Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)

Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield tr...
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Autor*in:	Siyuan Zhu [verfasserIn] Xiaojun Chen [verfasserIn] Xia Liu [verfasserIn] Jian Zhao [verfasserIn] Touming Liu [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL)

Übergeordnetes Werk:	In: BMC Genomics - BMC, 2003, 20(2019), 1, Seite 9
Übergeordnetes Werk:	volume:20 ; year:2019 ; number:1 ; pages:9

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s12864-019-6025-2

Katalog-ID:	DOAJ044420498

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520			\|a Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding.
650		4	\|a Garlic
650		4	\|a Bulb yield
650		4	\|a Association mapping
650		4	\|a Expression quantitative trait locus (eQTL)
653		0	\|a Biotechnology
653		0	\|a Genetics
700	0		\|a Xiaojun Chen \|e verfasserin \|4 aut
700	0		\|a Xia Liu \|e verfasserin \|4 aut
700	0		\|a Jian Zhao \|e verfasserin \|4 aut
700	0		\|a Touming Liu \|e verfasserin \|4 aut
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allfields	10.1186/s12864-019-6025-2 doi (DE-627)DOAJ044420498 (DE-599)DOAJbdcdc5c3d1a2454db5df308d23335ec0 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Siyuan Zhu verfasserin aut Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding. Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL) Biotechnology Genetics Xiaojun Chen verfasserin aut Xia Liu verfasserin aut Jian Zhao verfasserin aut Touming Liu verfasserin aut In BMC Genomics BMC, 2003 20(2019), 1, Seite 9 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:20 year:2019 number:1 pages:9 https://doi.org/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/article/bdcdc5c3d1a2454db5df308d23335ec0 kostenfrei http://link.springer.com/article/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA 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 20 2019 1 9
spelling	10.1186/s12864-019-6025-2 doi (DE-627)DOAJ044420498 (DE-599)DOAJbdcdc5c3d1a2454db5df308d23335ec0 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Siyuan Zhu verfasserin aut Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding. Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL) Biotechnology Genetics Xiaojun Chen verfasserin aut Xia Liu verfasserin aut Jian Zhao verfasserin aut Touming Liu verfasserin aut In BMC Genomics BMC, 2003 20(2019), 1, Seite 9 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:20 year:2019 number:1 pages:9 https://doi.org/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/article/bdcdc5c3d1a2454db5df308d23335ec0 kostenfrei http://link.springer.com/article/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA 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 20 2019 1 9
allfields_unstemmed	10.1186/s12864-019-6025-2 doi (DE-627)DOAJ044420498 (DE-599)DOAJbdcdc5c3d1a2454db5df308d23335ec0 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Siyuan Zhu verfasserin aut Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding. Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL) Biotechnology Genetics Xiaojun Chen verfasserin aut Xia Liu verfasserin aut Jian Zhao verfasserin aut Touming Liu verfasserin aut In BMC Genomics BMC, 2003 20(2019), 1, Seite 9 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:20 year:2019 number:1 pages:9 https://doi.org/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/article/bdcdc5c3d1a2454db5df308d23335ec0 kostenfrei http://link.springer.com/article/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA 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 20 2019 1 9
allfieldsGer	10.1186/s12864-019-6025-2 doi (DE-627)DOAJ044420498 (DE-599)DOAJbdcdc5c3d1a2454db5df308d23335ec0 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Siyuan Zhu verfasserin aut Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding. Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL) Biotechnology Genetics Xiaojun Chen verfasserin aut Xia Liu verfasserin aut Jian Zhao verfasserin aut Touming Liu verfasserin aut In BMC Genomics BMC, 2003 20(2019), 1, Seite 9 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:20 year:2019 number:1 pages:9 https://doi.org/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/article/bdcdc5c3d1a2454db5df308d23335ec0 kostenfrei http://link.springer.com/article/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA 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 20 2019 1 9
allfieldsSound	10.1186/s12864-019-6025-2 doi (DE-627)DOAJ044420498 (DE-599)DOAJbdcdc5c3d1a2454db5df308d23335ec0 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Siyuan Zhu verfasserin aut Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding. Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL) Biotechnology Genetics Xiaojun Chen verfasserin aut Xia Liu verfasserin aut Jian Zhao verfasserin aut Touming Liu verfasserin aut In BMC Genomics BMC, 2003 20(2019), 1, Seite 9 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:20 year:2019 number:1 pages:9 https://doi.org/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/article/bdcdc5c3d1a2454db5df308d23335ec0 kostenfrei http://link.springer.com/article/10.1186/s12864-019-6025-2 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA 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 20 2019 1 9
language	English
source	In BMC Genomics 20(2019), 1, Seite 9 volume:20 year:2019 number:1 pages:9
sourceStr	In BMC Genomics 20(2019), 1, Seite 9 volume:20 year:2019 number:1 pages:9
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL) Biotechnology Genetics
isfreeaccess_bool	true
container_title	BMC Genomics
authorswithroles_txt_mv	Siyuan Zhu @@aut@@ Xiaojun Chen @@aut@@ Xia Liu @@aut@@ Jian Zhao @@aut@@ Touming Liu @@aut@@
publishDateDaySort_date	2019-01-01T00:00:00Z
hierarchy_top_id	326644954
id	DOAJ044420498
language_de	englisch
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Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. 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callnumber-first	T - Technology
author	Siyuan Zhu
spellingShingle	Siyuan Zhu misc TP248.13-248.65 misc QH426-470 misc Garlic misc Bulb yield misc Association mapping misc Expression quantitative trait locus (eQTL) misc Biotechnology misc Genetics Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)
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topic_title	TP248.13-248.65 QH426-470 Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL)
topic	misc TP248.13-248.65 misc QH426-470 misc Garlic misc Bulb yield misc Association mapping misc Expression quantitative trait locus (eQTL) misc Biotechnology misc Genetics
topic_unstemmed	misc TP248.13-248.65 misc QH426-470 misc Garlic misc Bulb yield misc Association mapping misc Expression quantitative trait locus (eQTL) misc Biotechnology misc Genetics
topic_browse	misc TP248.13-248.65 misc QH426-470 misc Garlic misc Bulb yield misc Association mapping misc Expression quantitative trait locus (eQTL) misc Biotechnology misc Genetics
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title	Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)
ctrlnum	(DE-627)DOAJ044420498 (DE-599)DOAJbdcdc5c3d1a2454db5df308d23335ec0
title_full	Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)
author_sort	Siyuan Zhu
journal	BMC Genomics
journalStr	BMC Genomics
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author_browse	Siyuan Zhu Xiaojun Chen Xia Liu Jian Zhao Touming Liu
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author-letter	Siyuan Zhu
doi_str_mv	10.1186/s12864-019-6025-2
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title_sort	transcriptome-wide association study and eqtl analysis to assess the genetic basis of bulb-yield traits in garlic (allium sativum)
callnumber	TP248.13-248.65
title_auth	Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)
abstract	Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding.
abstractGer	Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding.
abstract_unstemmed	Abstract Background Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. Results In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. Conclusion This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding.
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title_short	Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)
url	https://doi.org/10.1186/s12864-019-6025-2 https://doaj.org/article/bdcdc5c3d1a2454db5df308d23335ec0 http://link.springer.com/article/10.1186/s12864-019-6025-2 https://doaj.org/toc/1471-2164
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up_date	2024-07-03T22:55:32.450Z
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Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)

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