Genotyping of the Q locus in wheat by a simple PCR-RFLP method

Abstract

The Q locus located on the long arm of chromosome 5A is a key factor in evolution and widespread cultivation of domesticated wheat. The Q locus pleiotropically affects many agronomically important traits including threshability, glume shape and tenacity, rachis fragility and others. Genotyping of the Q locus based on the complex traits is ambiguous due to their multi-genetic control through interactions with the Q locus. To determine the Q locus genotype of wheat accessions possessing A genome, we developed a method based on polymerase chain reaction -restriction fragment length polymorphism (PCR-RFLP) analysis. The Q and q alleles were clearly distinguished by PCR-RFLP analysis at six conserved single nucleotide polymorphisms in common wheat and wild and cultivated einkorn, emmer and timopheevi wheat. The Q locus genotype of Triticum sinskajae, which is one of the einkorn wheat species and exhibits free-threshing trait, was determined to be qq as expected. This simple PCR-RLFP-based genotyping method should serve as a useful tool in studying the origin of Q and thus wheat evolution after domestication and the following widespread cultivation.

Evidence from principal component analysis for improvement of grain shape- and spikelet morphology-related traits after hexaploid wheat speciation

“…The genotype at the q locus was also confirmed using restriction site polymorphisms as previously reported (Asakura et al, 2009). Three intragenic regions were amplified using q-specific primers, and then the amplified products were digested with MspI, TaqI or MboI.…”

“…Three intragenic regions were amplified using q-specific primers, and then the amplified products were digested with MspI, TaqI or MboI. After separation of the digested fragments by electrophoresis through a 2% agarose gel and staining with ethidium bromide, the presence or absence of the three restriction sites was determined with reference to the previous data (Asakura et al, 2009). …”

“…Norin 61 contained a photoperiod-insensitive allele at Ppd-D1 and the synthetic wheat line contained a sensitive allele. Similarly, genotypes of the q locus on chromosome 5A were compared between the mapping parents using allele-specific restriction sites (Asakura et al, 2009), but no polymorphisms were found. This indicated that Norin 61 and the synthetic wheat line share the same genotype (a dominant Q allele) at the q locus.…”

Discrimination of alleles and copy numbers at the Q locus in hexaploid wheat using quantitative pyrosequencing

“…SNP2299 seems to be closely related to the occurrence of domesticated free-threshing wheat. The restriction enzyme MboI can be used to differentiate between Q and q at this position (Asakura et al 2009). Plant breeders use both, cultivated and wild species, to select favorable new traits in elite cultivar candidates.…”

“…Simons et al (2006) showed that one variation in the DNA sequence of exon 8 leads to the amino acid substitution Valine (5Aq allele) to Isoleucine (5AQ allele), which seems to be closely related to the domestication of free-threshing wheat. Recently, Asakura et al (2009) used a PCR based CAPS marker assay to genotype the 5AQ locus. Since the Q (5A chromosome) and q gene sequences (5B and 5D chromosomes) are available (Simons et al 2006;Ning et al 2009), it is now possible to align the homoeoalleles from each genome including the primitive allele 5Aq and design differentiating pyrosequencing primers.…”