Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail
<p>Abstract</p> <p>Background</p> <p>As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first geno...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-10-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/551 |
| _version_ | 1818141492503379968 |
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| author | Frésard Laure Leroux Sophie Dehais Patrice Servin Bertrand Gilbert Hélène Bouchez Olivier Klopp Christophe Cabau Cédric Vignoles Florence Feve Katia Ricros Amélie Gourichon David Diot Christian Richard Sabine Leterrier Christine Beaumont Catherine Vignal Alain Minvielle Francis Pitel Frédérique |
| author_facet | Frésard Laure Leroux Sophie Dehais Patrice Servin Bertrand Gilbert Hélène Bouchez Olivier Klopp Christophe Cabau Cédric Vignoles Florence Feve Katia Ricros Amélie Gourichon David Diot Christian Richard Sabine Leterrier Christine Beaumont Catherine Vignal Alain Minvielle Francis Pitel Frédérique |
| author_sort | Frésard Laure |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on <it>Coturnix japonica</it> chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome.</p> <p>Results</p> <p>The sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene.</p> <p>Conclusions</p> <p>These data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the <it>DMD</it> (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in <it>Coturnix</it>.</p> |
| first_indexed | 2024-12-11T11:00:44Z |
| format | Article |
| id | doaj.art-77c12169a7e0461292c24da64e1dd9ab |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T11:00:44Z |
| publishDate | 2012-10-01 |
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| series | BMC Genomics |
| spelling | doaj.art-77c12169a7e0461292c24da64e1dd9ab2022-12-22T01:09:54ZengBMCBMC Genomics1471-21642012-10-0113155110.1186/1471-2164-13-551Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quailFrésard LaureLeroux SophieDehais PatriceServin BertrandGilbert HélèneBouchez OlivierKlopp ChristopheCabau CédricVignoles FlorenceFeve KatiaRicros AmélieGourichon DavidDiot ChristianRichard SabineLeterrier ChristineBeaumont CatherineVignal AlainMinvielle FrancisPitel Frédérique<p>Abstract</p> <p>Background</p> <p>As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on <it>Coturnix japonica</it> chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome.</p> <p>Results</p> <p>The sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene.</p> <p>Conclusions</p> <p>These data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the <it>DMD</it> (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in <it>Coturnix</it>.</p>http://www.biomedcentral.com/1471-2164/13/551QuailTonic immobilitySequencingAFLPTranscriptsSNPAIL |
| spellingShingle | Frésard Laure Leroux Sophie Dehais Patrice Servin Bertrand Gilbert Hélène Bouchez Olivier Klopp Christophe Cabau Cédric Vignoles Florence Feve Katia Ricros Amélie Gourichon David Diot Christian Richard Sabine Leterrier Christine Beaumont Catherine Vignal Alain Minvielle Francis Pitel Frédérique Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail BMC Genomics Quail Tonic immobility Sequencing AFLP Transcripts SNP AIL |
| title | Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail |
| title_full | Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail |
| title_fullStr | Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail |
| title_full_unstemmed | Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail |
| title_short | Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail |
| title_sort | fine mapping of complex traits in non model species using next generation sequencing and advanced intercross lines in japanese quail |
| topic | Quail Tonic immobility Sequencing AFLP Transcripts SNP AIL |
| url | http://www.biomedcentral.com/1471-2164/13/551 |
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