Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection
Hemerocallis spp. commonly known as daylilies and night lilies, are among the most popular ornamental crops worldwide. In Eastern Asia, H. citrina is also widely cultivated as both a vegetable crop and for medicinal use. However, limited genetic and genomic resources are available in Hemerocallis. K...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2020.00686/full |
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| author | Sen Li Sen Li Fangfang Ji Fangfang Ji Feifan Hou Feifan Hou Huliang Cui Huliang Cui Qingqing Shi Qingqing Shi Guoming Xing Guoming Xing Yiqun Weng Xiuping Kang Xiuping Kang |
| author_facet | Sen Li Sen Li Fangfang Ji Fangfang Ji Feifan Hou Feifan Hou Huliang Cui Huliang Cui Qingqing Shi Qingqing Shi Guoming Xing Guoming Xing Yiqun Weng Xiuping Kang Xiuping Kang |
| author_sort | Sen Li |
| collection | DOAJ |
| description | Hemerocallis spp. commonly known as daylilies and night lilies, are among the most popular ornamental crops worldwide. In Eastern Asia, H. citrina is also widely cultivated as both a vegetable crop and for medicinal use. However, limited genetic and genomic resources are available in Hemerocallis. Knowledge on the genetic diversity and population structure of this species-rich genus is very limited. In this study, we reported transcriptome sequencing of H. citrina cv. ‘Datonghuanghua’ which is a popular, high-yielding variety in China. We mined the transcriptome data, identified and characterized the microsatellite or simple sequence repeat (SSR) sequences in the expressed genome. From ∼14.15 Gbp clean reads, we assembled 92,107 unigenes, of which 41,796 were annotated for possible functions. From 41,796 unigenes, we identified and characterized 3,430 SSRs with varying motifs. Forty-three SSRs were used to fingerprint 155 Hemerocallis accessions. Clustering and population structure analyses with the genotypic data among the 155 accessions reveal broader genetic variation of daylilies than the night lily accessions which form a subgroup in the phylogenetic tree. The night lily group included accessions from H. citrina, H. lilioasphodelus, and H. minor, the majority of which bloom in the evening/night, whereas the ∼100 daylily accessions bloomed in the early morning suggesting flowering time may be a major force in the selection of night lily. The utility of these SSRs was further exemplified in association analysis of blooming time among these accessions. Twelve SSRs were found to have significant associations with this horticulturally important trait. |
| first_indexed | 2024-12-10T18:11:00Z |
| format | Article |
| id | doaj.art-aecdb9a252e845dfbfdaf4e9ef4f1631 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-10T18:11:00Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-aecdb9a252e845dfbfdaf4e9ef4f16312022-12-22T01:38:26ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-06-011110.3389/fpls.2020.00686512555Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis CollectionSen Li0Sen Li1Fangfang Ji2Fangfang Ji3Feifan Hou4Feifan Hou5Huliang Cui6Huliang Cui7Qingqing Shi8Qingqing Shi9Guoming Xing10Guoming Xing11Yiqun Weng12Xiuping Kang13Xiuping Kang14College of Horticulture, Shanxi Agricultural University, Taigu, ChinaCollaborative Innovation Center for Improving Quality and Increase Profits of Protected Vegetables in Shanxi, Taigu, ChinaCollege of Horticulture, Shanxi Agricultural University, Taigu, ChinaCollaborative Innovation Center for Improving Quality and Increase Profits of Protected Vegetables in Shanxi, Taigu, ChinaCollege of Horticulture, Shanxi Agricultural University, Taigu, ChinaCollaborative Innovation Center for Improving Quality and Increase Profits of Protected Vegetables in Shanxi, Taigu, ChinaCollege of Horticulture, Shanxi Agricultural University, Taigu, ChinaCollaborative Innovation Center for Improving Quality and Increase Profits of Protected Vegetables in Shanxi, Taigu, ChinaCollege of Horticulture, Shanxi Agricultural University, Taigu, ChinaCollaborative Innovation Center for Improving Quality and Increase Profits of Protected Vegetables in Shanxi, Taigu, ChinaCollege of Horticulture, Shanxi Agricultural University, Taigu, ChinaCollaborative Innovation Center for Improving Quality and Increase Profits of Protected Vegetables in Shanxi, Taigu, ChinaAgricultural Research Service, United States Department of Agriculture (USDA-ARS), Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, United StatesCollege of Horticulture, Shanxi Agricultural University, Taigu, ChinaCollaborative Innovation Center for Improving Quality and Increase Profits of Protected Vegetables in Shanxi, Taigu, ChinaHemerocallis spp. commonly known as daylilies and night lilies, are among the most popular ornamental crops worldwide. In Eastern Asia, H. citrina is also widely cultivated as both a vegetable crop and for medicinal use. However, limited genetic and genomic resources are available in Hemerocallis. Knowledge on the genetic diversity and population structure of this species-rich genus is very limited. In this study, we reported transcriptome sequencing of H. citrina cv. ‘Datonghuanghua’ which is a popular, high-yielding variety in China. We mined the transcriptome data, identified and characterized the microsatellite or simple sequence repeat (SSR) sequences in the expressed genome. From ∼14.15 Gbp clean reads, we assembled 92,107 unigenes, of which 41,796 were annotated for possible functions. From 41,796 unigenes, we identified and characterized 3,430 SSRs with varying motifs. Forty-three SSRs were used to fingerprint 155 Hemerocallis accessions. Clustering and population structure analyses with the genotypic data among the 155 accessions reveal broader genetic variation of daylilies than the night lily accessions which form a subgroup in the phylogenetic tree. The night lily group included accessions from H. citrina, H. lilioasphodelus, and H. minor, the majority of which bloom in the evening/night, whereas the ∼100 daylily accessions bloomed in the early morning suggesting flowering time may be a major force in the selection of night lily. The utility of these SSRs was further exemplified in association analysis of blooming time among these accessions. Twelve SSRs were found to have significant associations with this horticulturally important trait.https://www.frontiersin.org/article/10.3389/fpls.2020.00686/fulldaylilygenetic diversityHemerocallisnight lilypopulation structureSSR |
| spellingShingle | Sen Li Sen Li Fangfang Ji Fangfang Ji Feifan Hou Feifan Hou Huliang Cui Huliang Cui Qingqing Shi Qingqing Shi Guoming Xing Guoming Xing Yiqun Weng Xiuping Kang Xiuping Kang Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection Frontiers in Plant Science daylily genetic diversity Hemerocallis night lily population structure SSR |
| title | Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection |
| title_full | Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection |
| title_fullStr | Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection |
| title_full_unstemmed | Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection |
| title_short | Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection |
| title_sort | characterization of hemerocallis citrina transcriptome and development of est ssr markers for evaluation of genetic diversity and population structure of hemerocallis collection |
| topic | daylily genetic diversity Hemerocallis night lily population structure SSR |
| url | https://www.frontiersin.org/article/10.3389/fpls.2020.00686/full |
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