Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits
Abstract Background High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of east...
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| Format: | Article |
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BMC
2019-07-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5981-x |
| _version_ | 1818332232721367040 |
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| author | Jitao Li Jianjian Lv Ping Liu Ping Chen Jiajia Wang Jian Li |
| author_facet | Jitao Li Jianjian Lv Ping Liu Ping Chen Jiajia Wang Jian Li |
| author_sort | Jitao Li |
| collection | DOAJ |
| description | Abstract Background High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species. Results In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8–15.7% of the total growth-traits variation. Conclusions The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps. |
| first_indexed | 2024-12-13T13:32:29Z |
| format | Article |
| id | doaj.art-2701feb73f074c978af5ea36746be378 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T13:32:29Z |
| publishDate | 2019-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-2701feb73f074c978af5ea36746be3782022-12-21T23:44:07ZengBMCBMC Genomics1471-21642019-07-0120111510.1186/s12864-019-5981-xGenome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traitsJitao Li0Jianjian Lv1Ping Liu2Ping Chen3Jiajia Wang4Jian Li5Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine FisheriesMinistry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine FisheriesMinistry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine FisheriesMinistry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine FisheriesMinistry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine FisheriesMinistry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine FisheriesAbstract Background High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species. Results In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8–15.7% of the total growth-traits variation. Conclusions The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.http://link.springer.com/article/10.1186/s12864-019-5981-xExopalaemon carinicaudaGenomeSNPHigh-resolution linkage mapQTL mapping |
| spellingShingle | Jitao Li Jianjian Lv Ping Liu Ping Chen Jiajia Wang Jian Li Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits BMC Genomics Exopalaemon carinicauda Genome SNP High-resolution linkage map QTL mapping |
| title | Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits |
| title_full | Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits |
| title_fullStr | Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits |
| title_full_unstemmed | Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits |
| title_short | Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits |
| title_sort | genome survey and high resolution backcross genetic linkage map construction of the ridgetail white prawn exopalaemon carinicauda applications to qtl mapping of growth traits |
| topic | Exopalaemon carinicauda Genome SNP High-resolution linkage map QTL mapping |
| url | http://link.springer.com/article/10.1186/s12864-019-5981-x |
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