QTL analysis of leaf morphology in tetraploid Gossypium (cotton)

Jiang, Chunxiao; Wright, Robert J.; Woo, Sung Sick; Delmonte, Terrye A.; Paterson, Andrew H.

doi:10.1007/s001220050054

Cited by 105 publications

(86 citation statements)

References 26 publications

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“…The traits represented in (B) are indicated in (A) by a red box. development are rare in any species (Jiang et al, 2000;Holtan and Hake, 2003;Kimura et al, 2008;Tian et al, 2011). Even rarer are studies of variation in leaf morphology by a quantitative means capable of describing total shape variance (Iwata et al, 1998;Iwata and Ukai, 2002;Langlade et al, 2005;Chitwood et al, 2012bChitwood et al, , 2012cChitwood et al, , 2012d.…”

Section: Discussionmentioning

confidence: 99%

“…Such phenotypes are associated with water use efficiency and thermoregulation, traits important to yield (Nicotra et al, 2011;Chitwood et al, 2012a). Studies examining leaf morphology are often limited to analyses of size, dimensions of length and width, and complexity (Jiang et al, 2000;Pérez-Pérez et al, 2002;Holtan and Hake, 2003;Frary et al, 2004). Recently, a genome-wide association study using the maize (Zea mays) nested association mapping population identified liguleless genes as regulators of upright leaf angles.…”

Section: Introductionmentioning

confidence: 99%

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A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines

et al. 2013

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Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement. Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line. To take advantage of this information, we determine IL phenotypes for a suite of vegetative traits, ranging from leaf complexity, shape, and size to cellular traits, such as stomatal density and epidermal cell phenotypes. Elliptical Fourier descriptors on leaflet outlines provide a global analysis of highly heritable, intricate aspects of leaf morphology. We also demonstrate constraints between leaflet size and leaf complexity, pavement cell size, and stomatal density and show independent segregation of traits previously assumed to be genetically coregulated. Meta-analysis of previously measured traits in the ILs shows an unexpected relationship between leaf morphology and fruit sugar levels, which RNA-Seq data suggest may be attributable to genetically coregulated changes in fruit morphology or the impact of leaf shape on photosynthesis. Together, our results both improve upon the utility of an important genetic resource and attest to a complex, genetic basis for differences in leaf morphology between natural populations.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines

et al. 2013

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“…The inferred map is an excellent resource from which markers can be selected for marker assisted selection, identification of introgression lines, QTL mapping, and SNP discovery using sensitive new techniques that permit identification of informative DNA marker alleles in sequence-tagged sites such as these that had previously been mapped as RFLPs. A growing number of such studies have been done or are in progress (Jiang et al 1998(Jiang et al , 2000aWright et al 1998Wright et al , 1999Saranga et al 2004).…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy

Rong

Bowers²,

Schulze³

et al. 2005

Genome Res.

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Both ancient and recent polyploidy, together with post-polyploidization loss of many duplicated gene copies, complicates angiosperm comparative genomics. To explore an approach by which these challenges might be mitigated, genetic maps of extant diploid and tetraploid cottons (Gossypium spp.) were used to infer the approximate order of 3016 loci along the chromosomes of their hypothetical common ancestor. The inferred Gossypium gene order corresponded more closely than the original maps did to a similarly inferred ancestral gene order predating an independent paleopolyploidization (␣) in Arabidopsis. At least 59% of the cotton map and 53% of the Arabidopsis transcriptome showed correspondence in multilocus gene arrangements based on one or both of two software packages (CrimeStatII, FISH). Genomic regions in which chromosome structural rearrangement has been rapid (obscuring gene order correspondence) have also been subject to greater divergence of individual gene sequences. About 26%-44% of corresponding regions involved multiple Arabidopsis or cotton chromosomes, in some cases consistent with known, more ancient, duplications. The genomic distributions of multiple-locus probes provided early insight into the consequences for chromosome structure of an ancient large-scale duplication in cotton. Inferences that mitigate the consequences of ancient duplications improve leveraging of genomic information for model organisms in the study of more complex genomes.

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“…Using a high-density reference genetic map which consists of 3475 loci in total, herein we report the alignment of 432 QTL involving cotton fiber quality ( Jiang et al 1998;Paterson et al 2003;Chee et al 2005a,b;Draye et al 2005), yield ( Jiang et al 1998;Saranga et al 2001Saranga et al , 2004Rong et al 2005b), leaf morphology ( Jiang et al 2000;Waghmare et al 2005), flower morphology, resistance to bacteria , trichome distribution and density (Wright et al 1999), and other traits that were mapped in 11 populations. All QTL were also projected onto a consensus map, which was inferred to resemble the DNA marker arrangement of the hypothetical ancestor of the two subgenomes of tetraploid cotton (Rong et al 2005a).…”

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confidence: 99%

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

Feltus²,

et al. 2007

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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-fiberproducing 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, the number 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 of QTL representing a myriad of traits have been mapped in agronomically important crops, and also in botanical models 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 wit...

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QTL analysis of leaf morphology in tetraploid Gossypium (cotton)

Cited by 105 publications

References 26 publications

A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines

A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines

Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy

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

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