Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development

Abstract

QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks.

Figure 1.—

A CMap display of the comparison between an individual map and a consensus map. The left map is chromosome 16 from the n2 population including one QTL (MIC) shown on the left side of the map. The right map is consensus chromosomes C4, reconstructed from the At and Dt maps as described (Rong et al. 2005a). To the immediate right of this map, blocks of inferred synteny with Arabidopsis are shown. D (or Ds) number indicates correspondence to the accordingly numbered Arabidopsis α-duplicated segment (Bowers et al. 2003), and the number after the dot indicates the span of this particular segment of correspondence in the α-duplicated segment (which can be visualized at our CMAP website; also see Rong et al. 2005a for further details). To the right of blocks of inferred synteny, QTL likelihood intervals are plotted, labeled as described in the text. Where appropriate, parenthetical information indicates experimental treatments (for example, ww, well-watered, and bt, both treatments: Paterson et al. 2003), or alternate name of the trait if different in prior publications are presented in parenthesis after each QTL name. Detailed explanation of these descriptions can be found in the references cited.

Figure 2.—

Number and distribution of genetic markers and fiber-related QTL in 20-cM bins along chromosomes 1 and 2 of a reference genetic map (Rong et al. 2004). Open bars represent marker number and solid bars are 2-LOD likelihood intervals for fiber QTL.

Figure 3.—

Genetic map and Arabidopsis syntenic regions of a segment of cotton consensus chromosome C12 (from 54.1 to 73.1 cM) showing the locations of fiber-related QTL, Arabidopsis orthologs of cotton fiber-related cDNAs, and Arabidopsis genes functioning in trichome development. Vertical bars on the left side of C12 represent the locations of QTL for fiber elongation (Paterson et al. 2003), fiber length (Chee et al. 2005b), and mass of seed cotton (log transformed) (Jiang et al. 1998). Solid lines link putative orthologs between cotton and Arabidopsis which were used to infer correspondence in this region. The numbers on the left side of the Arabidopsis segments are consecutive numbers assigned to genes in each α-duplicated segment, provided to permit one to know (by subtraction) the number of intervening genes between two anchor points. Values in parentheses to the right of Arabidopsis gene designations indicate gene identifier and e-value for match to a candidate gene identified based on expression pattern (as detailed in supplemental Table 7 at http://www.genetics.org/supplemental/) or a role in Arabidopsis trichome development (supplemental Table 8).