Leaf morphology in Cowpea [<it>Vigna unguiculata</it> (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species
<p>Abstract</p> <p>Background</p> <p>Cowpea [<it>Vigna unguiculata</it> (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot he...
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BMC
2012-06-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/234 |
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| author | Pottorff Marti Ehlers Jeffrey D Fatokun Christian Roberts Philip A Close Timothy J |
| author_facet | Pottorff Marti Ehlers Jeffrey D Fatokun Christian Roberts Philip A Close Timothy J |
| author_sort | Pottorff Marti |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Cowpea [<it>Vigna unguiculata</it> (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa.</p> <p>Results</p> <p>Leaf morphology was studied in the cowpea RIL population, Sanzi (sub-globose leaf shape) x Vita 7 (hastate leaf shape). A QTL for leaf shape, <it>Hls</it> (hastate leaf shape), was identified on the Sanzi x Vita 7 genetic map spanning from 56.54 cM to 67.54 cM distance on linkage group 15. SNP marker 1_0910 was the most significant over the two experiments, accounting for 74.7% phenotypic variance (LOD 33.82) in a greenhouse experiment and 71.5% phenotypic variance (LOD 30.89) in a field experiment. The corresponding <it>Hls</it> locus was positioned on the cowpea consensus genetic map on linkage group 4, spanning from 25.57 to 35.96 cM. A marker-trait association of the <it>Hls</it> region identified SNP marker 1_0349 alleles co-segregating with either the hastate or sub-globose leaf phenotype. High co-linearity was observed for the syntenic <it>Hls</it> region in <it>Medicago truncatula</it> and <it>Glycine max.</it> One syntenic locus for <it>Hls</it> was identified on Medicago chromosome 7 while syntenic regions for <it>Hls</it> were identified on two soybean chromosomes, 3 and 19. In all three syntenic loci, an ortholog for the EZA1/SWINGER (AT4G02020.1) gene was observed and is the candidate gene for the <it>Hls</it> locus. The <it>Hls</it> locus was identified on the cowpea physical map via SNP markers 1_0910, 1_1013 and 1_0992 which were identified in three BAC contigs; contig926, contig821 and contig25.</p> <p>Conclusions</p> <p>This study has demonstrated how integrated genomic resources can be utilized for a candidate gene approach. Identification of genes which control leaf morphology may be utilized to improve the quality of cowpea leaves for vegetable and or forage markets as well as contribute to more fundamental research understanding the control of leaf shape in legumes.</p> |
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| spelling | doaj.art-71ab4695e28e4802a048dcc59686863a2022-12-21T21:49:54ZengBMCBMC Genomics1471-21642012-06-0113123410.1186/1471-2164-13-234Leaf morphology in Cowpea [<it>Vigna unguiculata</it> (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume speciesPottorff MartiEhlers Jeffrey DFatokun ChristianRoberts Philip AClose Timothy J<p>Abstract</p> <p>Background</p> <p>Cowpea [<it>Vigna unguiculata</it> (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa.</p> <p>Results</p> <p>Leaf morphology was studied in the cowpea RIL population, Sanzi (sub-globose leaf shape) x Vita 7 (hastate leaf shape). A QTL for leaf shape, <it>Hls</it> (hastate leaf shape), was identified on the Sanzi x Vita 7 genetic map spanning from 56.54 cM to 67.54 cM distance on linkage group 15. SNP marker 1_0910 was the most significant over the two experiments, accounting for 74.7% phenotypic variance (LOD 33.82) in a greenhouse experiment and 71.5% phenotypic variance (LOD 30.89) in a field experiment. The corresponding <it>Hls</it> locus was positioned on the cowpea consensus genetic map on linkage group 4, spanning from 25.57 to 35.96 cM. A marker-trait association of the <it>Hls</it> region identified SNP marker 1_0349 alleles co-segregating with either the hastate or sub-globose leaf phenotype. High co-linearity was observed for the syntenic <it>Hls</it> region in <it>Medicago truncatula</it> and <it>Glycine max.</it> One syntenic locus for <it>Hls</it> was identified on Medicago chromosome 7 while syntenic regions for <it>Hls</it> were identified on two soybean chromosomes, 3 and 19. In all three syntenic loci, an ortholog for the EZA1/SWINGER (AT4G02020.1) gene was observed and is the candidate gene for the <it>Hls</it> locus. The <it>Hls</it> locus was identified on the cowpea physical map via SNP markers 1_0910, 1_1013 and 1_0992 which were identified in three BAC contigs; contig926, contig821 and contig25.</p> <p>Conclusions</p> <p>This study has demonstrated how integrated genomic resources can be utilized for a candidate gene approach. Identification of genes which control leaf morphology may be utilized to improve the quality of cowpea leaves for vegetable and or forage markets as well as contribute to more fundamental research understanding the control of leaf shape in legumes.</p>http://www.biomedcentral.com/1471-2164/13/234QTL analysisLeaf morphologyGenomicsGeneticsPhysical mapSyntenyCandidate genesCowpeaLegumesEZA1/SWINGER |
| spellingShingle | Pottorff Marti Ehlers Jeffrey D Fatokun Christian Roberts Philip A Close Timothy J Leaf morphology in Cowpea [<it>Vigna unguiculata</it> (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species BMC Genomics QTL analysis Leaf morphology Genomics Genetics Physical map Synteny Candidate genes Cowpea Legumes EZA1/SWINGER |
| title | Leaf morphology in Cowpea [<it>Vigna unguiculata</it> (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species |
| title_full | Leaf morphology in Cowpea [<it>Vigna unguiculata</it> (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species |
| title_fullStr | Leaf morphology in Cowpea [<it>Vigna unguiculata</it> (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species |
| title_full_unstemmed | Leaf morphology in Cowpea [<it>Vigna unguiculata</it> (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species |
| title_short | Leaf morphology in Cowpea [<it>Vigna unguiculata</it> (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species |
| title_sort | leaf morphology in cowpea it vigna unguiculata it l walp qtl analysis physical mapping and identifying a candidate gene using synteny with model legume species |
| topic | QTL analysis Leaf morphology Genomics Genetics Physical map Synteny Candidate genes Cowpea Legumes EZA1/SWINGER |
| url | http://www.biomedcentral.com/1471-2164/13/234 |
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