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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-6025-2 |
| _version_ | 1828837190365347840 |
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| author | Siyuan Zhu Xiaojun Chen Xia Liu Jian Zhao Touming Liu |
| author_facet | Siyuan Zhu Xiaojun Chen Xia Liu Jian Zhao Touming Liu |
| author_sort | Siyuan Zhu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T18:37:01Z |
| format | Article |
| id | doaj.art-bdcdc5c3d1a2454db5df308d23335ec0 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T18:37:01Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-bdcdc5c3d1a2454db5df308d23335ec02022-12-22T00:15:46ZengBMCBMC Genomics1471-21642019-08-012011910.1186/s12864-019-6025-2Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)Siyuan Zhu0Xiaojun Chen1Xia Liu2Jian Zhao3Touming Liu4Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural SciencesInstitute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural SciencesNovogene Bioinformatics InstituteNovogene Bioinformatics InstituteInstitute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural SciencesAbstract 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.http://link.springer.com/article/10.1186/s12864-019-6025-2GarlicBulb yieldAssociation mappingExpression quantitative trait locus (eQTL) |
| spellingShingle | Siyuan Zhu Xiaojun Chen Xia Liu Jian Zhao Touming Liu Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) BMC Genomics Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL) |
| title | Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) |
| title_full | Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) |
| title_fullStr | Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) |
| title_full_unstemmed | Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) |
| title_short | Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum) |
| title_sort | transcriptome wide association study and eqtl analysis to assess the genetic basis of bulb yield traits in garlic allium sativum |
| topic | Garlic Bulb yield Association mapping Expression quantitative trait locus (eQTL) |
| url | http://link.springer.com/article/10.1186/s12864-019-6025-2 |
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