K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

Ziarsolo, Peio; Hasing, Tomas; Hilario, Rebeca; García‐Carpintero, Victor; Esteras, Cristina; Bombarely, Aureliano

doi:10.1186/s13007-021-00733-6

Cited by 4 publications

(8 citation statements)

References 25 publications

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“…Most of the SNPs identified in our study (86.4%) lies within genes. This is consistent with the notion that GBS libraries prepared with the methylation-sensitive enzyme ApeK I tends to avoid repetitive sequences, which are extremely abundant in the pea genome [ 10 , 13 , 37 , 38 ]. Genic SNPs have higher chance to reveal significant marker-trait associations [ 39 , 40 ], therefore we envisage that our SNP dataset, allowing the correct mapping of the Mendelian genes A and R in demo studies ( Fig.…”

Section: Discussionsupporting

confidence: 88%

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history

Pavan

Delvento

et al. 2022

Horticulture Research

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Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections – a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.

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Section: Discussionsupporting

confidence: 88%

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history

Pavan

Delvento

et al. 2022

Horticulture Research

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“…The genotyping was performed using a targeted genotyping-by-sequencing approach called SeqSNP, which has been successfully used in several crops ( Zhang et al., 2020 ; Jo et al., 2021 ; Ziarsolo et al., 2021 ). Sequence reads were aligned to the sequences (300bp) flanking the SNP markers, using Bowtie2 (version 2.4.5) ( Langmead and Salzberg, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers

Park,

Zhang,

Ali

2024

Front. Plant Sci.

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The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., ‘Saccharum spp’, ‘unknown’, and ‘hybrid’). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor-joining clustering analysis. Analysis of Molecular Variance revealed that within-species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement.

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“…Their panel of 5k target SNPs enabled high-throughput genotyping, generating many SNPs, including novel ones, with cross-transferability between related species. Finally, Ziarsolo et al (2021) presented the K-seq, a costeffective genotyping methodology based on Klenow amplification and Illumina sequencing. K-seq demonstrated reproducibility and reliability, providing valuable genetic data for diverse species, including tomato.…”

Section: Tomatomentioning

confidence: 99%

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

Martina,

De Rosa,

Magon

et al. 2024

Front. Plant Sci.

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This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.

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K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

Cited by 4 publications

References 25 publications

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history

Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

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