Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers
Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However...
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| Format: | Journal Article |
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Springer Publishing
2014
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| Online Access: | http://hdl.handle.net/20.500.11937/17463 |
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curtin-20.500.11937-17463 |
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curtin-20.500.11937-174632017-09-13T15:43:06Z Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers Kamphuis, L. Hane, James Nelson, M. Gao, L. Atkins, C. Singh, K. next-generation sequencing molecular marker SNP indel lupin Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome-derived gene-based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome-derived markers and 66 BAC-end sequence-derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map. 2014 Journal Article http://hdl.handle.net/20.500.11937/17463 10.1111/pbi.12229 Springer Publishing unknown |
| repository_type |
Digital Repository |
| institution_category |
Local University |
| institution |
Curtin University Malaysia |
| building |
Curtin Institutional Repository |
| collection |
Online Access |
| topic |
next-generation sequencing molecular marker SNP indel lupin |
| spellingShingle |
next-generation sequencing molecular marker SNP indel lupin Kamphuis, L. Hane, James Nelson, M. Gao, L. Atkins, C. Singh, K. Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers |
| description |
Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome-derived gene-based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome-derived markers and 66 BAC-end sequence-derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map. |
| format |
Journal Article |
| author |
Kamphuis, L. Hane, James Nelson, M. Gao, L. Atkins, C. Singh, K. |
| author_facet |
Kamphuis, L. Hane, James Nelson, M. Gao, L. Atkins, C. Singh, K. |
| author_sort |
Kamphuis, L. |
| title |
Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers |
| title_short |
Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers |
| title_full |
Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers |
| title_fullStr |
Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers |
| title_full_unstemmed |
Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers |
| title_sort |
transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers |
| publisher |
Springer Publishing |
| publishDate |
2014 |
| url |
http://hdl.handle.net/20.500.11937/17463 |
| first_indexed |
2018-09-06T19:44:20Z |
| last_indexed |
2018-09-06T19:44:20Z |
| _version_ |
1610888574995005440 |