The construction of a high-density consensus genetic map for soybean based on SNP markers derived from genotyping-by-sequencing

Fallah, Manel; Jean, Martine; St-Amour, Vincent Thomas Boucher; O’Donoughue, Louise S.; Belzile, François

doi:10.1139/gen-2021-0054

Cited by 4 publications

(5 citation statements)

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“… a Fraction of the genome captured across all 16 libraries b Average number of read at each sequenced position c Inferred from the closest corresponding SNP on the consensus genetic map [ 16 ] …”

Section: Resultsmentioning

confidence: 99%

“…The distribution of markers across the physical map was based on the VCF files generated after Fast-GBS analysis and SNP filtration, using the rMVP package in R [ 70 ]. For genetic maps, the genetic position of each SNP was inferred from the closest corresponding SNP on the consensus genetic map based on GBS-derived SNP markers [ 16 ]. Then, the distribution of markers across the genetic maps was evaluated using the QTL IciMapping v4.1 software [ 40 ].…”

Section: Methodsmentioning

confidence: 99%

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3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

et al. 2023

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Despite the increased efficiency of sequencing technologies and the development of reduced-representation sequencing (RRS) approaches allowing high-throughput sequencing (HTS) of multiplexed samples, the per-sample genotyping cost remains the most limiting factor in the context of large-scale studies. For example, in the context of genomic selection (GS), breeders need genome-wide markers to predict the breeding value of large cohorts of progenies, requiring the genotyping of thousands candidates. Here, we introduce 3D-GBS, an optimized GBS procedure, to provide an ultra-high-throughput and ultra-low-cost genotyping solution for species with small to medium-sized genome and illustrate its use in soybean. Using a combination of three restriction enzymes (PstI/NsiI/MspI), the portion of the genome that is captured was reduced fourfold (compared to a “standard” ApeKI-based protocol) while reducing the number of markers by only 40%. By better focusing the sequencing effort on limited set of restriction fragments, fourfold more samples can be genotyped at the same minimal depth of coverage. This GBS protocol also resulted in a lower proportion of missing data and provided a more uniform distribution of SNPs across the genome. Moreover, we investigated the optimal number of reads per sample needed to obtain an adequate number of markers for GS and QTL mapping (500–1000 markers per biparental cross). This optimization allows sequencing costs to be decreased by ~ 92% and ~ 86% for GS and QTL mapping studies, respectively, compared to previously published work. Overall, 3D-GBS represents a unique and affordable solution for applications requiring extremely high-throughput genotyping where cost remains the most limiting factor.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

et al. 2023

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show abstract

“…The distribution of markers across the physical map was based on the VCF les generated after Fast-GBS analysis and SNP ltration, using the rMVP package in R (Yin et al 2021). For genetic maps, the genetic position of each SNP was inferred from the closest corresponding SNP on the consensus genetic map based on GBS-derived SNP markers (Fallah et al 2022). Then, the distribution of markers across the genetic maps was evaluated using the QTL IciMapping v4.1 software (Meng et al 2015).…”

Section: Discussionmentioning

confidence: 99%

“…¥Average number of read at each sequenced position. § Inferred from the closest corresponding SNP on the consensus genetic map(Fallah et al 2022). …”

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3D-GBS: A universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

Ronne

Légaré

Belzile

et al. 2022

Preprint

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Despite the increased efficiency of sequencing technologies and the development of reduced-representation sequencing (RRS) approaches allowing high-throughput sequencing (HTS) of multiplexed samples, the per-sample genotyping cost remains the most limiting factor in the context of large-scale studies. For example, in the context of genomic selection (GS), breeders need genome-wide markers to predict the breeding value of large cohorts of progenies, requiring the genotyping of thousands candidates. Here, we introduce 3D-GBS, an optimized GBS procedure, to provide an ultra-high-throughput and ultra-low-cost genotyping solution for species with small to medium-sized genome and illustrate its use in soybean. Using a combination of three restriction enzymes (PstI/NsiI/MspI), the portion of the genome that is captured was reduced 4-fold (compared to a “standard” ApeKI-based protocol) while reducing the number of markers by only 40%. By better focusing the sequencing effort on limited set of restriction fragments, 4-fold more samples can be genotyped at the same minimal depth of coverage. This GBS protocol also resulted in a lower proportion of missing data and provided a more uniform distribution of SNPs across the genome. Moreover, we investigated the optimal number of reads per sample needed to obtain an adequate number of markers for GS and QTL mapping (500-1,000 markers per biparental cross). This optimization allows sequencing costs to be decreased by ~ 92% and ~ 86% for GS and QTL mapping studies, respectively, compared to previously published work. Overall, 3D-GBS represents a unique and affordable solution for applications requiring extremely high-throughput genotyping where cost remains the most limiting factor.

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Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus

Ollitrault,

Hufnagel,

Curk

et al. 2024

Front. Plant Sci.

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IntroductionUseful germplasm for citrus breeding includes all sexually compatible species of the former genera Citrus, Clymenia, Eremocitrus, Fortunella, Microcitrus, Oxanthera, and Poncirus, now merged in the single Citrus genus. An improved knowledge on the synteny/collinearity between the genome of these different species, and on their recombination landscapes, is essential to optimize interspecific breeding schemes.MethodWe have performed a large comparative genetic mapping study including several main clades of the Citrus genus. It concerns five species (C. maxima, C. medica, C. reticulata, C. trifoliata and C. glauca), two horticultural groups resulting from interspecific admixture (clementine and lemon) and two recent interspecific hybrids (C. australis x C. australasica and C. maxima x C. reticulata). The nine individual genetic maps were established from GBS data of 1,216 hybrids.Results and discussionThe number of SNPs mapped for each parent varies from 760 for C. medica to 4,436 for the C. maxima x C. reticulata hybrid, with an average of 2,162.3 markers by map. Their comparison with C. clementina v1.0 assembly and inter-map comparisons revealed a high synteny and collinearity between the nine genetic maps. Non-Mendelian segregation was frequent and specific for each parental combination. The recombination landscape was similar for the nine mapped parents, and large genomic regions with very low recombination were identified. A consensus genetic map was successfully established. It encompasses 10,756 loci, including 7,915 gene-based markers and 2,841 non-genic SNPs. The anchoring of the consensus map on 15 published citrus chromosome-scale genome assemblies revealed a high synteny and collinearity for the most recent assemblies, whereas discrepancies were observed for some older ones. Large structural variations do not seem to have played a major role in the differentiation of the main species of the Citrus genus. The consensus genetic map is a useful tool to check the accuracy of genome assemblies, identify large structural variation and focus on analyzing potential relationships with phenotypic variations. It should also be a reference framework to integrate the positions of QTLs and useful genes identified in different analyses.

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The construction of a high-density consensus genetic map for soybean based on SNP markers derived from genotyping-by-sequencing

Cited by 4 publications

References 36 publications

3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

3D-GBS: A universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes

Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the Citrus genus

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