Academic journal article Genetics

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

Academic journal article Genetics

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

Article excerpt

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.

MOST naturally occurring genetic variation in populations reflects polymorphic alleles that individually have relatively small effects but collectively result in continuous variation among members of the population. Through genetic mapping, thenumber and location of loci associated with complex trait variation, i.e., quantitative trait loci or QTL, can be estimated and used to infer the genetic basis of traits that differ between varieties and/or species (PATERSON et al. 1988). DNA markers linked to QTL can also be used as diagnostic tools in the selection of desirable genotypes (markerassisted selection) and as a starting point for cloning of QTL. For these reasons, vast numbers ofQTL representing a myriad of traits have been mapped in agronomically important crops, and also in botanicalmodels and animals. A handful of genes underlying QTL have been cloned (e.g., FRARY et al. 2000) based largely on fine mapping (PATERSON et al. 1990).

A recurring complication in the use of QTL data is that different parental combinations and/or experiments conducted in different environments often result in identification of partly or wholly nonoverlapping sets of QTL. The majority of such differences in the QTL landscape are presumed to be due to environment sensitivity of genes. The use of stringent statistical thresholds to infer QTL while controlling experiment-wise error rates (LANDER and BOTSTEIN 1989; CHURCHILL and DOERGE 1994) implies that only a small fraction of these nonoverlapping QTL can be attributed to falsepositive results. Small QTL with opposite phenotypic effects might occasionally be closely linked in coupling in early-generation populations, and separated only in advanced-generation populations after additional recombination.

Comparison of multiple QTL mapping experiments by alignment to a common reference map offers amore complete picture of the genetic control of a trait than can be obtained in any one study. One such trait, the genetic control of variation in growth and development of seed-borne epidermal "lint" fibers, is a natural priority in cotton genome analysis. All 50 Gossypium species have seed-borne epidermal trichomes, often referred to as "fuzz" fibers. "A" genome diploid cottons are distinct from their sister "F" and "B" genomes in that both wild and cultivated forms have longer lint fibers with secondary thickening, which are spinnable; this feature can thus be inferred to have evolved after the divergence of the A, B, and F genomes from a common ancestor ~5-7 MYA (WENDEL 1989). …

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