Genetic Mapping and Comparative Expression Analysis of Transcription Factors in Cotton

<div><p>Transcription factors (TFs) play an important role in the regulation of plant growth and development. The study of the structure and function of TFs represents a research frontier in plant molecular biology. The findings of these studies will provide significant information regarding genetic improvement traits in crops. Currently, a large number of TFs have been cloned, and their function has been verified. However, relatively few studies that genetically map TFs in cotton are available. To genetically map TFs in cotton in this study, specific primers were designed for TF genes that were published in the Plant Transcription Factor Database. A total of 977 TF primers were obtained, and 31 TF polymorphic loci were mapped on 15 cotton chromosomes. These polymorphic loci were clearly preferentially distributed on chromosomes 5, 11, 19 and 20; and TFs from the same family mapped to homologous cotton chromosomes. <i>In-silico</i> mapping verified that many mapped TFs were mapped on their corresponding chromosomes or their homologous chromosomes’ corresponding chromosomes in the diploid genomes. QTL mapping for fiber quality revealed that TF-Ghi005602-2 mapped on Chr19 was associated with fiber length. Eighty-five TF genes were selected for RT-PCR analysis, and 4 TFs were selected for qRT-PCR analysis, revealing unique expression patterns across different stages of fiber development between the mapping parents. Our data offer an overview of the chromosomal distribution of TFs in cotton, and the comparative expression analysis between <i>Gossypium hirsutum</i> and <i>G</i>. <i>barbadense</i> provides a rough understanding of the regulation of TFs during cotton fiber development.</p></div

Genome-wide recombination rate variation in a recombination map of cotton

<div><p>Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species’ genomes, and it is particularly unclear in <i>Gossypium</i>. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton.</p></div

Additional file 1: Table S1. of Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

Distribution statistics of SLAFs and polymorphic SLAFs on each chromosome. (XLS 25 kb

The correlation of genetic and physical maps, the estimated local recombination rates and its distribution in chromosomal rearrangement regions.

<p>The red dots represent the genetic and physical positions of markers. The red curves below the scatter plots of SSRs represent the estimated local recombination rates. The value of R² represent the correlation between the genetic and physical maps. Shadow represents the centromere regions, inversion regions and translocation regions.</p

The physical distribution statistics of markers on 26 chromosomes in cotton.

<p>The physical distribution statistics of markers on 26 chromosomes in cotton.</p

RT-PCR analysis of TFs between mapping parents.

<p>The numbers on the top represent fibers at 0 DPA, 5 DPA, 10 DPA, 15 DPA, 20 DPA, and 25 DPA for Emian22 and 3–79. Similar expression trends between Emian22 and 3–79 were classified as similar expression patterns. Apparent differences in expression between Emian22 and 3–79 were classified as different expression patterns. Obvious differences in expression levels between Emian22 and 3–79 were classified as obvious differences. Minor or no differences in expression levels between Emian22 and 3–79 were classified as no difference. Gene primers and their family names are indicated on the left.</p

Primer design strategies for TFs.

<p>(a) TFs with one motif (GenBank acc No. Ghi003408); (b) TFs with two motifs (GenBank acc No. Ghi003040). *: Target sequence; >>>>>: Primer region.</p

Additional file 6: Table S4. of Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

Non-synonymous SNPs present in the coding region of genes among the five cotton species. (XLS 220 kb

Chromosomal location of TFs in the A₂ genome of <i>G</i>. <i>arboretum</i> (a) and D₅ genome of <i>G</i>. <i>raimondii</i> (b).

<p>Chromosomal location of TFs in the A₂ genome of <i>G</i>. <i>arboretum</i> (a) and D₅ genome of <i>G</i>. <i>raimondii</i> (b).</p

Collinearity of the genetic and physical maps and genomic distribution of TEs, markers, recombination rate and genes on each chromosome.

<p>Collinearity of the genetic and physical maps and genomic distribution of TEs, markers, recombination rate and genes on each chromosome in At (A) and Dt (B). (A, B)I-IV: The genomic distribution of TEs, markers, recombination rate and genes on each chromosome are shown in heat map, red bar graphs, blue bar graphs and green bar graphs;V: The chromosomes;VI: Collinearity of the genetic and physical maps.</p