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

Locations of polymorphic TF loci on the BC₁ genetic linkage map.

<p>TF markers are underlined and bolded. The loci on each chromosome with an average of 10 cM of the original map were selected shown. The top and bottom markers and markers that were closely linked to the TF markers were retained for simplicity.</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

Distribution of TFs in various families.

<p>Distribution of TFs in various families.</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

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

Fiber quality of Emian22 and 3–79.

**<p><i>P</i>≤0.01.</p

Additional file 2: Table S2. of Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects

MHIs in (3E) F2 population. (XLS 26 kb

Genetic Mapping and Characteristics of Genes Specifically or Preferentially Expressed during Fiber Development in Cotton

<div><p>Cotton fiber is an ideal model to study cell elongation and cell wall construction in plants. During fiber development, some genes and proteins have been reported to be specifically or preferentially expressed. Mapping of them will reveal the genomic distribution of these genes, and will facilitate selection in cotton breeding. Based on previous reports, we designed 331 gene primers and 164 protein primers, and used single-strand conformation polymorphism (SSCP) to map and integrate them into our interspecific BC₁ linkage map. This resulted in the mapping of 57 loci representing 51 genes or proteins on 22 chromosomes. For those three markers which were tightly linked with quantitative trait loci (QTLs), the QTL functions obtained in this study and gene functions reported in previous reports were consistent. Reverse transcription-polymerase chain reaction (RT-PCR) analysis of 52 polymorphic functional primers showed that 21 gene primers and 17 protein primers had differential expression between Emian22 (<em>Gossypium hirsutum</em>) and 3–79 (<em>G. barbadense</em>). Both RT-PCR and quantitative real-time PCR (qRT-PCR) analyses of the three markers tightly linked with QTLs were consistent with QTL analysis and field experiments. Gene Ontology (GO) categorization revealed that almost all 51 mapped genes belonged to multiple categories that contribute to fiber development, indicating that fiber development is a complex process regulated by various genes. These 51 genes were all specifically or preferentially expressed during fiber cell elongation and secondary wall biosynthesis. Therefore, these functional gene-related markers would be beneficial for the genetic improvement of cotton fiber length and strength.</p> </div