Letter to the Editor: Methods for mapping quantitative trait loci in autotetraploid species.

Mapping quantitative trait loci (QTL) in autotetraploid species represents a timely and challenging task. Two papers published by Wu and his colleagues proposed statistical methods for QTL mapping in these evolutionarily and economically important species. In this Letter to the Editor, we present critical comments on the fundamental conceptual errors involved, from both statistical and genetic points of view.

A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations.

This optimized approach provides both a computational tool and a library construction protocol, which can maximize the number of genomic sequence reads that uniformly cover a plant genome and minimize the number of sequence reads representing chloroplast DNA and rRNA genes. One can implement the developed computational tool to feasibly design their own RAD-seq experiment to achieve expected coverage of sequence variant markers for large plant populations using information of the genome sequence and ideally, though not necessarily, information of the sequence polymorphism distribution in the genome. Advent of the next generation sequencing techniques motivates recent interest in developing sequence-based identification and genotyping of genome-wide genetic variants in large populations, with RAD-seq being a typical example.

Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.

Background: Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution 'nullisomic-tetrasomic' lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression.

3' Untranslated regions mediate transcriptional interference between convergent genes both locally and ectopically in Saccharomyces cerevisiae.

Paired sense and antisense (S/AS) genes located in cis represent a structural feature common to the genomes of both prokaryotes and eukaryotes, and produce partially complementary transcripts. We used published genome and transcriptome sequence data and found that over 20% of genes (645 pairs) in the budding yeast Saccharomyces cerevisiae genome are arranged in convergent pairs with overlapping 3'-UTRs. Using published microarray transcriptome data from the standard laboratory strain of S.

HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.

Background: The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies.

Results: We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): 'HSP base Assignment using NGS data through Diploid Similarity' (HANDS).

Multilocus tetrasomic linkage analysis using hidden Markov chain model.

The availability of reliable genetic linkage maps is crucial for functional and evolutionary genomic analyses. Established theory and methods of genetic linkage analysis have made map construction a routine exercise in diploids. However, many evolutionarily, ecologically, and/or agronomically important species are autopolyploids, with autotetraploidy being a typical example.

Robust detection and genotyping of single feature polymorphisms from gene expression data.

It is well known that Affymetrix microarrays are widely used to predict genome-wide gene expression and genome-wide genetic polymorphisms from RNA and genomic DNA hybridization experiments, respectively. It has recently been proposed to integrate the two predictions by use of RNA microarray data only. Although the ability to detect single feature polymorphisms (SFPs) from RNA microarray data has many practical implications for genome study in both sequenced and unsequenced species, it raises enormous challenges for statistical modelling and analysis of microarray gene expression data for this objective.

The role of cis-regulatory motifs and genetical control of expression in the divergence of yeast duplicate genes.

Expression divergence of duplicate genes is widely believed to be important for their retention and evolution of new function, although the mechanism that determines their expression divergence remains unclear. We use a genetical genomics approach to explore divergence in genetical control of yeast duplicate genes created by a whole-genome duplication that occurred about 100 MYA and those with a younger duplication age. The analysis reveals that duplicate genes have a significantly higher probability of sharing common genetic control than pairs of singleton genes.