Exome capture sequencing and variant calling of the AGILE Lentil diversity panel: 324 lentil lines analyzed in 2017-2020
Overview
Objectives
- Contribute a high-quality genotypic dataset to expand the genetic diversity of the Canadian lentil breeding program.
To determine which of the 324 LDP accessions are the best candidates to contribute to that genetic diversity in Lentil.
To contribute to developing markers to efficiently select against poor adaptation.
Experiment Summary
The lentil diversity panel (LDP) consists of 324 cultivated lentil lines that represent the diversity of lentils globally. Samples selected were derived from landraces in addition to bred varieties from a selections of genebanks. Targeted-exome resequencing of the LDP will provide the information needed to determine which germplasm can contribute to further genetic diversity in lentil, in addition to developing markers for selecting against poor adaptation.
Germplasm
| Germplasm Genus |
Lens
|
|---|---|
| Germplasm Scientific Name |
Lens culinaris
|
| Germplasm Collection |
AGILE LDP
|
Phenomics
Key Measurements
SNPs and short indels
Methodology
The raw reads were initially filtered using the following parameters: maximum N content error of 10%; minimum base median quality PHRED score = 28; minimum per-sequence quality = 25; minimum quality in a four-base window = 30; and reads longer than 50 bp.
These trimmed reads were aligned to the CDC Redberry reference genome v2.0 (Lcu.2RBY) using Bowtie2 2.3.3.1. PCR duplicates were removed with the rmdup function of SAMtools 1.3.1, and variants were called with the same version of SAMtools, where the minimum number of gapped reads to call an indel was set to 10.
SNPs were filtered with VCFtools 0.1.15 using a minimum quality = 30, minimum mean depth = 3×, maximum missingness per site = 0.10, minimum allele count (MAC) = 5, the SNPs within the CNV were removed, and only biallelic loci were kept.
Experimental Design
Experimental Design
The lentil diversity panel (LDP) consists of 324 cultivated lentil accessions. These accessions were selected to represent global diversity of cultivated lentils from a combination of landraces and bred varieties gathered from various genebanks.
One plant per accession of the LDP Genotyping was genotyped using the exome capture assay developed by Ogutcen et al. (2018). The exome probes were designed from the CDC Redberry reference genome v1.2.
Attribution
Researchers
| Data Collector |
Larissa Ramsay
|
|---|---|
| Data Custodian |
Kirstin E Bett
|
| Data Curator |
|
Publication(s)
- Ogutcen Ezgi, Ramsay Larissa, von Wettberg Eric, Bett Kirstin. Capturing variation in Lens (Fabaceae): development and utility of an exome capture array for lentil.. Applications in Plant Science. 2018.
- 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.
Associated Datasets
Dataset
Filtered Variant Set: Compressed VCF (.gz), CSI index (.csi)
This VCF was compressed using bgzip and indexed using tabix --csi.
The variants were filtered using VCFtools 0.1.15 and the following filtering criteria:
- minimum SNP quality of 30
- minimum mean depth = 3×
- maximum missingness per site = 0.10
- minimum allele count (MAC) = 5
- the SNPs within the CNV (Copy Number Variants) were removed
- only biallelic loci
Funding
Research Organization
Funding Grant
Grant Logo
Title
AGILE: Application of Genomic Innovation in the Lentil Economy
Data Custodian
- Kirstin E Bett
- Albert Vandenberg
Research Organization
Funding Range
2014-2019