Crop evolution: from genetics to genomics

Burke, John M.; Burger, Jutta C.; Chapman, Mark A.

doi:10.1016/j.gde.2007.09.003

Cited by 71 publications

(55 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Population bottlenecks are predicted to result in a genome-wide reduction in genetic diversity in domesticated species (Tanksley and McCouch, 1997;Yamasaki et al, 2005;Burke et al, 2007). Consistent with this expectation, and with previous findings both in sunflower (Tang and Knapp, 2003;Liu and Burke, 2006) and in other crops (Olsen and Schaal, 2001;Vigouroux et al, 2002;Casa et al, 2005;Caicedo et al, 2007;Sangiri et al, 2007;Zhu et al, 2007), we found that genetic diversity was highest among the wild lines and lowest among the improved lines, with the primitive domesticates being intermediate.…”

Section: Discussion Genetic Diversity and Relatednesssupporting

confidence: 91%

A Genomic Scan for Selection Reveals Candidates for Genes Involved in the Evolution of Cultivated Sunflower (Helianthus annuus)

et al. 2008

View full text Add to dashboard Cite

Genomic scans for selection are a useful tool for identifying genes underlying phenotypic transitions. In this article, we describe the results of a genome scan designed to identify candidates for genes targeted by selection during the evolution of cultivated sunflower. This work involved screening 492 loci derived from ESTs on a large panel of wild, primitive (i.e., landrace), and improved sunflower (Helianthus annuus) lines. This sampling strategy allowed us to identify candidates for selectively important genes and investigate the likely timing of selection. Thirty-six genes showed evidence of selection during either domestication or improvement based on multiple criteria, and a sequence-based test of selection on a subset of these loci confirmed this result. In view of what is known about the structure of linkage disequilibrium across the sunflower genome, these genes are themselves likely to have been targeted by selection, rather than being merely linked to the actual targets. While the selection candidates showed a broad range of putative functions, they were enriched for genes involved in amino acid synthesis and protein catabolism. Given that a similar pattern has been detected in maize (Zea mays), this finding suggests that selection on amino acid composition may be a general feature of the evolution of crop plants. In terms of genomic locations, the selection candidates were significantly clustered near quantitative trait loci (QTL) that contribute to phenotypic differences between wild and cultivated sunflower, and specific instances of QTL colocalization provide some clues as to the roles that these genes may have played during sunflower evolution.

show abstract

Section: Discussion Genetic Diversity and Relatednesssupporting

confidence: 91%

A Genomic Scan for Selection Reveals Candidates for Genes Involved in the Evolution of Cultivated Sunflower (Helianthus annuus)

et al. 2008

View full text Add to dashboard Cite

show abstract

“…Insights into the genetic basis of morphological change in nature are often facilitated using crop models, as Darwin famously noted in the introduction to On the Origin of Species when he wrote "At the commencement of my observations it seemed to me probable that a careful study of domesticated animals and of cultivated plants would offer the best chance of making out this obscure problem." Since Darwin's time, numerous mutations have been identified that control traits selected by humans during the domestication process, including loss-of-function alleles, changes in coding sequence, or altered levels or domains of expression (42)(43)(44)(45)(46). Notwithstanding these striking discoveries, relatively little is understood about the downstream effects on domestication mutations or transcriptional and physiological networks, nor how these are propagated into the phenotypes being subjected to directional selection.…”

Section: Discussionmentioning

confidence: 99%

Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton ( Gossypium )

Bao

Flagel

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Cotton is remarkable among our major crops in that four species were independently domesticated, two allopolyploids and two diploids. In each case thousands of years of human selection transformed sparsely flowering, perennial shrubs into highly productive crops with seeds bearing the vastly elongated and abundant single-celled hairs that comprise modern cotton fiber. The genetic underpinnings of these transformations are largely unknown, but comparative gene expression profiling experiments have demonstrated up-regulation of profilin accompanying domestication in all three species for which wild forms are known. Profilins are actin monomer binding proteins that are important in cytoskeletal dynamics and in cotton fiber elongation. We show that Gossypium diploids contain six profilin genes (GPRF1-GPRF6), located on four different chromosomes (eight chromosomes in the allopolyploid). All but one profilin (GPRF6) are expressed during cotton fiber development, and both homeologs of GPRF1-GPRF5 are expressed in fibers of the allopolyploids. Remarkably, quantitative RT-PCR and RNAseq data demonstrate that GPRF1-GPRF5 are all up-regulated, in parallel, in the three independently domesticated cottons in comparison with their wild counterparts. This result was additionally supported by iTRAQ proteomic data. In the allopolyploids, there This usage of novel should be fine, since it refers to a novel evolutionary process, not a novel discovery has been novel recruitment of the sixth profilin gene (GPRF6) as a result of domestication. This parallel up-regulation of an entire gene family in multiple species in response to strong directional selection is without precedent and suggests unwitting selection on one or more upstream transcription factors or other proteins that coordinately exercise control over profilin expression.polyploidy | crop evolution | fiber | directional selection

show abstract

“…Archeological and multilocus sequence data provide complementary information to understand the demographic and evolutionary events associated with the domestication of a species (Doebley et al 2006;Burke et al 2007). Recent population genomics studies suggest that domestication affects the entire genome and that selection acts on a large number of loci Caicedo et al 2007), so a multilocus approach is appropriate to study the effects of domestication and selection.…”

Section: Introductionmentioning

confidence: 99%

Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

Mamidi

Rossi

Annam

et al. 2011

Functional Plant Biol.

View full text Add to dashboard Cite

Abstract. Multilocus sequence data collected from domesticated and related wild relatives provides a rich source of information on the effect of human selection on the diversity and adaptability of a species to complex environments. To evaluate the domestication history of common bean (Phaseolus vulgaris L.), multilocus sequence data from landraces representing the various races within the Middle American (MA) and Andean gene pools was evaluated. Across 13 loci, nucleotide diversity was similar between landraces and wild germplasm in both gene pools. The diversity data were evaluated using the approximate Bayesian computation approach to test multiple domestication models and estimate population demographic parameters. A model with a single domestication event coupled with bidirectional migration between wild and domesticated genotypes fitted the data better than models consisting of two or three domestication events in each genepool. The effective bottleneck population size was~50% of the base population in each genepool. The bottleneck began~8200 and 8500 years before present and ended at~6300 and~7000 years before present in MA and Andean gene pools respectively. Linkage disequilibrium decayed to a greater extent in the MA genepool. Given the (1) geographical adaptation bottleneck in each wild gene pool, (2) a subsequent domestication bottleneck within each gene pool, (3) differentiation into gene-pool specific races and (4) variable extents of linkage disequilibrium, association mapping experiments for common bean would more appropriately be performed within each genepool.

show abstract

Crop evolution: from genetics to genomics

Cited by 71 publications

References 59 publications

A Genomic Scan for Selection Reveals Candidates for Genes Involved in the Evolution of Cultivated Sunflower (Helianthus annuus)

A Genomic Scan for Selection Reveals Candidates for Genes Involved in the Evolution of Cultivated Sunflower (Helianthus annuus)

Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton ( Gossypium )

Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

Contact Info

Product

Resources

About