55 results on '"Shunxue Tang"'
Search Results
52. Genetic analysis of sunflower domestication
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John M. Burke, Loren H. Rieseberg, Shunxue Tang, and Steven J. Knapp
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Genetic Markers ,Genetics ,education.field_of_study ,DNA, Plant ,Genetic Linkage ,Directional selection ,Quantitative Trait Loci ,Population ,Chromosome Mapping ,food and beverages ,Quantitative trait locus ,Biology ,Genetic architecture ,Phenotype ,Family-based QTL mapping ,Helianthus ,Allele ,Plant Structures ,Association mapping ,education ,Domestication ,Research Article - Abstract
Quantitative trait loci (QTL) controlling phenotypic differences between cultivated sunflower and its wild progenitor were investigated in an F3 mapping population. Composite interval mapping revealed the presence of 78 QTL affecting the 18 quantitative traits of interest, with 2–10 QTL per trait. Each QTL explained 3.0–68.0% of the phenotypic variance, although only 4 (corresponding to 3 of 18 traits) had effects >25%. Overall, 51 of the 78 QTL produced phenotypic effects in the expected direction, and for 13 of 18 traits the majority of QTL had the expected effect. Despite being distributed across 15 of the 17 linkage groups, there was a substantial amount of clustering among QTL controlling different traits. In several cases, regions influencing multiple traits harbored QTL with antagonistic effects, producing a cultivar-like phenotype for some traits and a wild-like phenotype for others. On the basis of the directionality of QTL, strong directional selection for increased achene size appears to have played a central role in sunflower domestication. None of the other traits show similar evidence of selection. The occurrence of numerous wild alleles with cultivar-like effects, combined with the lack of major QTL, suggests that sunflower was readily domesticated.
53. EST and EST-SSR marker resources for Iris
- Author
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Marie-Michèle Cordonnier-Pratt, Michael L. Arnold, Rebecca A Okashah, Christopher A Taylor, Steven J. Knapp, Virgil E. Johnson, Shunxue Tang, and Lee H. Pratt
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Genetic Markers ,0106 biological sciences ,DNA, Plant ,Iris Plant ,Plant Science ,01 natural sciences ,Genetic analysis ,03 medical and health sciences ,Gene mapping ,lcsh:Botany ,Databases, Genetic ,Genotyping ,Gene Library ,030304 developmental biology ,Expressed Sequence Tags ,2. Zero hunger ,Genetics ,0303 health sciences ,Expressed sequence tag ,Polymorphism, Genetic ,biology ,Ecotype ,food and beverages ,biology.organism_classification ,lcsh:QK1-989 ,Genetic marker ,Louisiana iris ,Microsatellite ,Research Article ,Microsatellite Repeats ,010606 plant biology & botany - Abstract
BackgroundLimited DNA sequence and DNA marker resources have been developed forIris(Iridaceae), a monocot genus of 200–300 species in the Asparagales, several of which are horticulturally important. We mined anI. brevicaulis-I. fulvaEST database for simple sequence repeats (SSRs) and developed ortholog-specific EST-SSR markers for genetic mapping and other genotyping applications inIris. Here, we describe the abundance and other characteristics of SSRs identified in the transcript assembly (EST database) and the cross-species utility and polymorphisms ofI. brevicaulis-I. fulvaEST-SSR markers among wild collected ecotypes and horticulturally important cultivars.ResultsCollectively, 6,530 ESTs were produced from normalized leaf and root cDNA libraries ofI. brevicaulis(IB72) andI. fulva(IF174), and assembled into 4,917 unigenes (1,066 contigs and 3,851 singletons). We identified 1,447 SSRs in 1,162 unigenes and developed 526 EST-SSR markers, each tracing a different unigene. Three-fourths of the EST-SSR markers (399/526) amplified alleles from IB72 and IF174 and 84% (335/399) were polymorphic between IB25 and IF174, the parents ofI. brevicaulis×I. fulvamapping populations. Forty EST-SSR markers were screened for polymorphisms among 39 ecotypes or cultivars of seven species – 100% amplified alleles from wild collected ecotypes of Louisiana Iris (I.brevicaulis,I.fulva,I. nelsonii, andI. hexagona), whereas 42–52% amplified alleles from cultivars of three horticulturally important species (I. pseudacorus,I. germanica, andI. sibirica). Ecotypes and cultivars were genetically diverse – the number of alleles/locus ranged from two to 18 and mean heterozygosity was 0.76.ConclusionNearly 400 ortholog-specific EST-SSR markers were developed for comparative genetic mapping and other genotyping applications inIris, were highly polymorphic among ecotypes and cultivars, and have broad utility for genotyping applications within the genus.
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54. Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower.
- Author
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Kolkman, Judith M., Berry, Simon T., Leon, Aiberto J., Slabaugh, Mary B., Shunxue Tang, Wenxiang Gao, Shintani, David K., Burke, John M., and Knapp, Steven J.
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GENETIC polymorphisms , *GENETIC research , *GENE mapping , *CULTIVARS , *GENETIC mutation , *GENOTYPE-environment interaction - Abstract
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 (θ = 0.0094) than wild populations (θ = 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 domes- tication 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. [ABSTRACT FROM AUTHOR]
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- 2007
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55. Extensive Chromosomal Repatterning and the Evolution of Sterility Barriers in Hybrid Sunflower Species.
- Author
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Zhao Lai, Nakazato, Takuya, Salmaso, Marzia, Burke, John M., Shunxue Tang, Knapp, Steven J., and Rieseberg, Loren H.
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SUNFLOWERS , *PLANT genetics , *PLANT chromosomes , *POLLEN , *POLLINATION - Abstract
New species may arise via hybridization and without a change in ploidy. This process, termed homoploid hybrid speciation, is theoretically difficult because it requires the development of reproductive barriers in sympatry or parapatry. Theory suggests that isolation may arise through rapid karyotypic evolution and/or ecological divergence of hybrid neospecies. Here, we investigate the role of karyotypic change in homoploid hybrid speciation by generating detailed genetic linkage maps for three hybrid sunflower species, Helianthus anomalus, H. deserticola, and H. paradoxus, and comparing these maps to those previously generated for the parental species, H. annuus and H. petiolaris. We also conduct a quantitative trait locus (QTL) analysis of pollen fertility in a BC2 population between the parental species and assess levels of pollen and seed fertility in all cross-combinations of the hybrid and parental species. The three hybrid species are massively divergent from their parental species in karyotype; gene order differences were observed for between 9 and 11 linkage groups (of 17 total), depending on the comparison. About one-third of the karyoypic differences arose through the sorting of chromosomal rearrangements that differentiate the parental species, but the remainder appear to have arisen de novo (six breakages/six fusions in H. anomalus, four breakages/three fusions in H. deserticola, and five breakages/five fusions in H. paradoxus). QTL analyses indicate that the karyotypic differences contribute to reproductive isolation. Nine of 11 pollen viability QTL occur on rearranged chromosomes and all but one map close to a rearrangement breakpoint. Finally, pollen and seed fertility estimates for F1's between the hybrid and parental species fall below 11%, which is sufficient for evolutionary independence of the hybrid neospecies. [ABSTRACT FROM AUTHOR]
- Published
- 2005
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