Exploring structural variation in the genus Lens
Objectives
Develop high quality structural variant datasets for 23 key Lens germplasm including 8 cultivars 9 RIL population parents.
Study existing and new trait-associated regions (e.g. QTL) within the context of structural variation for a more complete picture of the causation of some phenotypes.
Germplasm
| Germplasm Genus |
Lens
|
|---|---|
| Germplasm Scientific Name |
Lens spp.
|
| Germplasm Collection |
23 Lens germplasm including 8 cultivars 9 RIL population parents
|
Executive Summary
We will generate approximately 10X coverage of all the parents of our recombinant inbred line (RIL) populations and an additional 9 cultivated lines with significance to Activities 2 and 3. This additional data will be used to further clarify the structural variant landscape and inform our association studies.
We will explore existing software for their ability to predict structural variants in Lens sequencing data. Results will be confirmed through random visual evaluation and cross referencing with known or suspected structural variants. Additionally, regions detected in Activity 2 and 3 association studies will be visual explored for structural variants which may play a role in these traits. Once a reasonable set of software and parameters has been determined, structural variants will be detected for all the chosen germplasm.
Attribution
The following researchers and their organizations were involved in this work and should be credited for their role in any resulting or related publications.
| Data Custodian |
Kirstin E Bett
|
|---|---|
| Collaborator |
|
| Data Curator |
|
| Research Organization |
Publication
- Guerra-Garcia A, Haile T, Ogutcen E, Bett KE, von Wettberg EJ. An evolutionary look into the history of lentil reveals unexpected diversity. Evolutionary applications. 2022 Aug; 15(8):1313-1325.
- Ramsay L, Koh CS, Kagale S, Gao D, Kaur S, Haile T, Gela TS, Chen LA, Cao Z, Konkin DJ, Toegelová H, Doležel J, Rosen BD, Stonehouse R, Humann JL, Main D, Coyne CJ, McGee RJ, Cook DR, Penmetsa RV, Vandenberg A, Chan C, Banniza S, Edwards D, Bayer PE, Batley J, Udupa SM, Bett KE. Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species.. bioRxiv. 2021 Jul 24.
Research Outputs
The following research outputs are specific to the study as a whole. There are additional research outputs associated with the linked experiments.
Datasets
Structural variant sets for parents of key RIL populations used in Activity 2 and 3.
The following table indicates the structural variant datasets available. For each indicated as available there are minimap2 alignments, low quality break-ends, low quality inversions, high/low quality deletions, and high/low quality insertions datasets. These are made available for exploration in our JBrowse2 for Lens culinaris CDC Redberry v2.0 (Lcu.2RBY).
RIL Population Maternal Parent Paternal Parent See on JBrowse2 LR-06 1294M-23 1048-8R High-quality variants LR-11 BM4 CDC Milestone High-quality variants LR-18 CDC Robin 964a-46 High-quality Variants LR-26 Eston High-quality Variants LR-68 Lupa 3339-3 High-quality Variants LR-70 Eston High-quality Variants LR-86 Lupa High-quality Variants NOTE: The missing parents in the above table where excluded as we have full genome assemblies for these accessions: Lens ervoides IG 72815 (Ler.1DRT; paternal parent LR-26), Lens odemensis IG 72623 (Lod.1TUR; paternal parent LR-70), Lens orientalis BGE 016880 (Lor.1WPS; paternal parent LR-86).
Structural variant sets for key germplasm.
The following list indicates the structural variant datasets available representing germplasm of particular significance to Activities 2 and 3. For each indicated as available there are minimap2 alignments, low quality break-ends, low quality inversions, high/low quality deletions, and high/low quality insertions datasets. These are made available for exploration in our JBrowse2 for Lens culinaris CDC Redberry v2.0 (Lcu.2RBY).
- Blaze-BC
- CDC Greenstar
- CDC KR-1
- CDC Maxim
- CDC Viceroy
- 1245S-1
- IBC 929
- ILL 1704
See the high-quality variants (insertions and deletions) for these germplasm on JBrowse2.
Grant Activity
Grant Logo
Title
EVOLVES: Enhancing the Value of Lentil Variation for Ecosystem Survival
Data Custodian
- Kirstin E Bett
- Albert Vandenberg
Research Organization
Funding Range
2019-2023