TY - JOUR
T1 - Combining genetical genomics and bulked segregant analysis-based diverential expression
T2 - An approach to gene localization
AU - Chen, Xinwei
AU - Hedley, Peter E.
AU - Morris, Jenny
AU - E, Hui Liu Rients
AU - Waugh, Niks Robbie
PY - 2011/5/1
Y1 - 2011/5/1
N2 - Positional gene isolation in unsequenced species generally requires either a reference genome sequence or an inference of gene content based on conservation of synteny with a genomic model. In the large unsequenced genomes of the Triticeae cereals the latter, i.e. conservation of synteny with the rice and Brachypodium genomes, provides a powerful proxy for establishing local gene content and order. However, eYcient exploitation of conservation of synteny requires 'homology bridges' between the model genome and the target region that contains a gene of interest. As eVective homology bridges are generally the sequences of genetically mapped genes, increasing the density of these genes around a target locus is an important step in the process. We used bulked segregant analysis (BSA) of transcript abundance data to identify genes located in a speciWc region of the barley genome. The approach is valuable because only a relatively small proportion of barley genes are currently placed on a genetic map. We analyzed eQTL datasets from the reference Steptoe £ Morex doubled haploid population and showed a strong association between diVerential gene expression and cis-regulation, with 83% of diVerentially expressed genes co-locating with their eQTL. We then performed BSA by assembling allele-speciWc pools based on the genotypes of individuals at the partial resistance QTL Rphq11. BSA identiWed a total of 411 genes as diVerentially expressed, including HvPHGPx, a gene previously identiWed as a promising candidate for Rphq11. The genetic location of 276 of these genes could be determined from both eQTL datasets and conservation of synteny, and 254 (92%) of these were located on the target chromosome. We conclude that the identiWcation of diVerential expression by BSA constitutes a novel method to identify genes located in speciWc regions of interest. The datasets obtained from such studies provide a robust set of candidate genes for the analysis and serve as valuable resources for targeted marker development and comparative mapping with other grass species.
AB - Positional gene isolation in unsequenced species generally requires either a reference genome sequence or an inference of gene content based on conservation of synteny with a genomic model. In the large unsequenced genomes of the Triticeae cereals the latter, i.e. conservation of synteny with the rice and Brachypodium genomes, provides a powerful proxy for establishing local gene content and order. However, eYcient exploitation of conservation of synteny requires 'homology bridges' between the model genome and the target region that contains a gene of interest. As eVective homology bridges are generally the sequences of genetically mapped genes, increasing the density of these genes around a target locus is an important step in the process. We used bulked segregant analysis (BSA) of transcript abundance data to identify genes located in a speciWc region of the barley genome. The approach is valuable because only a relatively small proportion of barley genes are currently placed on a genetic map. We analyzed eQTL datasets from the reference Steptoe £ Morex doubled haploid population and showed a strong association between diVerential gene expression and cis-regulation, with 83% of diVerentially expressed genes co-locating with their eQTL. We then performed BSA by assembling allele-speciWc pools based on the genotypes of individuals at the partial resistance QTL Rphq11. BSA identiWed a total of 411 genes as diVerentially expressed, including HvPHGPx, a gene previously identiWed as a promising candidate for Rphq11. The genetic location of 276 of these genes could be determined from both eQTL datasets and conservation of synteny, and 254 (92%) of these were located on the target chromosome. We conclude that the identiWcation of diVerential expression by BSA constitutes a novel method to identify genes located in speciWc regions of interest. The datasets obtained from such studies provide a robust set of candidate genes for the analysis and serve as valuable resources for targeted marker development and comparative mapping with other grass species.
UR - http://www.scopus.com/inward/record.url?scp=79958753915&partnerID=8YFLogxK
U2 - 10.1007/s00122-011-1538-3
DO - 10.1007/s00122-011-1538-3
M3 - Article
C2 - 21267709
AN - SCOPUS:79958753915
SN - 0040-5752
VL - 122
SP - 1375
EP - 1383
JO - Theoretical and Applied Genetics
JF - Theoretical and Applied Genetics
IS - 7
ER -