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Purpose: Site-specific modeling with consideration of land-use types is required to evaluate the effectiveness of different farming practices on organic carbon (OC) sequestration by soil. In this study, a comprehensive model for different cropland types fitting to the relationship between bulk density (Bd) and OC was used to evaluate carbon sequestration by soil. Materials and methods: Six cropland sites for crop cultivation (i.e., lettuce, lisianthus, pineapple, multigrain, tea, and coffee) in southwest Taiwan were utilized for illustration. The linear (L) and exponential decay (ED) models fL(x) and fED(x) were fitted to the relationship between Bd and OC. The integrations of fL(x) and fED(x) associated with site-specific boundaries DL* and DED* were in expression as FL*(x) and FED*(x), respectively to predict OC stock (OCS) for each cropland site. Results and discussion: The results showed a significantly negative correlation between Bd and OC. According to the validation results, the site-specific predictions of OCS by both FL*(x) and FED*(x) were reliable for the cropland sites. Also, further OC sequestration to increase OCS by 0.4% in a 20-cm depth of soil would more efficiently occur in deeper soil than in upper soil. Current practices for cultivating lisianthus, tea, and coffee, increasing OC would be more conservational and result in a significantly decreasing Bd trend. Conclusions: In contrast, croplands for the cultivation of lettuce, multigrain, and pineapple, which have much less OC saturation, could efficiently increase OCS by 0.4% in a 20-cm soil depth for further OC sequestration. [ABSTRACT FROM AUTHOR]

The genus Sorghum consists of 25 species, including Sorghum bicolor (L.) Moench, one of the top five cereal crops cultivated globally, and S. halepense, one of the most noxious weeds. Weedy Sorghum possesses outstanding adaptability and drought tolerance thrives in diverse environments and becomes an invasive plant worldwide. Taiwan is a unique place possessing suitable habitats for four Sorghum taxa, S. bicolor ssp. bicolor, var. technicum, ssp. verticilliflorum and S. halepense, which were identified by key morphological features. The four Sorghum taxa showed distinct geographic distributions, revealing that invasiveness was influenced by their own characteristics and human activities. The sporadic distributions of cultivated S. bicolor ssp. bicolor and var. technicum may be attributed to human disturbance and agricultural activities. The rhizomatous S. halepense was widely distributed and showed the highest genetic diversity (He > 0.776) among the four taxa, with its strong adaptation to various environments threatening the agricultural practices and ecosystem in Taiwan. In contrast, the newly naturalised S. bicolor ssp. verticilliflorum was confined to and dominant in southern Taiwan, with the lowest genetic diversity (He < 0.272). Significant genetic differentiation (FST = 0.5207) between the two ssp. verticilliflorum subpopulations was associated with natural geographic isolation. This study concretely elucidated the geographic distributions, genetic diversity and relatedness of invasive and escaped Sorghum taxa, indicating the potential aggressiveness and hazard of weedy Sorghum in Taiwan. [ABSTRACT FROM AUTHOR]

Rice domestication/adaptation is a good model for studies of the development and spread of this important crop. Mutations that caused morphological and physiological change, followed by human selection/expansion, finally led to the improvement of phenotypes suitable for different kinds of environments. We used the sequence information for Heading date 1 (Hd1) gene to reveal the association between sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes had been reported. By data-mining the genome sequencing information in the public domain, we discovered 3 other types. These loss-of-function allele haplotypes are present in subtropical and tropical regions, which indicates human selection. Some of these haplotypes are present locally. However, types 7 and 13 are present in more than one-third of the world's rice accessions, including landraces and modern varieties. In the present study, phylogenetic, allele network and selection pressure analyses revealed that these two haplotypes might have occurred early in Southeastern Asia and then were introgressed in many local landraces in nearby regions. We also demonstrate that these haplotypes are present in weedy rice populations, which again indicates that these alleles were present in rice cultivation for long time. In comparing the wild rice sequence information, these loss-of-function haplotypes occurred in agro but were not from wild rice. [ABSTRACT FROM AUTHOR]

Foxtail millet (Setaria italica (L.) P. Beauv.), the second most cultivated millet species, is well adapted to diverse environments and remains an important cereal food and forage crop in arid and semiarid regions worldwide. A symbolic crop for indigenous Austronesian peoples, foxtail millet has been cultivated in Taiwan for more than 5,000 years, and landraces reflect diversifying selection for various food applications. A total of 124 accessions collected within Taiwan were assessed for Wx genotypes. Four identified Wx alleles, I, III, IV, and IX were caused by insertion of various transposable elements (TEs) and resulted in endosperm with non-waxy, low amylose content (AC), and waxy, respectively. A total of 16.9%, 4.0%, 49.2%, and 29.8% of accessions were classified as type I, III, IV, and IX, respectively; approximately half of the accessions belonged to the waxy type, indicating that glutinous grains were favored for making traditional food and wine. The TE insertion affected splicing efficiency rather than accuracy, leading to significantly reduced expression of wx in types III, IV, and IX, although their transcripts were the same as wild-type, type I. Consequently, the granule-bound starch synthase I (GBSSI) contents of the three mutated genotypes were relatively low, leading to waxy or low AC endosperm, and the Wx genotypes could explain 78% of variance in AC. The geographic distribution of Wx genotypes are associated with culinary preferences and migration routes of Taiwanese indigenous peoples—in particular, the genotype of landraces collected from Orchid Island was distinct from those from Taiwan Island. This information on the major gene regulating starch biosynthesis in foxtail millet endosperm can be applied to breeding programs for grain quality, and contributes to knowledge of Austronesian cultures. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Archaeobotanical remains of millet were found at the Nan-kuan-li East site in Tainan Science Park, southern Taiwan. This site, dated around 5000-4300 BP, is characterized by remains of the Tapenkeng culture, the earliest Neolithic culture found so far in Taiwan. A large number of millet-like carbonized and charred seeds with varied sizes and shapes were unearthed from the site by the flotation method. Since no millet grain was ever found archaeologically in Taiwan previously, this discovery is of great importance and significance. This paper is in an attempt to further analyze these plant remains for a clearer understanding of the agricultural practice of the ancient inhabitants of the Nan-kuan-li East site. Result: We used light and scanning electron microscopy to examine the morphological features of some modern domesticated and unearthed seeds to compare and identify the archaeobotanical remains by three criteria: caryopsis shape, embryo notch, and morphology of lemma and palea. We also developed a new methodology for distinguishing the excavated foxtail and broomcorn millet seeds. Conclusion: Two domesticated millet, including broomcorn millet ( Panicum miliaceum) and foxtail millet ( Setaria italica), as well as one wild millet species, yellow foxtail ( Setaria glauca), were identified in the unearthed seeds. Together with the millet remains, rice was also cultivated in the area. Archaeological evidence shows that millet and rice farming may have been important food sources for people living about 5000 years ago in southern Taiwan. [ABSTRACT FROM AUTHOR]

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 D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations. [ABSTRACT FROM AUTHOR]

The repeat sequences occupied more than 50 % of soybean genome. In order to understand where these repeat sequences distributed in soybean genome and its related Glycine species, we examined three new repeat sequences-soybean repeat sequence (SBRS1, SBRS2 and SBRS3), some nonspecific repeat sequences and 45S rDNA on several Glycine species, including annual and perennial accessions in this study. In the annual species, G. soja, signals for SBRS1 and ATT repeat can be found on each chromosome in GG genome, but those for SBRS2 and SBRS3 were located at three specific loci. In perennial Glycine species, these three SBR repeat frequently co-localized with 45S rDNA, two major 45S rDNA loci were found in all tetraploid species. However, an extra minor locus was found in one accession of the G. pescadrensis (Tab074), but not in another accession (Tab004). We demonstrate that some repetitive sequences are present in all Glycine species used in the study, but the abundancy is different in annual or perennial species. We suggest this study may provide additional information in investigations of the phylogeny in the Glycine species. [ABSTRACT FROM AUTHOR]

The repeat sequences occupied more than 50 % of soybean genome. In order to understand where these repeat sequences distributed in soybean genome and its related Glycine species, we examined three new repeat sequences-soybean repeat sequence (SBRS1, SBRS2 and SBRS3), some nonspecific repeat sequences and 45S rDNA on several Glycine species, including annual and perennial accessions in this study. In the annual species, G. soja, signals for SBRS1 and ATT repeat can be found on each chromosome in GG genome, but those for SBRS2 and SBRS3 were located at three specific loci. In perennial Glycine species, these three SBR repeat frequently co-localized with 45S rDNA, two major 45S rDNA loci were found in all tetraploid species. However, an extra minor locus was found in one accession of the G. pescadrensis (Tab074), but not in another accession (Tab004). We demonstrate that some repetitive sequences are present in all Glycine species used in the study, but the abundancy is different in annual or perennial species. We suggest this study may provide additional information in investigations of the phylogeny in the Glycine species. [ABSTRACT FROM AUTHOR]

Foxtail millet is considered a 'smart food' because of nutrient richness and resilience to environments. A diversity panel of 92 foxtail millet landraces preserved by Taiwan indigenous peoples containing amylose content (AC) in the range of 0.7% to 16.9% exhibited diverse physiochemical properties revealed by a rapid viscosity analyzer (RVA). AC was significantly correlated with 5 RVA parameters, and some RVA parameters were also highly correlated with one another. In comparison to rice, foxtail millet contained less starch (65.9–73.1%) and no significant difference in totals of resistant starch (RS), slowly digestible starch (SDS), hydrolysis index (HI), and expected glycemic index (eGI) according to in vitro digestibility assays of raw flour with similar AC. RS was significantly positively correlated with AC and four RVA parameters, cold paste viscosity (CPV), setback viscosity (SBV), peak time (PeT), and pasting temperature (PaT), implying that suitable food processing to alter physicochemical properties of foxtail millet might mitigate hyperglycemia. This investigation of pasting properties and digestibility of diverse foxtail millet germplasm revealed much variation and showed potential for multi-dimensional utilizations in daily staple food and food industries. [ABSTRACT FROM AUTHOR]

Background: Endosperm is a triploid tissue in seed resulting from a sperm nucleus fused with the binucleate central cell after double fertilization. Endosperm may be involved in metabolite production, solute transport, nutrient storage, and germination. In the legume family (Fabaceae), with the greatest number of domesticated crops, approximately 60% of genera contain well-differentiated endosperm in mature seeds. Soybean seeds, the most important legume crop in the worlds, have endosperm surrounding embryos during all stages of seed development. However, the function of soybean endosperm is still unknown. Results: Flow cytometry assay confirmed that soybean endosperm was triploid. Cytobiological observation showed that soybean endosperm cells were alive with zigzag-shape cell wall. Soybean endosperm cells allowed fusion proteins (42 kDa) to move from bombarded cells to adjacent unbombarded-cells. Such movement is not simple diffusion because the fusion proteins failed to move into dead cells. We used symplastic tracers to test the transport potential of soybean endosperm. Small organic dye and low-molecular-weight symplastic tracers revealed fast symplastic transport. After a treatment of an inhibitor of ATPase, N,N′-dicyclohexylcarbodiimide (DCCD), symplastic transport was blocked, but all tracers still showed fast apolopastic transport. The transport speed of 8-hydroxypyrene-1,3,6-trisulfonic acid in endosperm was 1.5 to 3 times faster than in cotyledon cells or Arabidopsis embryos. Conclusions: Soybean endosperm is a membrane-like, semi-transparent, and fully active tissue located between the seed coat and cotyledon. Soybean endosperm cells allowed macromolecules to move fast via plasmodesmata transport. The size exclusion limit is larger for soybean endosperm cells than its cotyledon or even Arabidopsis embryo cells. Soybean endosperm may be involved in fast and horizontal transport during the mid-developmental stage of seeds. [ABSTRACT FROM AUTHOR]

Background: Rice (Oryza sativa) is one of the main crops in the world, and more than 3.9 billion people will consume rice by 2025. Sterility significantly affects rice production and leads to yield defects. The undeveloped anthers or abnormal pollen represent serious defects in rice male sterility. Therefore, understanding the mechanism of male sterility is an important task. Here, we investigated a rice sterile mutant according to its developmental morphology and transcriptional profiles. Results: An untagged T-DNA insertional mutant showed defective pollen and abnormal anthers as compared with its semi-sterile mutant (sstl) progeny segregates. Transcriptomic analysis of sterile sstl-s revealed several biosynthesis pathways, such as downregulated cell wall, lipids, secondary metabolism, and starch synthesis. This downregulation is consistent with the morphological characterization of sstl-s anthers with irregular exine, absence of intine, no starch accumulation in pollen grains and no accumulated flavonoids in anthers. Moreover, defective microsporangia development led to abnormal anther locule and aborted microspores. The downregulated lipids, starch, and cell wall synthesis-related genes resulted in loss of fertility. Conclusions: We illustrate the importance of microsporangia in the development of anthers and functional microspores. Abnormal development of pollen grains, pollen wall, anther locule, etc. result in severe yield reduction. [ABSTRACT FROM AUTHOR]

Background: Genetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. Three main models for the origins of the Taiwanese Neolithic have been proposed: origins in coastal north China (Shandong); in coastal central China (Yangtze Valley), and in coastal south China. A combination of linguistic and agricultural evidence helps resolve this controversial issue.Results: We report on botanically informed linguistic fieldwork of the agricultural vocabulary of Formosan aborigines, which converges with earlier findings in archaeology, genetics and historical linguistics to assign a lesser role for rice than was earlier thought, and a more important one for the millets. We next present the results of an investigation of domestication genes in a collection of traditional rice landraces maintained by the Formosan aborigines over a hundred years ago. The genes controlling awn length, shattering, caryopsis color, plant and panicle shapes contain the same mutated sequences as modern rice varieties everywhere else in the world, arguing against an independent domestication in south China or Taiwan. Early and traditional Formosan agriculture was based on foxtail millet, broomcorn millet and rice. We trace this suite of cereals to northeastern China in the period 6000-5000 BCE and argue, following earlier proposals, that the precursors of the Austronesians, expanded south along the coast from Shandong after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. This expansion introduced to Taiwan a mixed farming, fishing and intertidal foraging subsistence strategy; domesticated foxtail millet, broomcorn millet and japonica rice; a belief in the sacredness of foxtail millet; ritual ablation of the upper incisors in adolescents of both sexes; domesticated dogs; and a technological package including inter alia houses, nautical technology, and loom weaving.Conclusion: We suggest that the pre-Austronesians expanded south along the coast from that region after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]