Reference "Development and implementation of high-throughput SNP genotyping in barley"

Reference ID

48114

Title

Development and implementation of high-throughput SNP genotyping in barley

Source

BMC Genomics, 2009, vol. 10, pp. 582-582

Authors (28)

Close-T-J	Bhat-P-R	Lonardi-S	Wu-Y	Rostoks-N	Ramsay-L
Druka-A	Stein-N	Svensson-J-T	Wanamaker-S	Bozdag-S	Roose-M-L
Moscou-M-J	Chao-S	Varshney-R-K	Szucs-P	Sato-K	Hayes-P-M
Matthews-D-E	Kleinhofs-A	Muehlbauer-G-J	DeYoung-J	Marshall-D-F	Madishetty-K
Fenton-R-D	Condamine-P	Graner-A	Waugh-R

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.