The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop
Abstract Background Yellow lupin (Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key ad...
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | BMC Genetics |
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| Online Access: | http://link.springer.com/article/10.1186/s12863-019-0767-3 |
| _version_ | 1811234136843616256 |
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| author | Muhammad Munir Iqbal Mark Huynh Joshua A. Udall Andrzej Kilian Kedar N. Adhikari Jens D. Berger William Erskine Matthew N. Nelson |
| author_facet | Muhammad Munir Iqbal Mark Huynh Joshua A. Udall Andrzej Kilian Kedar N. Adhikari Jens D. Berger William Erskine Matthew N. Nelson |
| author_sort | Muhammad Munir Iqbal |
| collection | DOAJ |
| description | Abstract Background Yellow lupin (Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key adaptation traits such as phenology and enhanced stress tolerance are often complex and controlled by several genes. Genomic-enabled technologies may help to improve our basic understanding of these traits and to provide selective markers in breeding. However, in yellow lupin there are very limited genomic resources to support research and no published information is available on the genetic control of adaptation traits. Results We aimed to address these deficiencies by developing the first linkage map for yellow lupin and conducting quantitative trait locus (QTL) analysis of yield under well-watered (WW) and water-deficit (WT) conditions. Two next-generation sequencing marker approaches - genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) sequencing - were employed to genotype a recombinant inbred line (RIL) population developed from a bi-parental cross between wild and domesticated parents. A total of 2,458 filtered single nucleotide polymorphism (SNP) and presence / absence variation (PAV) markers were used to develop a genetic map comprising 40 linkage groups, the first reported for this species. A number of significant QTLs controlling total biomass and 100-seed weight under two water (WW and WD) regimes were found on linkage groups YL-03, YL-09 and YL-26 that together explained 9 and 28% of total phenotypic variability. QTLs associated with length of the reproductive phase and time to flower were found on YL-01, YL-21, YL-35 and YL-40 that together explained a total of 12 and 44% of total phenotypic variation. Conclusion These genomic resources and the QTL information offer significant potential for use in marker-assisted selection in yellow lupin. |
| first_indexed | 2024-04-12T11:32:40Z |
| format | Article |
| id | doaj.art-fd7a75c52bfd4ae6848c3c365fd131af |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-12T11:32:40Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-fd7a75c52bfd4ae6848c3c365fd131af2022-12-22T03:34:59ZengBMCBMC Genetics1471-21562019-08-0120111310.1186/s12863-019-0767-3The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume cropMuhammad Munir Iqbal0Mark Huynh1Joshua A. Udall2Andrzej Kilian3Kedar N. Adhikari4Jens D. Berger5William Erskine6Matthew N. Nelson7School of Agriculture and Environment, The University of Western AustraliaThe College of Life Sciences, Brigham Young UniversityUSDA-ARS Southern Plains Agricultural Research CenterDiversity Arrays Technology, University of CanberraSchool of Life and Environmental Sciences, I A Watson Grains Research Centre, The University of SydneyAgriculture and Food, CSIROSchool of Agriculture and Environment, The University of Western AustraliaAgriculture and Food, CSIROAbstract Background Yellow lupin (Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key adaptation traits such as phenology and enhanced stress tolerance are often complex and controlled by several genes. Genomic-enabled technologies may help to improve our basic understanding of these traits and to provide selective markers in breeding. However, in yellow lupin there are very limited genomic resources to support research and no published information is available on the genetic control of adaptation traits. Results We aimed to address these deficiencies by developing the first linkage map for yellow lupin and conducting quantitative trait locus (QTL) analysis of yield under well-watered (WW) and water-deficit (WT) conditions. Two next-generation sequencing marker approaches - genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) sequencing - were employed to genotype a recombinant inbred line (RIL) population developed from a bi-parental cross between wild and domesticated parents. A total of 2,458 filtered single nucleotide polymorphism (SNP) and presence / absence variation (PAV) markers were used to develop a genetic map comprising 40 linkage groups, the first reported for this species. A number of significant QTLs controlling total biomass and 100-seed weight under two water (WW and WD) regimes were found on linkage groups YL-03, YL-09 and YL-26 that together explained 9 and 28% of total phenotypic variability. QTLs associated with length of the reproductive phase and time to flower were found on YL-01, YL-21, YL-35 and YL-40 that together explained a total of 12 and 44% of total phenotypic variation. Conclusion These genomic resources and the QTL information offer significant potential for use in marker-assisted selection in yellow lupin.http://link.springer.com/article/10.1186/s12863-019-0767-3Yellow lupinLinkage mapAdaptation traitsPhenologyQTL analysis |
| spellingShingle | Muhammad Munir Iqbal Mark Huynh Joshua A. Udall Andrzej Kilian Kedar N. Adhikari Jens D. Berger William Erskine Matthew N. Nelson The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop BMC Genetics Yellow lupin Linkage map Adaptation traits Phenology QTL analysis |
| title | The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop |
| title_full | The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop |
| title_fullStr | The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop |
| title_full_unstemmed | The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop |
| title_short | The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop |
| title_sort | first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop |
| topic | Yellow lupin Linkage map Adaptation traits Phenology QTL analysis |
| url | http://link.springer.com/article/10.1186/s12863-019-0767-3 |
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