RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum)

Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging...
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Gespeichert in:

Autor*in:	Qingqing Yu [verfasserIn] Yao Ling [verfasserIn] Yanli Xiong [verfasserIn] Wenda Zhao [verfasserIn] Yi Xiong [verfasserIn] Zhixiao Dong [verfasserIn] Jian Yang [verfasserIn] Junming Zhao [verfasserIn] Xinquan Zhang [verfasserIn] Xiao Ma [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	Lolium multiflorum Variety identification RAD-seq Phylogenetic analysis SNP markers

Übergeordnetes Werk:	In: BMC Plant Biology - BMC, 2003, 22(2022), 1, Seite 12
Übergeordnetes Werk:	volume:22 ; year:2022 ; number:1 ; pages:12

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s12870-022-03617-6

Katalog-ID:	DOAJ029509211

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allfields	10.1186/s12870-022-03617-6 doi (DE-627)DOAJ029509211 (DE-599)DOAJfd2a8dda9fa64f939f40ecd32d445216 DE-627 ger DE-627 rakwb eng QK1-989 Qingqing Yu verfasserin aut RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum) 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety ‘Changjiang No.2’ had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species. Lolium multiflorum Variety identification RAD-seq Phylogenetic analysis SNP markers Botany Yao Ling verfasserin aut Yanli Xiong verfasserin aut Wenda Zhao verfasserin aut Yi Xiong verfasserin aut Zhixiao Dong verfasserin aut Jian Yang verfasserin aut Junming Zhao verfasserin aut Xinquan Zhang verfasserin aut Xiao Ma verfasserin aut In BMC Plant Biology BMC, 2003 22(2022), 1, Seite 12 (DE-627)335489060 (DE-600)2059868-3 14712229 nnns volume:22 year:2022 number:1 pages:12 https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/article/fd2a8dda9fa64f939f40ecd32d445216 kostenfrei https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/toc/1471-2229 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_224 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 22 2022 1 12
spelling	10.1186/s12870-022-03617-6 doi (DE-627)DOAJ029509211 (DE-599)DOAJfd2a8dda9fa64f939f40ecd32d445216 DE-627 ger DE-627 rakwb eng QK1-989 Qingqing Yu verfasserin aut RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum) 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety ‘Changjiang No.2’ had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species. Lolium multiflorum Variety identification RAD-seq Phylogenetic analysis SNP markers Botany Yao Ling verfasserin aut Yanli Xiong verfasserin aut Wenda Zhao verfasserin aut Yi Xiong verfasserin aut Zhixiao Dong verfasserin aut Jian Yang verfasserin aut Junming Zhao verfasserin aut Xinquan Zhang verfasserin aut Xiao Ma verfasserin aut In BMC Plant Biology BMC, 2003 22(2022), 1, Seite 12 (DE-627)335489060 (DE-600)2059868-3 14712229 nnns volume:22 year:2022 number:1 pages:12 https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/article/fd2a8dda9fa64f939f40ecd32d445216 kostenfrei https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/toc/1471-2229 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_224 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 22 2022 1 12
allfields_unstemmed	10.1186/s12870-022-03617-6 doi (DE-627)DOAJ029509211 (DE-599)DOAJfd2a8dda9fa64f939f40ecd32d445216 DE-627 ger DE-627 rakwb eng QK1-989 Qingqing Yu verfasserin aut RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum) 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety ‘Changjiang No.2’ had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species. Lolium multiflorum Variety identification RAD-seq Phylogenetic analysis SNP markers Botany Yao Ling verfasserin aut Yanli Xiong verfasserin aut Wenda Zhao verfasserin aut Yi Xiong verfasserin aut Zhixiao Dong verfasserin aut Jian Yang verfasserin aut Junming Zhao verfasserin aut Xinquan Zhang verfasserin aut Xiao Ma verfasserin aut In BMC Plant Biology BMC, 2003 22(2022), 1, Seite 12 (DE-627)335489060 (DE-600)2059868-3 14712229 nnns volume:22 year:2022 number:1 pages:12 https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/article/fd2a8dda9fa64f939f40ecd32d445216 kostenfrei https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/toc/1471-2229 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_224 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 22 2022 1 12
allfieldsGer	10.1186/s12870-022-03617-6 doi (DE-627)DOAJ029509211 (DE-599)DOAJfd2a8dda9fa64f939f40ecd32d445216 DE-627 ger DE-627 rakwb eng QK1-989 Qingqing Yu verfasserin aut RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum) 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety ‘Changjiang No.2’ had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species. Lolium multiflorum Variety identification RAD-seq Phylogenetic analysis SNP markers Botany Yao Ling verfasserin aut Yanli Xiong verfasserin aut Wenda Zhao verfasserin aut Yi Xiong verfasserin aut Zhixiao Dong verfasserin aut Jian Yang verfasserin aut Junming Zhao verfasserin aut Xinquan Zhang verfasserin aut Xiao Ma verfasserin aut In BMC Plant Biology BMC, 2003 22(2022), 1, Seite 12 (DE-627)335489060 (DE-600)2059868-3 14712229 nnns volume:22 year:2022 number:1 pages:12 https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/article/fd2a8dda9fa64f939f40ecd32d445216 kostenfrei https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/toc/1471-2229 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_224 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 22 2022 1 12
allfieldsSound	10.1186/s12870-022-03617-6 doi (DE-627)DOAJ029509211 (DE-599)DOAJfd2a8dda9fa64f939f40ecd32d445216 DE-627 ger DE-627 rakwb eng QK1-989 Qingqing Yu verfasserin aut RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum) 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety ‘Changjiang No.2’ had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species. Lolium multiflorum Variety identification RAD-seq Phylogenetic analysis SNP markers Botany Yao Ling verfasserin aut Yanli Xiong verfasserin aut Wenda Zhao verfasserin aut Yi Xiong verfasserin aut Zhixiao Dong verfasserin aut Jian Yang verfasserin aut Junming Zhao verfasserin aut Xinquan Zhang verfasserin aut Xiao Ma verfasserin aut In BMC Plant Biology BMC, 2003 22(2022), 1, Seite 12 (DE-627)335489060 (DE-600)2059868-3 14712229 nnns volume:22 year:2022 number:1 pages:12 https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/article/fd2a8dda9fa64f939f40ecd32d445216 kostenfrei https://doi.org/10.1186/s12870-022-03617-6 kostenfrei https://doaj.org/toc/1471-2229 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_224 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 22 2022 1 12
language	English
source	In BMC Plant Biology 22(2022), 1, Seite 12 volume:22 year:2022 number:1 pages:12
sourceStr	In BMC Plant Biology 22(2022), 1, Seite 12 volume:22 year:2022 number:1 pages:12
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Lolium multiflorum Variety identification RAD-seq Phylogenetic analysis SNP markers Botany
isfreeaccess_bool	true
container_title	BMC Plant Biology
authorswithroles_txt_mv	Qingqing Yu @@aut@@ Yao Ling @@aut@@ Yanli Xiong @@aut@@ Wenda Zhao @@aut@@ Yi Xiong @@aut@@ Zhixiao Dong @@aut@@ Jian Yang @@aut@@ Junming Zhao @@aut@@ Xinquan Zhang @@aut@@ Xiao Ma @@aut@@
publishDateDaySort_date	2022-01-01T00:00:00Z
hierarchy_top_id	335489060
id	DOAJ029509211
language_de	englisch
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callnumber-first	Q - Science
author	Qingqing Yu
spellingShingle	Qingqing Yu misc QK1-989 misc Lolium multiflorum misc Variety identification misc RAD-seq misc Phylogenetic analysis misc SNP markers misc Botany RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum)
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topic_title	QK1-989 RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum) Lolium multiflorum Variety identification RAD-seq Phylogenetic analysis SNP markers
topic	misc QK1-989 misc Lolium multiflorum misc Variety identification misc RAD-seq misc Phylogenetic analysis misc SNP markers misc Botany
topic_unstemmed	misc QK1-989 misc Lolium multiflorum misc Variety identification misc RAD-seq misc Phylogenetic analysis misc SNP markers misc Botany
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title	RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum)
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title_full	RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum)
author_sort	Qingqing Yu
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author_browse	Qingqing Yu Yao Ling Yanli Xiong Wenda Zhao Yi Xiong Zhixiao Dong Jian Yang Junming Zhao Xinquan Zhang Xiao Ma
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title_sort	rad-seq as an effective strategy for heterogenous variety identification in plants—a case study in italian ryegrass (lolium multiflorum)
callnumber	QK1-989
title_auth	RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum)
abstract	Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety ‘Changjiang No.2’ had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species.
abstractGer	Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety ‘Changjiang No.2’ had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species.
abstract_unstemmed	Abstract The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety ‘Changjiang No.2’ had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species.
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title_short	RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum)
url	https://doi.org/10.1186/s12870-022-03617-6 https://doaj.org/article/fd2a8dda9fa64f939f40ecd32d445216 https://doaj.org/toc/1471-2229
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RAD-seq as an effective strategy for heterogenous variety identification in plants—a case study in Italian Ryegrass (Lolium multiflorum)

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