Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings

Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and e...
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Autor*in:	Jia Li [verfasserIn] Wei Xin [verfasserIn] Weiping Wang [verfasserIn] Shijiao Zhao [verfasserIn] Lu Xu [verfasserIn] Xingdong Jiang [verfasserIn] Yuxuan Duan [verfasserIn] Hongliang Zheng [verfasserIn] Luomiao Yang [verfasserIn] Hualong Liu [verfasserIn] Yan Jia [verfasserIn] Detang Zou [verfasserIn] Jingguo Wang [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	Rice Genome-wide association study RNA-seq Low-nitrogen tolerance

Übergeordnetes Werk:	In: Rice - SpringerOpen, 2016, 15(2022), 1, Seite 16
Übergeordnetes Werk:	volume:15 ; year:2022 ; number:1 ; pages:16

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.1186/s12284-022-00597-x

Katalog-ID:	DOAJ021209332

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520			\|a Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.
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allfields	10.1186/s12284-022-00597-x doi (DE-627)DOAJ021209332 (DE-599)DOAJ7e1b6c1024f0482eb05ff76f012d08e2 DE-627 ger DE-627 rakwb eng SB1-1110 Jia Li verfasserin aut Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency. Rice Genome-wide association study RNA-seq Low-nitrogen tolerance Plant culture Wei Xin verfasserin aut Weiping Wang verfasserin aut Shijiao Zhao verfasserin aut Lu Xu verfasserin aut Xingdong Jiang verfasserin aut Yuxuan Duan verfasserin aut Hongliang Zheng verfasserin aut Luomiao Yang verfasserin aut Hualong Liu verfasserin aut Yan Jia verfasserin aut Detang Zou verfasserin aut Jingguo Wang verfasserin aut In Rice SpringerOpen, 2016 15(2022), 1, Seite 16 (DE-627)582026636 (DE-600)2457103-9 19398433 nnns volume:15 year:2022 number:1 pages:16 https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/article/7e1b6c1024f0482eb05ff76f012d08e2 kostenfrei https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/toc/1939-8425 Journal toc kostenfrei https://doaj.org/toc/1939-8433 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4367 GBV_ILN_4700 AR 15 2022 1 16
spelling	10.1186/s12284-022-00597-x doi (DE-627)DOAJ021209332 (DE-599)DOAJ7e1b6c1024f0482eb05ff76f012d08e2 DE-627 ger DE-627 rakwb eng SB1-1110 Jia Li verfasserin aut Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency. Rice Genome-wide association study RNA-seq Low-nitrogen tolerance Plant culture Wei Xin verfasserin aut Weiping Wang verfasserin aut Shijiao Zhao verfasserin aut Lu Xu verfasserin aut Xingdong Jiang verfasserin aut Yuxuan Duan verfasserin aut Hongliang Zheng verfasserin aut Luomiao Yang verfasserin aut Hualong Liu verfasserin aut Yan Jia verfasserin aut Detang Zou verfasserin aut Jingguo Wang verfasserin aut In Rice SpringerOpen, 2016 15(2022), 1, Seite 16 (DE-627)582026636 (DE-600)2457103-9 19398433 nnns volume:15 year:2022 number:1 pages:16 https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/article/7e1b6c1024f0482eb05ff76f012d08e2 kostenfrei https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/toc/1939-8425 Journal toc kostenfrei https://doaj.org/toc/1939-8433 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4367 GBV_ILN_4700 AR 15 2022 1 16
allfields_unstemmed	10.1186/s12284-022-00597-x doi (DE-627)DOAJ021209332 (DE-599)DOAJ7e1b6c1024f0482eb05ff76f012d08e2 DE-627 ger DE-627 rakwb eng SB1-1110 Jia Li verfasserin aut Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency. Rice Genome-wide association study RNA-seq Low-nitrogen tolerance Plant culture Wei Xin verfasserin aut Weiping Wang verfasserin aut Shijiao Zhao verfasserin aut Lu Xu verfasserin aut Xingdong Jiang verfasserin aut Yuxuan Duan verfasserin aut Hongliang Zheng verfasserin aut Luomiao Yang verfasserin aut Hualong Liu verfasserin aut Yan Jia verfasserin aut Detang Zou verfasserin aut Jingguo Wang verfasserin aut In Rice SpringerOpen, 2016 15(2022), 1, Seite 16 (DE-627)582026636 (DE-600)2457103-9 19398433 nnns volume:15 year:2022 number:1 pages:16 https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/article/7e1b6c1024f0482eb05ff76f012d08e2 kostenfrei https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/toc/1939-8425 Journal toc kostenfrei https://doaj.org/toc/1939-8433 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4367 GBV_ILN_4700 AR 15 2022 1 16
allfieldsGer	10.1186/s12284-022-00597-x doi (DE-627)DOAJ021209332 (DE-599)DOAJ7e1b6c1024f0482eb05ff76f012d08e2 DE-627 ger DE-627 rakwb eng SB1-1110 Jia Li verfasserin aut Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency. Rice Genome-wide association study RNA-seq Low-nitrogen tolerance Plant culture Wei Xin verfasserin aut Weiping Wang verfasserin aut Shijiao Zhao verfasserin aut Lu Xu verfasserin aut Xingdong Jiang verfasserin aut Yuxuan Duan verfasserin aut Hongliang Zheng verfasserin aut Luomiao Yang verfasserin aut Hualong Liu verfasserin aut Yan Jia verfasserin aut Detang Zou verfasserin aut Jingguo Wang verfasserin aut In Rice SpringerOpen, 2016 15(2022), 1, Seite 16 (DE-627)582026636 (DE-600)2457103-9 19398433 nnns volume:15 year:2022 number:1 pages:16 https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/article/7e1b6c1024f0482eb05ff76f012d08e2 kostenfrei https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/toc/1939-8425 Journal toc kostenfrei https://doaj.org/toc/1939-8433 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4367 GBV_ILN_4700 AR 15 2022 1 16
allfieldsSound	10.1186/s12284-022-00597-x doi (DE-627)DOAJ021209332 (DE-599)DOAJ7e1b6c1024f0482eb05ff76f012d08e2 DE-627 ger DE-627 rakwb eng SB1-1110 Jia Li verfasserin aut Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency. Rice Genome-wide association study RNA-seq Low-nitrogen tolerance Plant culture Wei Xin verfasserin aut Weiping Wang verfasserin aut Shijiao Zhao verfasserin aut Lu Xu verfasserin aut Xingdong Jiang verfasserin aut Yuxuan Duan verfasserin aut Hongliang Zheng verfasserin aut Luomiao Yang verfasserin aut Hualong Liu verfasserin aut Yan Jia verfasserin aut Detang Zou verfasserin aut Jingguo Wang verfasserin aut In Rice SpringerOpen, 2016 15(2022), 1, Seite 16 (DE-627)582026636 (DE-600)2457103-9 19398433 nnns volume:15 year:2022 number:1 pages:16 https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/article/7e1b6c1024f0482eb05ff76f012d08e2 kostenfrei https://doi.org/10.1186/s12284-022-00597-x kostenfrei https://doaj.org/toc/1939-8425 Journal toc kostenfrei https://doaj.org/toc/1939-8433 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4367 GBV_ILN_4700 AR 15 2022 1 16
language	English
source	In Rice 15(2022), 1, Seite 16 volume:15 year:2022 number:1 pages:16
sourceStr	In Rice 15(2022), 1, Seite 16 volume:15 year:2022 number:1 pages:16
format_phy_str_mv	Article
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topic_facet	Rice Genome-wide association study RNA-seq Low-nitrogen tolerance Plant culture
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authorswithroles_txt_mv	Jia Li @@aut@@ Wei Xin @@aut@@ Weiping Wang @@aut@@ Shijiao Zhao @@aut@@ Lu Xu @@aut@@ Xingdong Jiang @@aut@@ Yuxuan Duan @@aut@@ Hongliang Zheng @@aut@@ Luomiao Yang @@aut@@ Hualong Liu @@aut@@ Yan Jia @@aut@@ Detang Zou @@aut@@ Jingguo Wang @@aut@@
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callnumber-first	S - Agriculture
author	Jia Li
spellingShingle	Jia Li misc SB1-1110 misc Rice misc Genome-wide association study misc RNA-seq misc Low-nitrogen tolerance misc Plant culture Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings
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topic_title	SB1-1110 Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings Rice Genome-wide association study RNA-seq Low-nitrogen tolerance
topic	misc SB1-1110 misc Rice misc Genome-wide association study misc RNA-seq misc Low-nitrogen tolerance misc Plant culture
topic_unstemmed	misc SB1-1110 misc Rice misc Genome-wide association study misc RNA-seq misc Low-nitrogen tolerance misc Plant culture
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title	Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings
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title_full	Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings
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title_sort	mapping of candidate genes in response to low nitrogen in rice seedlings
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title_auth	Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings
abstract	Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.
abstractGer	Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.
abstract_unstemmed	Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.
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title_short	Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings
url	https://doi.org/10.1186/s12284-022-00597-x https://doaj.org/article/7e1b6c1024f0482eb05ff76f012d08e2 https://doaj.org/toc/1939-8425 https://doaj.org/toc/1939-8433
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Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. 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Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings

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