After reviewing recent evidence from related disciplines arguing for an origin of the Austronesia... more After reviewing recent evidence from related disciplines arguing for an origin of the Austronesian peoples in northeastern China, this paper discusses the Proto-Austronesian and Old Chinese names of the millets, Setaria italica and Panicum miliaceum. Partly based on linguistic data collected in Taiwan by the authors, proposed Proto-Austronesian cognate sets for millet terms are re-evaluated and the Proto-Austronesian sets are identified. The reasons for the earlier confusion among Old Chinese terms for the millets are explained: the Austronesian term for Panicum miliaceum and one of the Chinese terms for the same plant are shown to obey the sound correspondences between Proto-Austronesian and Chinese, earlier described, under a particular resolution of the phonological ambiguities in the oc reconstruction. Possession of the two kinds of millets (not just Setaria, as previously thought) places the pre-Austronesians in northeastern China, adjacent to the probable Sino-Tibetan homeland.
Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mut... more Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D...
Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical da... more Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical day length to get flowering. Sensitivity to photoperiod has been suggested as a major selection target in cultivated or weedy rice. The modern rice varieties in Taiwan may be cultivated twice a year. These varieties contain loss-of-function of two important flowering-time related genes, Heading date 1 (Hd1) and Early heading date 1 (Ehd1), and are mainly from a mega variety, Taichung 65. However, the parental lines of this variety were sensitive to photoperiod, thus, how Taichung 65 loss its sensitivity is a mystery. In this study, we used accession-specific single nucleotide polymorphism analysis to reveal the gene flow that occurred between different rice accessions decades ago and demonstrate that two landraces introgressed during the breeding process, which led to the loss of photoperiod sensitivity. Both Hd1 and Ehd1 may be important during artificial selection for flowering time, especially in a subtropical region such as Taiwan. This is a good example of introgression playing important roles during rice domestication.
Domestication is the selection process depending on human being’s demand. The domesticated genes ... more Domestication is the selection process depending on human being’s demand. The domesticated genes are the heredity unit to represent these selected traits. We would like to study how diversity the domestication genes and their nearby regions among the rice landraces with widely different characters but all been adopted in Taiwan. Totally 20 rice accessions, ranged from thousands of years to modern varieties which may be classified as landraces, upland races, old varieties and modern elite varieties, of Indica or Japonicarice. After quality control, mapping quality and variant calling quality, the mapped NGS data and BAM files were then transformed to variant calling format, the VCF files. Then we further processed decreasing false negative possibility on SNP-relative non-variant variety. The generic distance among whole genome and domesticated gene region were calculated and analyzed. A total of 25 domesticated genes, including heading day, grain and plant morphology, abiotic toleran...
Several annual and perennial species in the genus Glycine Willd., including G. soja, long-pod G. ... more Several annual and perennial species in the genus Glycine Willd., including G. soja, long-pod G. tomentella, short-pod G. tomentella and G. tabacina, collected in Taiwan and nearby islands were studied for variations of their seed proteins. SDS-PAGE and Western blotting were used to analyze the total proteins, the heat soluble proteins, six seed maturation proteins (GmPMs) and one seed storage
In this study, a novel method for spot detection is proposed with the addition of confidence eval... more In this study, a novel method for spot detection is proposed with the addition of confidence evaluation for each detected spot. The confidence of a spot will give useful hints for subsequent processing such as landmark selection, spot quantification, gel image registration, etc. The proposed method takes slices of a gel image in the gray level direction and build them
Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs ... more Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor 'no apical meristem' (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security.
After reviewing recent evidence from related disciplines arguing for an origin of the Austronesia... more After reviewing recent evidence from related disciplines arguing for an origin of the Austronesian peoples in northeastern China, this paper discusses the Proto-Austronesian and Old Chinese names of the millets, Setaria italica and Panicum miliaceum. Partly based on linguistic data collected in Taiwan by the authors, proposed Proto-Austronesian cognate sets for millet terms are re-evaluated and the Proto-Austronesian sets are identified. The reasons for the earlier confusion among Old Chinese terms for the millets are explained: the Austronesian term for Panicum miliaceum and one of the Chinese terms for the same plant are shown to obey the sound correspondences between Proto-Austronesian and Chinese, earlier described, under a particular resolution of the phonological ambiguities in the oc reconstruction. Possession of the two kinds of millets (not just Setaria, as previously thought) places the pre-Austronesians in northeastern China, adjacent to the probable Sino-Tibetan homeland.
Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mut... more Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D...
Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical da... more Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical day length to get flowering. Sensitivity to photoperiod has been suggested as a major selection target in cultivated or weedy rice. The modern rice varieties in Taiwan may be cultivated twice a year. These varieties contain loss-of-function of two important flowering-time related genes, Heading date 1 (Hd1) and Early heading date 1 (Ehd1), and are mainly from a mega variety, Taichung 65. However, the parental lines of this variety were sensitive to photoperiod, thus, how Taichung 65 loss its sensitivity is a mystery. In this study, we used accession-specific single nucleotide polymorphism analysis to reveal the gene flow that occurred between different rice accessions decades ago and demonstrate that two landraces introgressed during the breeding process, which led to the loss of photoperiod sensitivity. Both Hd1 and Ehd1 may be important during artificial selection for flowering time, especially in a subtropical region such as Taiwan. This is a good example of introgression playing important roles during rice domestication.
Domestication is the selection process depending on human being’s demand. The domesticated genes ... more Domestication is the selection process depending on human being’s demand. The domesticated genes are the heredity unit to represent these selected traits. We would like to study how diversity the domestication genes and their nearby regions among the rice landraces with widely different characters but all been adopted in Taiwan. Totally 20 rice accessions, ranged from thousands of years to modern varieties which may be classified as landraces, upland races, old varieties and modern elite varieties, of Indica or Japonicarice. After quality control, mapping quality and variant calling quality, the mapped NGS data and BAM files were then transformed to variant calling format, the VCF files. Then we further processed decreasing false negative possibility on SNP-relative non-variant variety. The generic distance among whole genome and domesticated gene region were calculated and analyzed. A total of 25 domesticated genes, including heading day, grain and plant morphology, abiotic toleran...
Several annual and perennial species in the genus Glycine Willd., including G. soja, long-pod G. ... more Several annual and perennial species in the genus Glycine Willd., including G. soja, long-pod G. tomentella, short-pod G. tomentella and G. tabacina, collected in Taiwan and nearby islands were studied for variations of their seed proteins. SDS-PAGE and Western blotting were used to analyze the total proteins, the heat soluble proteins, six seed maturation proteins (GmPMs) and one seed storage
In this study, a novel method for spot detection is proposed with the addition of confidence eval... more In this study, a novel method for spot detection is proposed with the addition of confidence evaluation for each detected spot. The confidence of a spot will give useful hints for subsequent processing such as landmark selection, spot quantification, gel image registration, etc. The proposed method takes slices of a gel image in the gray level direction and build them
Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs ... more Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor 'no apical meristem' (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security.
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Papers by Yuan-Ching Tsai