Recent Developments in Fiber Genomics of Tetraploid Cotton Species

Cotton (Gossypium spp.) produces naturally soft, single-celled trichomes as fiber on the seed coat supplying the main source of natural raw material for the textile industry. It is economically considered as one of the most leading cash crops in the world and evolutionarily very important as a model system for detailed scientific investigations. Cotton production is going through a big transition stage such as losing the market share in competition with the synthetic fibers, high popularity of Bt and herbicide resistance genes in cotton cultivars, and the recent shift of fiber demands to meet the standard fiber quality due to change of textile technologies to produce high superior quality of fibers in the global market. Recently, next-generation sequencing technologies through high-throughput sequencing at greatly reduced costs provided opportunities to sequence the diploid and tetraploid cotton genomes. With the availability of large volume of literatures on molecular mapping, new genomic resources, characterization of cotton genomes, discoveries of many novel genes, regulatory elements including small and microRNAs and new genetic tools such as gene silencing or gene editing technique for genome manipulation, this report attempted to provide the readers a comprehensive review on the recent advances of cotton fiber genomics research

QTL mapping for flowering-time and photoperiod insensitivity of cotton <i>Gossypium darwinii</i> Watt

<div><p>Most wild and semi-wild species of the genus <i>Gossypium</i> are exhibit photoperiod-sensitive flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic flowering was developed by crossing a photoperiod insensitive irradiation mutant line with its pre-mutagenesis photoperiodic wild-type <i>G</i>. <i>darwinii</i> Watt genotype. Individuals from the F₂ and F₃ generations were grown with their parental lines and F₁ hybrid progeny in the long day and short night summer condition (natural day-length) of Uzbekistan to evaluate photoperiod sensitivity, i.e., flowering-time during the seasons 2008–2009. Through genotyping the individuals of this bi-parental population segregating for flowering-time, linkage maps were constructed using 212 simple-sequence repeat (SSR) and three cleaved amplified polymorphic sequence (CAPS) markers. Six QTLs directly associated with flowering-time and photoperiodic flowering were discovered in the F₂ population, whereas eight QTLs were identified in the F₃ population. Two QTLs controlling photoperiodic flowering and duration of flowering were common in both populations. <i>In silico</i> annotations of the flanking DNA sequences of mapped SSRs from sequenced cotton (<i>G</i>. <i>hirsutum</i> L.) genome database has identified several potential ‘candidate’ genes that are known to be associated with regulation of flowering characteristics of plants. The outcome of this research will expand our understanding of the genetic and molecular mechanisms of photoperiodic flowering. Identified markers should be useful for marker-assisted selection in cotton breeding to improve early flowering characteristics.</p></div

Information of mapped SSR and CAPS markers.

<p>Information of mapped SSR and CAPS markers.</p

The cross-combination between the wild type of cotton species <i>G</i>. <i>darwinii</i> Watt with its photoperiod insensitive irradiation mutant line.

<p>A) Wild type, B) F₁ plant, and C) irradiation mutant line.</p

Linkage group (LG) / chromosome (Chr.) information in the F₂ population.

<p>Linkage group (LG) / chromosome (Chr.) information in the F₂ population.</p

Genomic distributions of SSR markers and photoperiod-related QTLs identified in the F_2:3 mapping population of this study.

<p>Genomic distributions of SSR markers and photoperiod-related QTLs identified in the F_2:3 mapping population of this study.</p

Histogram of all recorded traits of flowering-time, photoperiodic flowering, other related to flowering and some morphological traits.

<p>a) flowering-time, b) node of first fruiting branch, c) number of buds, d) number of nodes, e) photoperiodic flowering, f) flowering duration Arrows show means for parental genotypes and F₁ hybrid; black arrow—wild type, white arrow—irradiation mutant, and arrow with patterned fill—F₁ plant.</p

Genetic variances and estimated broad-sense heritability of traits in the F₃ population.

<p>Genetic variances and estimated broad-sense heritability of traits in the F₃ population.</p

Genetic linkage map of the F₂ population showing the location of QTL for photoperiodic flowering.

<p>Genetic linkage map of the F₂ population showing the location of QTL for photoperiodic flowering.</p

Examples of SSR markers (JESPR270), segregating in F₂ population.

<p>(M)—Molecular-weight size marker, ‘P₁’ and ‘P₂’—parents, F₁—first-generation hybrid, 1–32—individuals of the F₂ generation.</p