Development and implementation of high-throughput SNP genotyping in barley

Timothy J. Close, Prasanna R. Bhat, Stefano Lonardi, Yonghui Wu, Nils Rostoks, Luke Ramsay, Arnis Druka, Nils Stein, Jan T. Svensson, Steve Wanamaker, Serdar Bozdag, Mikeal L. Roose, Matthew J. Moscou, Shiaoman Chao, Rajeev K. Varshney, Péter Szucs, Kazuhiro Sato, Patrick M. Hayes, David E. Matthews, Andris Kleinhofs & 8 others Gary J. Muehlbauer, Joseph DeYoung, David F. Marshall, Kavitha Madishetty, Raymond D. Fenton, Pascal Condamine, Andreas Graner, Robbie Waugh

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Abstract

Background: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. Conclusion: The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.

Original languageEnglish
Article number582
JournalBMC Genomics
Volume10
DOIs
Publication statusPublished - 4 Dec 2009

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Hordeum
Single Nucleotide Polymorphism
Gene Frequency
Breeding
Genome
Genetic Loci
Haploidy
Expressed Sequence Tags
Genetic Recombination
Population
Organism Cloning
Chromosomes
Alleles
Genotype
Genes

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Close, T. J., Bhat, P. R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., ... Waugh, R. (2009). Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics, 10, [582]. https://doi.org/10.1186/1471-2164-10-582
Close, Timothy J. ; Bhat, Prasanna R. ; Lonardi, Stefano ; Wu, Yonghui ; Rostoks, Nils ; Ramsay, Luke ; Druka, Arnis ; Stein, Nils ; Svensson, Jan T. ; Wanamaker, Steve ; Bozdag, Serdar ; Roose, Mikeal L. ; Moscou, Matthew J. ; Chao, Shiaoman ; Varshney, Rajeev K. ; Szucs, Péter ; Sato, Kazuhiro ; Hayes, Patrick M. ; Matthews, David E. ; Kleinhofs, Andris ; Muehlbauer, Gary J. ; DeYoung, Joseph ; Marshall, David F. ; Madishetty, Kavitha ; Fenton, Raymond D. ; Condamine, Pascal ; Graner, Andreas ; Waugh, Robbie. / Development and implementation of high-throughput SNP genotyping in barley. In: BMC Genomics. 2009 ; Vol. 10.
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Close, TJ, Bhat, PR, Lonardi, S, Wu, Y, Rostoks, N, Ramsay, L, Druka, A, Stein, N, Svensson, JT, Wanamaker, S, Bozdag, S, Roose, ML, Moscou, MJ, Chao, S, Varshney, RK, Szucs, P, Sato, K, Hayes, PM, Matthews, DE, Kleinhofs, A, Muehlbauer, GJ, DeYoung, J, Marshall, DF, Madishetty, K, Fenton, RD, Condamine, P, Graner, A & Waugh, R 2009, 'Development and implementation of high-throughput SNP genotyping in barley', BMC Genomics, vol. 10, 582. https://doi.org/10.1186/1471-2164-10-582

Development and implementation of high-throughput SNP genotyping in barley. / Close, Timothy J.; Bhat, Prasanna R.; Lonardi, Stefano; Wu, Yonghui; Rostoks, Nils; Ramsay, Luke; Druka, Arnis; Stein, Nils; Svensson, Jan T.; Wanamaker, Steve; Bozdag, Serdar; Roose, Mikeal L.; Moscou, Matthew J.; Chao, Shiaoman; Varshney, Rajeev K.; Szucs, Péter; Sato, Kazuhiro; Hayes, Patrick M.; Matthews, David E.; Kleinhofs, Andris; Muehlbauer, Gary J.; DeYoung, Joseph; Marshall, David F.; Madishetty, Kavitha; Fenton, Raymond D.; Condamine, Pascal; Graner, Andreas; Waugh, Robbie.

In: BMC Genomics, Vol. 10, 582, 04.12.2009.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Development and implementation of high-throughput SNP genotyping in barley

AU - Close, Timothy J.

AU - Bhat, Prasanna R.

AU - Lonardi, Stefano

AU - Wu, Yonghui

AU - Rostoks, Nils

AU - Ramsay, Luke

AU - Druka, Arnis

AU - Stein, Nils

AU - Svensson, Jan T.

AU - Wanamaker, Steve

AU - Bozdag, Serdar

AU - Roose, Mikeal L.

AU - Moscou, Matthew J.

AU - Chao, Shiaoman

AU - Varshney, Rajeev K.

AU - Szucs, Péter

AU - Sato, Kazuhiro

AU - Hayes, Patrick M.

AU - Matthews, David E.

AU - Kleinhofs, Andris

AU - Muehlbauer, Gary J.

AU - DeYoung, Joseph

AU - Marshall, David F.

AU - Madishetty, Kavitha

AU - Fenton, Raymond D.

AU - Condamine, Pascal

AU - Graner, Andreas

AU - Waugh, Robbie

PY - 2009/12/4

Y1 - 2009/12/4

N2 - Background: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. Conclusion: The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.

AB - Background: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. Conclusion: The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.

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Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L et al. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics. 2009 Dec 4;10. 582. https://doi.org/10.1186/1471-2164-10-582