transparent Testa 8 (TT8) and Homeobox 12 (HB12) genes with univariate and multivariate analyses. TT8-silenced (TT8i), HB12-silenced (HB12i) and wild type (WT) alfalfa were grown in a greenhouse under normal conditions and were harvested at early-to-mid vegetative stage. Samples were free-dried and grounded through 0.02 mm sieve for spectra collections with attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Afterwards, both univariate and multivariate analyses were conducted on amide, carbohydrate and lipid regions. Univariate results showed that silencing of TT8 and HB12 genes affected peak heights of most total carbohydrate (TC) and structural carbohydrate (STC), and structural carbohydrate area (STCA) in carbohydrate regions; and β-sheet height, amide areas, and ratios of amide I/II and α-helix/β-sheet in amide region; and symmetric CH2 (SyCH2), asymmetric CH2 (AsCH2) and (a)symmetric CH2 and CH3 area (ASCCA) in the lipid region. Multivariate analysis showed that both hierarchy cluster analysis (HCA) and principal component analysis (PCA) clearly separated WT from transgenic plants in all carbohydrate regions and (a)symmetric CH2 and CH3 (ASCC) lipid region. In the amide region, PCA separated WT, TT8i and HB12i into different groups, while HCA clustered WT into a separate group. In conclusion, silencing of TT8 and HB12 affected intrinsic molecular structures of both amide and carbohydrate profiles in alfalfa, and multivariate analyses successfully distinguished gene-silenced alfalfa from its parental WT control.http://www.mdpi.com/1422-0067/19/4/1046gene silencingtransgenic alfalfaATR-FTRunivariate analysismultivariate analysis |
| spellingShingle | Yaogeng Lei Abdelali Hannoufa David Christensen Haitao Shi Luciana L. Prates Peiqiang Yu Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes International Journal of Molecular Sciences gene silencing transgenic alfalfa ATR-FTR univariate analysis multivariate analysis |
| title | Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes |
| title_full | Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes |
| title_fullStr | Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes |
| title_full_unstemmed | Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes |
| title_short | Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes |
| title_sort | molecular structural changes in alfalfa detected by atr ftir spectroscopy in response to silencing of tt8 and hb12 genes |
| topic | gene silencing transgenic alfalfa ATR-FTR univariate analysis multivariate analysis |
| url | http://www.mdpi.com/1422-0067/19/4/1046 |
| work_keys_str_mv | AT yaogenglei molecularstructuralchangesinalfalfadetectedbyatrftirspectroscopyinresponsetosilencingoftt8andhb12genes AT abdelalihannoufa molecularstructuralchangesinalfalfadetectedbyatrftirspectroscopyinresponsetosilencingoftt8andhb12genes AT davidchristensen molecularstructuralchangesinalfalfadetectedbyatrftirspectroscopyinresponsetosilencingoftt8andhb12genes AT haitaoshi molecularstructuralchangesinalfalfadetectedbyatrftirspectroscopyinresponsetosilencingoftt8andhb12genes AT lucianalprates molecularstructuralchangesinalfalfadetectedbyatrftirspectroscopyinresponsetosilencingoftt8andhb12genes AT peiqiangyu molecularstructuralchangesinalfalfadetectedbyatrftirspectroscopyinresponsetosilencingoftt8andhb12genes |