Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

The complete chloroplast genome of Actinidia latifolia, a species with high vitamin C content in fruit

Actinidia latifolia, known for its high vitamin C content in fruits, is widely distributed in the subtropical and tropical regions of eastern and southern Asia. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. latifolia to investigate its phylogenetic position in the gunus Actinidia. The complete cp genome sequence is 156,873 bp in length with 37.15% overall GC content and characterized by a typical quadripartite structure comprising one pair of inverted repeats (23,377 bp) separated by a small single-copy region (21,453 bp) and a large single-copy region (88,666 bp). The cp genome contains 132 unique genes, including 83 protein coding genes, 41 tRNA genes, and 8 rRNA genes. Phylogenetic analysis highly supported that A. latifolia evolutionarily close to A. eriantha

Comparative Transcriptome Analysis Revealed the Key Genes Regulating Ascorbic Acid Synthesis in Actinidia

Actinidia (kiwifruit) is known as ‘the king of vitamin C’ due to its rich ascorbic acid (AsA) concentration, which makes it an important model for studying the regulation of AsA metabolism. Herein, transcriptomic analysis was employed to identify candidate genes that regulate AsA synthesis in Actinidia species with 100-fold variations in fruit AsA content (A. latifolia and A. rufa). Approximately 1.16 billion high-quality reads were generated, and an average of 66.68% of the data was uniquely aligned against the reference genome. AsA-associated DEGs that predominately respond to abiotic signals, and secondary metabolic pathways were identified. The key candidate genes, for instance, GDP-L-galactose phosphorylase-3 (GGP3), were explored according to integrated analysis of the weighted gene co-expression network and L-galactose pathway. Transgenic kiwifruit plants were generated, and the leaves of GGP3 (OE-GGP3) overexpressing lines had AsA contents 2.0- to 6.4-fold higher than those of the wild type. Transcriptomic analysis of transgenic kiwifruit lines was further implemented to identify 20 potential downstream target genes and understand GGP3-regulated cellular processes. As a result, two transcription factors (AcESE3 and AcMYBR) were selected to carry out yeast two-hybrid and BiFC assays, which verified that there were obvious AcESE3–AcMYBR and AcESE3–AcGGP3 protein–protein interactions. This study provides insight into the mechanism of AsA synthesis and provides candidate factors and genes involved in AsA accumulation in kiwifruit

Comprehensive Analysis of Metabolome and Transcriptome in Fruits and Roots of Kiwifruit

Kiwifruit (Actinidia chinensis) roots instead of fruits are widely used as Chinese medicine, but the functional metabolites remain unclear. In this study, we conducted comparative metabolome analysis between root and fruit in kiwifruit. A total of 410 metabolites were identified in the fruit and root tissues, and of them, 135 metabolites were annotated according to the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway. Moreover, 54 differentially expressed metabolites (DEMs) were shared in root and fruit, with 17 DEMs involved in the flavonoid pathway. Of the 17 DEMs, three flavonols (kaempferol-3-rhamnoside, L-Epicatechin and trifolin) and one dihydrochalcone (phloretin) showed the highest differences in the content level, suggesting that flavonols and dihydrochalcones may act as functional components in kiwifruit root. Transcriptome analysis revealed that genes related to flavonols and dihydrochalcones were highly expressed in root. Moreover, two AP2 transcription factors (TFs), AcRAP2-4 and AcAP2-4, were highly expressed in root, while one bHLH TF AcbHLH62 showed extremely low expression in root. The expression profiles of these TFs were similar to those of the genes related to flavonols and dihydrochalcones, suggesting they are key candidate genes controlling the flavonoid accumulation in kiwifruit. Our results provided an insight into the functional metabolites and their regulatory mechanism in kiwifruit root

Phylogenetic relationship and characterization of the complete chloroplast genome of Actinidia callosa var. strigillosa

Actinidia callosa var. strigillosa is one of the endangered Actinidia species scattering across mountain areas in southwest China. Here, we assembled and characterized the complete chloroplast (cp) genome sequence of A. strigillosa to provide genomic resources for its identification, conservation and utilization. The cp genome is 155,957 bp in length, containing a pair of 23,119 bp inverted repeat (IR) regions, which is separated by a large single copy region (LSC) of 89,429 bp and a small single copy region (SSC) of 20,290 bp. A total of 132 genes were annotated in this cp genome, including 83 protein-coding genes, 41 tRNA genes and 8 rRNA genes. The phylogenetic position of A. strigillosa based the cp genome data was sister to the group A. deliciosa and A. chinensis

Characterizing Tetraploid Populations of <i>Actinidia chinensis</i> for Kiwifruit Genetic Improvement

Understanding genetic diversity and structure in natural populations and their suitable habitat response to environmental changes is critical for the protection and utilization of germplasm resources. We evaluated the genetic diversity and structure of 24 A. chinensis populations using simple sequence repeat (SSR) molecular markers. The potential suitable distribution of tetraploid A. chinensis estimated under the current climate and predicted for the future climate was generated with ecological niche modeling (ENM). The results indicated that the polyploid populations of A.chinensis have high levels of genetic diversity and that there are distinct eastern and western genetic clusters. The population structure of A. chinensis can be explained by an isolation-by-distance model. The results also revealed that potentially suitable areas of tetraploids will likely be gradually lost and the habitat will likely be increasingly fragmented in the future. This study provides an extensive overview of tetraploid A. chinensis across its distribution range, contributing to a better understanding of its germplasm resources. These results can also provide the scientific basis for the protection and sustainable utilization of kiwifruit wild resources

Agronomic Trait Variations and Ploidy Differentiation of Kiwiberries in Northwest China: Implication for Breeding

Polyploid plants often have higher biomass and superior crop qualities. Breeders therefore search for crop germplasm with higher ploidy levels; however, whether higher ploidy levels are associated with better performance remains unclear. Actinidia arguta and related species, whose commercialized fruit are referred to as kiwiberries, harbor a series of ploidy races in nature, offering an opportunity to determine the link between ploidy levels and agronomic traits. In the present study, we determined the ploidy levels of A. arguta var. arguta, A. arguta var. giraldii, and A. melanandra in 16 natural populations using flow cytometry, and examined 31 trait variations in fruits, leaves and flowers by field observations, microscopic examination and laboratory analyses. Our results showed that octaploid and decaploid A. arguta var. giraldii had larger dimension of leaves than tetraploid A. arguta var. arguta and A. melanandra, but their fruits were significantly smaller. In addition, A. arguta var. giraldii (8x and 10x) had higher contents of nutrients such as ascorbic acid and amino acids; however, some important agronomic traits, including the content of total sugar and total acid, were significantly lower in the octaploids and decaploids. Moreover, octaploids and decaploids did not result in greater ecological adaptability for the challenging environments and climates. In conclusion, the differentiation of ecological adaptability and traits among natural kiwiberries' cytotypes suggested that higher ploidy levels are not inevitably advantageous in plants. The findings of A. arguta and related taxa in geographical distribution and agronomic trait variations will facilitate their germplasm domestication

Maturity, Ripening and Quality of ‘Donghong’ Kiwifruit Evaluated by the Kiwi-Meter™

Traditional destructive fruit assessment methodologies are currently being replaced by non-destructive alternatives. The Kiwi-Meter™ is promoted as a non-destructive device for assessment of kiwifruit maturation and ripening. In this study, three trials evaluated the feasibility of using the Kiwi-Meter and its IAD™ index data for monitoring maturation, ripening, and quality of Actinidia chinensis var. chinensis ‘Donghong’ kiwifruit. The findings from the trials suggest that the Kiwi-Meter provides a non-destructive tool for measuring the color or chlorophyll content of the outer tissues of ‘Donghong’ kiwifruit. Since the timing of harvest of kiwifruit is not determined solely by flesh color, the utility of the Kiwi-Meter in any wider evaluation of fruit maturation (or ripening or quality) is dependent on there being a strong association between other fruit characteristics of interest with flesh color. The ‘Donghong’ fruit used in this trial degreened fully before ripening and thus the Kiwi-Meter could not provide a measure of maturation, ripening, or fruit quality. It is concluded that the Kiwi-Meter can assess fruit for flesh color, although even for this purpose, it must be considered that the IAD measurement may be limited to only the outer area of the fruit flesh