Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars

Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between diff...
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Autor*in:	Tang, Kang [verfasserIn] Li, Lin Zhang, Bowen Zhang, Wei Zeng, Ningbo Zhang, Hao Liu, Dengwang Luo, Zinan

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Peanut Transcriptome Weighted gene co-expression network analysis (WGCNA) Differentially expressed genes (DEGs) Hub genes

Anmerkung:	© The Author(s) 2023

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 24(2023), 1 vom: 27. Juli
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:1 ; day:27 ; month:07

Links:	Volltext

DOI / URN:	10.1186/s12864-023-09436-9

Katalog-ID:	SPR052554686

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520			\|a Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency.
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650		4	\|a Hub genes \|7 (dpeaa)DE-He213
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allfields	10.1186/s12864-023-09436-9 doi (DE-627)SPR052554686 (SPR)s12864-023-09436-9-e DE-627 ger DE-627 rakwb eng Tang, Kang verfasserin aut Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. Peanut (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Weighted gene co-expression network analysis (WGCNA) (dpeaa)DE-He213 Differentially expressed genes (DEGs) (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Li, Lin aut Zhang, Bowen aut Zhang, Wei aut Zeng, Ningbo aut Zhang, Hao aut Liu, Dengwang aut Luo, Zinan aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 27. Juli (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:27 month:07 https://dx.doi.org/10.1186/s12864-023-09436-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 27 07
spelling	10.1186/s12864-023-09436-9 doi (DE-627)SPR052554686 (SPR)s12864-023-09436-9-e DE-627 ger DE-627 rakwb eng Tang, Kang verfasserin aut Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. Peanut (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Weighted gene co-expression network analysis (WGCNA) (dpeaa)DE-He213 Differentially expressed genes (DEGs) (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Li, Lin aut Zhang, Bowen aut Zhang, Wei aut Zeng, Ningbo aut Zhang, Hao aut Liu, Dengwang aut Luo, Zinan aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 27. Juli (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:27 month:07 https://dx.doi.org/10.1186/s12864-023-09436-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 27 07
allfields_unstemmed	10.1186/s12864-023-09436-9 doi (DE-627)SPR052554686 (SPR)s12864-023-09436-9-e DE-627 ger DE-627 rakwb eng Tang, Kang verfasserin aut Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. Peanut (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Weighted gene co-expression network analysis (WGCNA) (dpeaa)DE-He213 Differentially expressed genes (DEGs) (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Li, Lin aut Zhang, Bowen aut Zhang, Wei aut Zeng, Ningbo aut Zhang, Hao aut Liu, Dengwang aut Luo, Zinan aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 27. Juli (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:27 month:07 https://dx.doi.org/10.1186/s12864-023-09436-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 27 07
allfieldsGer	10.1186/s12864-023-09436-9 doi (DE-627)SPR052554686 (SPR)s12864-023-09436-9-e DE-627 ger DE-627 rakwb eng Tang, Kang verfasserin aut Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. Peanut (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Weighted gene co-expression network analysis (WGCNA) (dpeaa)DE-He213 Differentially expressed genes (DEGs) (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Li, Lin aut Zhang, Bowen aut Zhang, Wei aut Zeng, Ningbo aut Zhang, Hao aut Liu, Dengwang aut Luo, Zinan aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 27. Juli (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:27 month:07 https://dx.doi.org/10.1186/s12864-023-09436-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 27 07
allfieldsSound	10.1186/s12864-023-09436-9 doi (DE-627)SPR052554686 (SPR)s12864-023-09436-9-e DE-627 ger DE-627 rakwb eng Tang, Kang verfasserin aut Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. Peanut (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Weighted gene co-expression network analysis (WGCNA) (dpeaa)DE-He213 Differentially expressed genes (DEGs) (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Li, Lin aut Zhang, Bowen aut Zhang, Wei aut Zeng, Ningbo aut Zhang, Hao aut Liu, Dengwang aut Luo, Zinan aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 27. Juli (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:27 month:07 https://dx.doi.org/10.1186/s12864-023-09436-9 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 27 07
language	English
source	Enthalten in BMC genomics 24(2023), 1 vom: 27. Juli volume:24 year:2023 number:1 day:27 month:07
sourceStr	Enthalten in BMC genomics 24(2023), 1 vom: 27. Juli volume:24 year:2023 number:1 day:27 month:07
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Peanut Transcriptome Weighted gene co-expression network analysis (WGCNA) Differentially expressed genes (DEGs) Hub genes
isfreeaccess_bool	true
container_title	BMC genomics
authorswithroles_txt_mv	Tang, Kang @@aut@@ Li, Lin @@aut@@ Zhang, Bowen @@aut@@ Zhang, Wei @@aut@@ Zeng, Ningbo @@aut@@ Zhang, Hao @@aut@@ Liu, Dengwang @@aut@@ Luo, Zinan @@aut@@
publishDateDaySort_date	2023-07-27T00:00:00Z
hierarchy_top_id	326644954
id	SPR052554686
language_de	englisch
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author	Tang, Kang
spellingShingle	Tang, Kang misc Peanut misc Transcriptome misc Weighted gene co-expression network analysis (WGCNA) misc Differentially expressed genes (DEGs) misc Hub genes Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars
authorStr	Tang, Kang
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topic_title	Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars Peanut (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Weighted gene co-expression network analysis (WGCNA) (dpeaa)DE-He213 Differentially expressed genes (DEGs) (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213
topic	misc Peanut misc Transcriptome misc Weighted gene co-expression network analysis (WGCNA) misc Differentially expressed genes (DEGs) misc Hub genes
topic_unstemmed	misc Peanut misc Transcriptome misc Weighted gene co-expression network analysis (WGCNA) misc Differentially expressed genes (DEGs) misc Hub genes
topic_browse	misc Peanut misc Transcriptome misc Weighted gene co-expression network analysis (WGCNA) misc Differentially expressed genes (DEGs) misc Hub genes
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title	Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars
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title_full	Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars
author_sort	Tang, Kang
journal	BMC genomics
journalStr	BMC genomics
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author_browse	Tang, Kang Li, Lin Zhang, Bowen Zhang, Wei Zeng, Ningbo Zhang, Hao Liu, Dengwang Luo, Zinan
container_volume	24
format_se	Elektronische Aufsätze
author-letter	Tang, Kang
doi_str_mv	10.1186/s12864-023-09436-9
title_sort	gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars
title_auth	Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars
abstract	Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. © The Author(s) 2023
abstractGer	Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. © The Author(s) 2023
abstract_unstemmed	Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. © The Author(s) 2023
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container_issue	1
title_short	Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars
url	https://dx.doi.org/10.1186/s12864-023-09436-9
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author2	Li, Lin Zhang, Bowen Zhang, Wei Zeng, Ningbo Zhang, Hao Liu, Dengwang Luo, Zinan
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up_date	2024-07-04T03:12:35.454Z
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Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars

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