Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids.
Three assays useful for detecting specific RNA transcripts are primer extension, S1 nuclease protection, and reverse-transcription-cleaved amplified polymorphic sequence (RT-CAPS) analysis. All three of these techniques are used routinely for gene expression analyses and allow insights not possible by RNA blot (northern blot) hybridization. In this chapter, we describe how the primer extension, S1 nuclease protection, and RT-CAPS methods can be used to discriminate one or more parental or progenitor alleles in hybrids or allopolyploids. We discuss the rationale for using the different techniques and provide examples of the data generated.
Pikaard
Craig S
CS
Biology Department, Washington University, Saint Louis, Missouri 63130, USA.
Preuss
Sasha
S
Earley
Keith
K
Lawrence
Richard J
RJ
Lewis
Michelle S
MS
Chen
Z Jeffrey
ZJ
D000483:Alleles; D001937:Brassica / Q000235:genetics; D017931:DNA Primers; D015870:Gene Expression; D017343:Genes, Plant; D005821:Genetic Techniques; D006824:Hybridization, Genetic; D021141:Nucleic Acid Amplification Techniques; D011110:Polymorphism, Genetic; D011123:Polyploidy; D018749:RNA, Plant / Q000235:genetics; D015719:Single-Strand Specific DNA and RNA Endonucleases; D014158:Transcription, Genetic
D017931:DNA Primers; D018749:RNA, Plant; D015719:Single-Strand Specific DNA and RNA Endonucleases