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 Szűcs, 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

Research output: Contribution to journalArticleResearchpeer-review

427 Citations (Scopus)

Abstract

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.
Original languageEnglish
Article number582
JournalBMC Genomics
Volume10
DOIs
Publication statusPrint publication - 4 Dec 2009
Externally publishedYes

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Hordeum
Single Nucleotide Polymorphism
Genetic Loci
Organism Cloning
Genotype
Genome
Datasets

Cite this

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 ; Szűcs, 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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abstract = "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.",
author = "Close, {Timothy J} and Bhat, {Prasanna R} and Stefano Lonardi and Yonghui Wu and Nils Rostoks and Luke Ramsay and Arnis Druka and Nils Stein and Svensson, {Jan T} and Steve Wanamaker and Serdar Bozdag and Roose, {Mikeal L} and Moscou, {Matthew J} and Shiaoman Chao and Varshney, {Rajeev K} and P{\'e}ter Szűcs and Kazuhiro Sato and Hayes, {Patrick M} and Matthews, {David E} and Andris Kleinhofs and Muehlbauer, {Gary J} and Joseph DeYoung and Marshall, {David F} and Kavitha Madishetty and Fenton, {Raymond D} and Pascal Condamine and Andreas Graner and Robbie Waugh",
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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, Szűcs, 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; Szűcs, 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 journalArticleResearchpeer-review

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 - Szűcs, 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 - 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.

AB - 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.

U2 - 10.1186/1471-2164-10-582

DO - 10.1186/1471-2164-10-582

M3 - Article

VL - 10

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 582

ER -

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