Quantitative Trait Loci for Genetically Correlated Seed Traits are Tightly Linked to Branching and Pericarp Pigment Loci in Sunflower

Tang, Shunxue; Leόn, Alberto J.; Bridges, William C.; Knapp, Steven J.

doi:10.2135/cropsci2005.0006-7

Cited by 78 publications

(92 citation statements)

References 49 publications

(68 reference statements)

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“…The 31 loci were distributed across 12 of the 17 linkage groups (LGs) with between one and six loci on each LG. A subset of our candidate genes were found in the same genomic interval as previously mapped QTL (Burke et al, 2002Tang et al, 2006;Wills and Burke, 2007). In fact, 23 of the 27 genes whose positions could be determined relative to the QTL mapped by Wills and Burke (2007) based on shared markers, colocalized with at least one QTL based on their one-LOD (log of the odds) confidence intervals.…”

Section: Genetic Mappingmentioning

confidence: 64%

“…Because a number of domestication-and improvement-related QTL have previously been mapped in sunflower (Burke et al, 2002Tang et al, 2006;Wills and Burke, 2007;Baack et al, 2008), the map positions of the selection candidates identified herein were of great interest. Chromosomal locations of 31 of the 36 selection candidates were determined via genetic mapping and are listed in Table 3.…”

Section: Genetic Mappingmentioning

confidence: 99%

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

et al. 2008

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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.

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Section: Genetic Mappingmentioning

confidence: 64%

Section: Genetic Mappingmentioning

confidence: 99%

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

et al. 2008

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“…However, in the one remaining case (number of heads produced; LG10), this is somewhat unexpected. Indeed, this QTL explains 28% of the segregating phenotypic variance and colocalizes with the B locus, which is known to influence apical branching (Tang et al 2006). In fact, the region harboring the B locus is known to have manifold effects, influencing not only plant architecture but also achene/seed morphology.…”

Section: Discussionmentioning

confidence: 99%

Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

2007

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Genetic analyses of the domestication syndrome have revealed that domestication-related traits typically have a very similar genetic architecture across most crops, being conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype. To date, the domestication of sunflower (Helianthus annuus L.) stands as the only counterexample to this pattern. In previous work involving a cross between wild sunflower (also H. annuus) and a highly improved oilseed cultivar, we found that domestication-related traits in sunflower are controlled by numerous QTL, typically of small effect. To provide insight into the minimum genetic changes required to transform the weedy common sunflower into a useful crop plant, we mapped QTL underlying domestication-related traits in a cross between a wild sunflower and a primitive Native American landrace that has not been the target of modern breeding programs. Consistent with the results of the previous study, our data indicate that the domestication of sunflower was driven by selection on a large number of loci, most of which had small to moderate phenotypic effects. Unlike the results of the previous study, however, nearly all of the QTL identified herein had phenotypic effects in the expected direction, with the domesticated allele producing a more crop-like phenotype and the wild allele producing a more wild-like phenotype. Taken together, these results are consistent with the hypothesis that selection during the post-domestication era has resulted in the introduction of apparently maladaptive alleles into the modern sunflower gene pool.

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“…Because the sunflower domestication syndrome is complex, the number of loci under selection in wide hybrids in contemporary oilseed sunflower breeding programs is predicted to be large; at least 14 of the 17 chromosomes are known to harbor phenotypic and quantitative trait loci for domestication and confectionery traits and should be under strong selection in oilseed sunflower breeding programs (Burke et al 2002(Burke et al , 2005Gandhi et al 2005;Tang et al 2006a). The introgression of wild alleles into modern oilseed sunflower inbred lines has produced a patchwork of elite and wild alleles.…”

Section: Discussionmentioning

confidence: 99%

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Kolkman

Berry²,

Leόn³

et al. 2007

Genetics

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Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression -the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/ 62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (u ¼ 0.0094) than wild populations (u ¼ 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome ($3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping.

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Quantitative Trait Loci for Genetically Correlated Seed Traits are Tightly Linked to Branching and Pericarp Pigment Loci in Sunflower

Cited by 78 publications

References 49 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)

Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

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