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

Abstract

Background: Cotton 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 x 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.

Results: The 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.

Conclusions: Meta-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.

Figure 1

Projections of QTLs and confidence interval positions on chromosome 3. Projections of 55 QTLs and confidence interval for various fiber traits on chromosome 3 (Figures for other chromosomes are shown in Additional file 3, Figure S1). Positions of putative QTLs (LOD > 2) and one-LOD drop off CI, as output data from QTL analysis with WinQTL Cartographer software, are projected on the Guazuncho-2 x VH8-4602, RIL-BC-consensus map. The QTL positions are arbitrarily centered (by the software) relative to the CI (input data). QTLs originate (i) from the 11 RIL experiments reported in this paper, (ii) from the 3 backcross generations reported in Lacape et al. [7] and re-analyzed using the consensus map and (iii) the fiber QTLs compiled in Rong et al. [16] that could be projected on the Guazuncho-2 x VH8-4602 consensus map. QTL nomenclature of RIL and BC data is a concatenation of the RIL experiment location (or BC generation), trait name, chromosome, rank on chromosome, LOD peak value and sign of additivity (shown in square brackets) relative to the Gh (Guazuncho-2) parent. The QTL name is bracketed when its LOD value is inferior to the permutation-based (1000) threshold but superior to LOD2. Names for other QTLs were kept as in their original reference [16]. Fiber quality categories comprise fiber length (grouping UHML, ML, UQLw), length uniformity (UI and SFI), fineness (H, Hs, MR and micronaire), color (Rd and + b), strength and elongation. Bars for QTLs of a given category on a given chromosome are filled in the same color, but colors may differ from one chromosome to the next (see color legends in Additional file 3, Figure S1).

Figure 2

Results of QTL clustering (meta-analysis) by MetaQTL. Results of QTL clustering (meta-analysis) by MetaQTL of QTLs for fiber length (LEN) on chromosome 3 with 26 QTLs (those displayed in blue in Figure 1) grouped as 4 clusters. QTLs belonging to the same cluster have the same color. QTLs common to two clusters are represented with the color of each cluster, the length of the color segments being proportional to the probability for the QTL of belonging to the cluster of the same color. The vertical lines provide approximate bounds for the clusters. Figures for all 30 individual trait x chromosome combinations are shown in Additional file 5, Figure S2.

Figure 3

Variation of the LOD score profiles along chromosome 4 for fiber length measurements. Graphical representation of the variation among 11 data sets of the LOD score profiles (upper panel) and of the observed additivity effect (in mm) as conferred by the Gh parent (lower panel) along chromosome 4 for fiber length measurements (either HVI-based, as Upper Half Mean Length, UHML or Mean Length, ML, or AFIS-based, as Upper Quartile Length per weight, UQLw). Phenotypic data were obtained from 11 experiments of the RIL population and analyzed with WinQTL Cartographer by composite interval mapping (loci positioned on the RIL map). The 2 horizontal lines correspond to 2 different LOD thresholds: the permutation-based (1000 permutations) threshold averaged from the 11 sets, ie LOD = 3.5 (dotted line), and an arbitrary value of LOD = 2 (solid line).