Background CBF/DREB duplicate genes are widely distributed in higher plants and encode transcript... more Background CBF/DREB duplicate genes are widely distributed in higher plants and encode transcriptional factors, or CBFs, which bind a DNA regulatory element and impart responsiveness to low temperatures and dehydration. Results We explored patterns of genetic variations of CBF1, -2, and -3 from 34 accessions of Arabidopsis thaliana. Molecular population genetic analyses of these genes indicated that CBF2 has much reduced nucleotide diversity in the transcriptional unit and promoter, suggesting that CBF2 has been subjected to a recent adaptive sweep, which agrees with reports of a regulatory protein of CBF2. Investigating the ratios of Ka/Ks between all paired CBF paralogus genes, high conservation of the AP2 domain was observed, and the major divergence of proteins was the result of relaxation in two regions within the transcriptional activation domain which was under positive selection after CBF duplication. With respect to the level of CBF gene expression, several mutated nucleotides in the promoters of CBF3 and -1 of specific ecotypes might be responsible for its consistently low expression. Conclusion We concluded from our data that important evolutionary changes in CBF1, -2, and -3 may have primarily occurred at the level of gene regulation as well as in protein function.
Proceedings of The National Academy of Sciences, 2006
Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding... more Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding more than half of the human population. Despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, Oryza rufipogon, remains unclear. In this study, DNA sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. Results indicate that India and Indochina may represent the ancestral center of diversity for O. rufipogon. Additionally, the data suggest that cultivated rice was domesticated at least twice from different O. rufipogon populations and that the products of these two independent domestication events are the two major rice varieties, Oryza sativa indica and Oryza sativa japonica. Based on this geographical analysis, O. sativa indica was domesticated within a region south of the Himalaya mountain range, likely eastern India, Myanmar, and Thailand, whereas O. sativa japonica was domesticated from wild rice in southern China.
Scutellaria austrotaiwanensis is a new species first described in 1997. It is a rare and endemic ... more Scutellaria austrotaiwanensis is a new species first described in 1997. It is a rare and endemic species in southern Taiwan. In this study, 16 polymorphic microsatellite loci were isolated from Scutellaria austrotaiwanensis using a magnetic bead enrichment method. Several genetic indices, including observed heterozygosity (Ho), expected heterozygosity (He), number of effective alleles (Ne), and polymorphism information content (PIC), were calculated. Deviation of heterozygosity was detected by the fixation index (Fis) and Hardy–Weinberg equilibrium was tested by possibilities (P HWE) using a chi-squared test. Allele numbers ranged from 4 to 8, with observed heterozygosity ranging from 0.611 to 1.000. Five microsatellite markers showed deficient heterozygosity by Fis > 0. No loci exhibited a departure from Hardy–Weinberg equilibrium, possibly due to a stable population. No loci pairs revealed significant linkage disequilibrium. The microsatellite markers reported here should be useful to evaluate the population structure of S. austrotaiwanensis for conservation efforts.
Background This study addresses the apportionment of genetic diversity between Cycas revoluta and... more Background This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China. Results The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atp B and rbc L genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic. Conclusion Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.
Ludwigia polycarpa is the only species of section Microcarpium occurring north of 37°N in the cen... more Ludwigia polycarpa is the only species of section Microcarpium occurring north of 37°N in the central midwest of the United States. Recently, the loss of wetlands in North America reduced the population number and size of L. polycarpa dramatically. In this study, for the purpose of the conservation of the endangered species, we described eight microsatellite DNA loci. High variabilities enable these molecular markers to assess the population structure. The number of alleles per locus ranged from 8 to 23. The expected (H E) and observed (H O) heterozygosities ranged from 0.86 to 0.96 and 0.00 to 1.00, respectively. Seven of the eight microsatellite loci displayed significant departures from Hardy–Weinberg expectations, likely due to the loss of habitats and the small population size. No linkage disequilibrium was observed in the pairwise comparisons of loci. The application of these microsatellite loci in L. polycarpa may provide a tool for understanding its demography and population structure.
The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal... more The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal DNA (rDNA) gene family was surveyed in Miscanthus sinensis var. glaber. Length heterogeneity, with sizes from 1782 to 2212 base pairs, of the IGS resulted from the variation of copy numbers of the A and B subrepeats. These repeated elements were located upstream of the presumptive polymeraseII promoter, which was the region corresponding to the nontranscribed spacer (NTS). Length heterogeneity was detected both within and between individuals of Miscanthus sinensis var. glaber. Neighbor-joining analyses of repetitive A elements indicated that both unequal crossing-over and preferential conversion may have affected the hot-spot regions of the IGS in concert. Within-individual polymorphism and the reconstructed phylogeny suggested that interspecific hybridization has also contributed to length heterogeneity.
Background CBF/DREB duplicate genes are widely distributed in higher plants and encode transcript... more Background CBF/DREB duplicate genes are widely distributed in higher plants and encode transcriptional factors, or CBFs, which bind a DNA regulatory element and impart responsiveness to low temperatures and dehydration. Results We explored patterns of genetic variations of CBF1, -2, and -3 from 34 accessions of Arabidopsis thaliana. Molecular population genetic analyses of these genes indicated that CBF2 has much reduced nucleotide diversity in the transcriptional unit and promoter, suggesting that CBF2 has been subjected to a recent adaptive sweep, which agrees with reports of a regulatory protein of CBF2. Investigating the ratios of Ka/Ks between all paired CBF paralogus genes, high conservation of the AP2 domain was observed, and the major divergence of proteins was the result of relaxation in two regions within the transcriptional activation domain which was under positive selection after CBF duplication. With respect to the level of CBF gene expression, several mutated nucleotides in the promoters of CBF3 and -1 of specific ecotypes might be responsible for its consistently low expression. Conclusion We concluded from our data that important evolutionary changes in CBF1, -2, and -3 may have primarily occurred at the level of gene regulation as well as in protein function.
Proceedings of The National Academy of Sciences, 2006
Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding... more Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding more than half of the human population. Despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, Oryza rufipogon, remains unclear. In this study, DNA sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. Results indicate that India and Indochina may represent the ancestral center of diversity for O. rufipogon. Additionally, the data suggest that cultivated rice was domesticated at least twice from different O. rufipogon populations and that the products of these two independent domestication events are the two major rice varieties, Oryza sativa indica and Oryza sativa japonica. Based on this geographical analysis, O. sativa indica was domesticated within a region south of the Himalaya mountain range, likely eastern India, Myanmar, and Thailand, whereas O. sativa japonica was domesticated from wild rice in southern China.
Scutellaria austrotaiwanensis is a new species first described in 1997. It is a rare and endemic ... more Scutellaria austrotaiwanensis is a new species first described in 1997. It is a rare and endemic species in southern Taiwan. In this study, 16 polymorphic microsatellite loci were isolated from Scutellaria austrotaiwanensis using a magnetic bead enrichment method. Several genetic indices, including observed heterozygosity (Ho), expected heterozygosity (He), number of effective alleles (Ne), and polymorphism information content (PIC), were calculated. Deviation of heterozygosity was detected by the fixation index (Fis) and Hardy–Weinberg equilibrium was tested by possibilities (P HWE) using a chi-squared test. Allele numbers ranged from 4 to 8, with observed heterozygosity ranging from 0.611 to 1.000. Five microsatellite markers showed deficient heterozygosity by Fis > 0. No loci exhibited a departure from Hardy–Weinberg equilibrium, possibly due to a stable population. No loci pairs revealed significant linkage disequilibrium. The microsatellite markers reported here should be useful to evaluate the population structure of S. austrotaiwanensis for conservation efforts.
Background This study addresses the apportionment of genetic diversity between Cycas revoluta and... more Background This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China. Results The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atp B and rbc L genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic. Conclusion Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.
Ludwigia polycarpa is the only species of section Microcarpium occurring north of 37°N in the cen... more Ludwigia polycarpa is the only species of section Microcarpium occurring north of 37°N in the central midwest of the United States. Recently, the loss of wetlands in North America reduced the population number and size of L. polycarpa dramatically. In this study, for the purpose of the conservation of the endangered species, we described eight microsatellite DNA loci. High variabilities enable these molecular markers to assess the population structure. The number of alleles per locus ranged from 8 to 23. The expected (H E) and observed (H O) heterozygosities ranged from 0.86 to 0.96 and 0.00 to 1.00, respectively. Seven of the eight microsatellite loci displayed significant departures from Hardy–Weinberg expectations, likely due to the loss of habitats and the small population size. No linkage disequilibrium was observed in the pairwise comparisons of loci. The application of these microsatellite loci in L. polycarpa may provide a tool for understanding its demography and population structure.
The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal... more The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal DNA (rDNA) gene family was surveyed in Miscanthus sinensis var. glaber. Length heterogeneity, with sizes from 1782 to 2212 base pairs, of the IGS resulted from the variation of copy numbers of the A and B subrepeats. These repeated elements were located upstream of the presumptive polymeraseII promoter, which was the region corresponding to the nontranscribed spacer (NTS). Length heterogeneity was detected both within and between individuals of Miscanthus sinensis var. glaber. Neighbor-joining analyses of repetitive A elements indicated that both unequal crossing-over and preferential conversion may have affected the hot-spot regions of the IGS in concert. Within-individual polymorphism and the reconstructed phylogeny suggested that interspecific hybridization has also contributed to length heterogeneity.
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Papers by Yu-Chung Chiang