Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum x G. barbadense RIL population

Abstract

BackgroundCotton fibers (produced by Gossypium species) are the premier natural fibers for textile production. The two tetraploid species, G. barbadense (Gb) and G. hirsutum (Gh), differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific Gh × Gb recombinant inbred line (RIL) population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years.ResultsThe RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a per-site basis by composite interval mapping. Among the 651 putative QTLs (LOD > 2), 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents) and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3.ConclusionsMeta-analysis provided a reliable means of integrating phenotypic and genetic mapping data across multiple populations and environments for complex fiber traits. The consistent chromosomal regions contributing to fiber quality traits constitute good candidates for the further dissection of the genetic and genomic factors underlying important fiber characteristics, and for marker-assisted selection.

A Review of QTL Mapping in Cotton: Molecular Markers, Mapping Populations and Statistical Methods

“…Such multiple generations of mating increases the potential number of recombination events and improves map resolution (i.e., sufficient meioses have occurred to reduce disequilibrium between moderately linked markers). In cotton a considerable number of studies have used RILs as mapping population for mapping yield and fibre quality related and other traits (Park et al, 2005;Shen et al, 2007;Wang et al, 2006;Abdurakhmonov et al, 2007;Wu et al, 2008;Zhang et al, 2009;Lacape et al, 2009Lacape et al, , 2010Gore et al, 2014andYu et al, 2013.DH populations have also been used for QTL mapping in several species (Bao et al, 2002;Mahmood et al, 2003;Behn et al, 2005;Semagn et al, 2006;Semagn et al, 2007 andCrouch, 2008).…”

Genetic Mapping in Cotton

“…However, association mapping achieved for crop improvement is not comparable to that in human genomics [89]. Over the decades, many QTLs have been identified using bi-parental populations for yield, yield components and other traits of interest [90,91]. However, only few were successfully used in plant improvement programs.…”

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

“…An RFLP map with 63 fiber QTLs linked to the A-subgenome (chromosome 3, 7, 9, 10, and 12) and 29 fiber QTLs associated with the D-subgenome (chromosome 14Lo, 20, and the long arm of chromosome 26) were reported in 2005 [12]. RFLP's were extensively used in identifying a wide-range of QTLs linked to fiber quality, length, strength, uniformity, wall thickness, micronaire, fineness, and maturity [13,14]). …”