Treatable Traits in Chronic Respiratory Disease: A Comprehensive Review.

Chronic respiratory diseases are major contributors to the global burden of disease. While understanding of these diseases has improved, treatment guidelines have continued to rely on severity and exacerbation-based approaches. A new personalised approach, termed the "treatable traits" approach, has been suggested to address the limitations of the existing treatment strategies. We aim to systematically review the current evidence regarding treatable traits in chronic respiratory diseases and to identify gaps in the current literature. We searched the PubMed and Embase databases and included studies on treatable traits and chronic respiratory diseases. We then extracted information on prevalence, prognostic implications, treatment options and benefits from these studies. A total of 58 papers was included for review. The traits identified were grouped into five broad themes: physiological, biochemical, psychosocial, microbiological, and comorbidity traits. Studies have shown advantages of the treatable traits paradigm in the clinical setting. However, few randomised controlled trials have been conducted. Findings from our review suggest that multidisciplinary management with therapies targeted at treatable traits has the potential to be efficacious when added to the best practices currently implemented. This paradigm has the potential to improve the holistic care of chronic respiratory diseases.

Floral morphs of Justicia adhatoda L. differ in fruit and seed, but not floral, traits or pollinator visitation.

Pigment patterns in corollas are common, and act as nectar guides for pollinators. We discovered multiple floral morphs of Justicia adhatoda L. (Acanthaceae) with variable extents of corolla vein pigmentation in a population in Sariska, Rajasthan. Two floral morphs, one completely white and the other white with dark purple vein pigmentation, were compared in order to investigate any possible differences relating to: (a) corolla surface structure, (b) pollinator visitation, (c) reward for the pollinator, and (d) fitness parameters in the morphs. Both morphs showed similar UV reflectance, had distally located conical cells in petals, indicated similar pollinator visitation and had similar nectar content. Contrastingly, seed germination and seed weight were significantly higher in the purple-veined morph, while fruit set and seed set were higher in the white morph which also showed higher amounts of saturated fatty acids in the seeds. The results about aborted seeds differed inconsistently. Thus, variation in corolla pigmentation in J. adhatoda suggests fitness trade-off between the morphs with higher fruit and seed set, but lower seed germination and seed weight in the white morph compared to the purple-veined. We are led to the possibility of different selective pressures acting on the morphs and resulting in adaptive polymorphism.

Effect of Botanical Extracts on the Growth and Nutritional Quality of Field-Grown White Head Cabbage (Brassica oleracea var. capitata).

Nutraceuticals and functional foods are gaining more attention amongst consumers interested in nutritious food. The consumption of foodstuffs with a high content of phytochemicals has been proven to provide various health benefits. The application of biostimulants is a potential strategy to fortify cultivated plants with beneficial bioactive compounds. Nevertheless, it has not yet been established whether the proposed higher plants (St. John's wort, giant goldenrod, common dandelion, red clover, nettle, and valerian) are appropriate for the production of potential bio-products enhancing the nutritional value of white cabbage. Therefore, this research examines the impact of botanical extracts on the growth and nutritional quality of cabbage grown under field conditions. Two extraction methods were used for the production of water-based bio-products, namely: ultrasound-assisted extraction and mechanical homogenisation. Bio-products were applied as foliar sprays to evaluate their impact on total yield, dry weight, photosynthetic pigments, polyphenols, antioxidant activity, vitamin C, nitrates, micro- and macroelements, volatile compounds, fatty acids, sterols, and sugars. Botanical extracts showed different effects on the examined parameters. The best results in terms of physiological and biochemical properties of cabbage were obtained for extracts from common dandelion, valerian, nettle, and giant goldenrod. When enriched with nutrients, vegetables can constitute a valuable component of functional food.

Magnetic Field Treatments Improves Sunflower Yield by Inducing Physiological and Biochemical Modulations in Seeds.

Magnetic seed enhancement has been practicing as a promising tool to improve germination and seedling growth of low vigor seeds stored under suboptimal conditions, but there is still ambiguity regarding the prospects for magnetism in oilseeds. Present study elucidates the potential of magnetic seed stimulation to improve sunflower germination, growth and yield. Germination and emergence tests were performed to optimize the strength of the magnetic field to sunflower seed enhancement. The seeds were directly exposed to magnetic field strengths of 50, 100 and 150 millitesla (mT) for 5, 10 and 15 min (min) and then standard germination tests were performed. Secondly, the emergence potential of untreated seeds was compared with seed exposed to hydropriming, priming with 3% moringa leaf extract (MLE), priming with magnetically treated water (MTW) for 10 min and priming with 3% MLE solution prepared in magnetically treated water (MTW + MLE). Germination, emergence, seedling growth and seed biochemical properties were used to select the best treatment for field evaluation. The results of the study revealed that magnetic seed treatment with 100 mT for 10 min and seed priming with 3% MLE solution in magnetically treated water (MTW + MLE) significantly improved emergence, crop growth rate and sunflower yield.

Genome-wide association study of fish oil supplementation on lipid traits in 81,246 individuals reveals new gene-diet interaction loci.

Fish oil supplementation is widely used for reducing serum triglycerides (TAGs) but has mixed effects on other circulating cardiovascular biomarkers. Many genetic polymorphisms have been associated with blood lipids, including high- and low-density-lipoprotein cholesterol (HDL-C, LDL-C), total cholesterol, and TAGs. Here, the gene-diet interaction effects of fish oil supplementation on these lipids were analyzed in a discovery cohort of up to 73,962 UK Biobank participants, using a 1-degree-of-freedom (1df) test for interaction effects and a 2-degrees-of-freedom (2df) test to jointly analyze interaction and main effects. Associations with P < 1×10-6 in either test (26,157; 18,300 unique variants) were advanced to replication in up to 7,284 participants from the Atherosclerosis Risk in Communities (ARIC) Study. Replicated associations reaching 1df P < 0.05 (2,175; 1,763 unique variants) were used in meta-analyses. We found 13 replicated and 159 non-replicated (UK Biobank only) loci with significant 2df joint tests that were predominantly driven by main effects and have been previously reported. Four novel interaction loci were identified with 1df P < 5×10-8 in meta-analysis. The lead variant in the GJB6-GJB2-GJA3 gene cluster, rs112803755 (A>G; minor allele frequency = 0.041), shows exclusively interaction effects. The minor allele is significantly associated with decreased TAGs in individuals with fish oil supplementation, but with increased TAGs in those without supplementation. This locus is significantly associated with higher GJB2 expression of connexin 26 in adipose tissue; connexin activity is known to change upon exposure to omega-3 fatty acids. Significant interaction effects were also found in three other loci in the genes SLC12A3 (HDL-C), ABCA6 (LDL-C), and MLXIPL (LDL-C), but highly significant main effects are also present. Our study identifies novel gene-diet interaction effects for four genetic loci, whose effects on blood lipids are modified by fish oil supplementation. These findings highlight the need and possibility for personalized nutrition.

Local adaptation to continuous mowing makes the noxious weed Solanum elaeagnifolium a superweed candidate by improving fitness and defense traits.

The role of disturbance in accelerating weed growth is well understood. While most studies have focused on soil mediated disturbance, mowing can also impact weed traits. Using silverleaf nightshade (Solanum elaeagnifolium), a noxious and invasive weed, through a series of field, laboratory, and greenhouse experiments, we asked whether continuous mowing influences growth and plant defense traits, expressed via different avenues, and whether they cascade into offspring. We found that mowed plants produced significantly less number of fruits, and less number of total seeds per plant, but had higher seed mass, and germinated more and faster. When three herbivores were allowed to feed, tobacco hornworm (Manduca sexta) caterpillars, gained more mass on seedlings from unmowed plants, while cow pea aphid (Aphis craccivora), a generalist, established better on mowed seedlings; however, leaf trichome density was higher on unmowed seedlings, suggesting possible negative cross talk in defense traits. Texas potato beetle (Leptinotarsa texana), a co-evolved specialist on S. elaeagnifolium, did not show any differential feeding effects. We also found that specific root length, an indicator of nutrient acquisition, was significantly higher in first generation seedlings from mowed plants. Taken together, we show that mowing is a selective pressure that enhances some fitness and defense traits and can contribute to producing superweeds.

Multiple-genotypes transcriptional analysis revealed candidates genes and nucleotide variants for improvement of quality characteristics in tea (Camellia sinensis (L.) O. Kuntze).

Tea quality is a polygenic trait that exhibits tremendous genetic variability due to accumulation of array of secondary metabolites. To elucidate global molecular insights controlling quality attributes, metabolite profiling and transcriptome sequencing of twelve diverse tea cultivars was performed in tea shoots harvested during quality season. RP-HPLC-DAD analysis of quality parameters revealed significant difference in catechins, theanine and caffeine contents. Transcriptome sequencing resulted into 50,107 non-redundant transcripts with functional annotations of 81.6% (40,847) of the transcripts. Interestingly, 2872 differentially expressed transcripts exhibited significant enrichment in 38 pathways (FDR ≤ 0.05) including secondary metabolism, amino acid and carbon metabolism. Thirty-eight key candidates reportedly involved in biosynthesis of fatty acid derived volatiles, volatile terpenes, glycoside hydrolysis and key quality related pathways (flavonoid, caffeine and theanine-biosynthesis) were highly expressed in catechins-rich tea cultivars. Furthermore, enrichment of candidates involved in flavonoid biosynthesis, transcriptional regulation, volatile terpene and biosynthesis of fatty acid derived volatile in Protein-Protein Interactome network revealed well-coordinated regulation of quality characteristics in tea. Additionally, ascertainment of 23,649 non-synonymous SNPs and validation of candidate SNPs present in quality related genes suggests their potential utility in genome-wide mapping and marker development for expediting breeding of elite compound-rich tea cultivars.

Genome-wide SNP discovery from Darjeeling tea cultivars - their functional impacts and application toward population structure and trait associations.

Genotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. Elite cultivars of Darjeeling tea were undergone SNP genotyping by double-digest restriction-site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from ~10.4 GB sequence data, encompassing 15 chromosomes of the reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology. A group of 95 genes was identified to be affected by high impact variants. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p < 0.05 and 0.001).

Differential physio-biochemical and yield responses of Camelina sativa L. under varying irrigation water regimes in semi-arid climatic conditions.

Camelina sativa L. is an oilseed crop with wide nutritional and industrial applications. Because of favorable agronomic characteristics of C. sativa in a water-limiting environment interest in its production has increased worldwide. In this study the effect of different irrigation regimes (I0 = three irrigations, I1 = two irrigations, I2 = one irrigation and I3 = one irrigation) on physio-biochemical responses and seed yield attributes of two C. sativa genotypes was explored under semi-arid conditions. Results indicated that maximum physio-biochemical activity, seed yield and oil contents appeared in genotype 7126 with three irrigations (I0). In contrast water deficit stress created by withholding irrigation (I1, I2 and I3) at different growth stages significantly reduced the physio-biochemical activity as well as yield responses in both C. sativa genotypes. Nonetheless the highest reduction in physio-biochemical and yield attributes were observed in genotype 8046 when irrigation was skipped at vegetative and flowering stages of crop (I3). In genotypic comparison, C. sativa genotype 7126 performed better than 8046 under all I1, I2 and I3 irrigation treatments. Because 7126 exhibited better maintenance of tissue water content, leaf gas exchange traits and chlorophyll pigment production, resulting in better seed yield and oil production. Findings of this study suggest that to achieve maximum yield potential in camelina three irrigations are needed under semi-arid conditions, however application of two irrigations one at flowering and second at silique development stage can ensure an economic seed yield and oil contents. Furthermore, genotype 7126 should be adopted for cultivation under water limited arid and semi-arid regions due to its better adaptability.

Major QTLs for Trunk Height and Correlated Agronomic Traits Provide Insights into Multiple Trait Integration in Oil Palm Breeding.

Superior oil yield is always the top priority of the oil palm industry. Short trunk height (THT) and compactness traits have become increasingly important to improve harvesting efficiency since the industry started to suffer yield losses due to labor shortages. Breeding populations with low THT and short frond length (FL) are actually available, such as Dumpy AVROS pisifera (DAV) and Gunung Melayu dura (GM). However, multiple trait stacking still remains a challenge for oil palm breeding, which usually requires 12-20 years to complete a breeding cycle. In this study, yield and height increment in the GM × GM (GM-3341) and the GM × DAV (GM-DAV-3461) crossing programs were evaluated and palms with good yield and smaller height increment were identified. In the GM-3341 family, non-linear THT growth between THT_2008 (seven years old) and THT_2014 (13 years old) was revealed by a moderate correlation, suggesting that inter-palm competition becomes increasingly important. In total, 19 quantitative trait loci (QTLs) for THT_2008 (8), oil per palm (O/P) (7) and FL (4) were localized on the GM-3341 linkage map, with an average mapping interval of 2.01 cM. Three major QTLs for THT_2008, O/P and FL are co-located on chromosome 11 and reflect the correlation of THT_2008 with O/P and FL. Multiple trait selection for high O/P and low THT (based on the cumulative effects of positive alleles per trait) identified one palm from 100 palms, but with a large starting population of 1000-1500 seedling per cross, this low frequency could be easily compensated for during breeding selection.

Morphological and metabolic profiling of a tropical-adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor.

Potato (Solanum tuberosum L.) is one of the world's most important crops, but it is facing major challenges due to climatic changes. To investigate the effects of intermittent drought on the natural variability of plant morphology and tuber metabolism in a novel potato association panel comprising 258 varieties we performed an augmented block design field study under normal irrigation and under water-deficit and recovery conditions in Ica, Peru. All potato genotypes were profiled for 45 morphological traits and 42 central metabolites via nuclear magnetic resonance. Statistical tests and norm of reaction analysis revealed that the observed variations were trait specific, that is, genotypic versus environmental. Principal component analysis showed a separation of samples as a result of conditional changes. To explore the relational ties between morphological traits and metabolites, correlation-based network analysis was employed, constructing one network for normal irrigation and one network for water-recovery samples. Community detection and difference network analysis highlighted the differences between the two networks, revealing a significant correlational link between fumarate and plant vigor. A genome-wide association study was performed for each metabolic trait. Eleven single nucleotide polymorphism (SNP) markers were associated with fumarate. Gene Ontology analysis of quantitative trait loci regions associated with fumarate revealed an enrichment of genes regulating metabolic processes. Three of the 11 SNPs were located within genes, coding for a protein of unknown function, a RING domain protein and a zinc finger protein ZAT2. Our findings have important implications for future potato breeding regimes, especially in countries suffering from climate change.

Genetic variants and underlying mechanisms influencing variance heterogeneity in maize.

Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance-heterogeneity genome-wide association study to examine the contribution of variance heterogeneity to oil-related quantitative traits. We identified 79 unique variance-controlling single nucleotide polymorphisms (vSNPs) from the sequences of 77 candidate variance-heterogeneity genes for 21 oil-related traits using the Levene test (P < 1.0 × 10-5 ). About 30% of the candidate genes encode enzymes that work in lipid metabolic pathways, most of which define clear expression variance quantitative trait loci. Of the vSNPs specifically associated with the genetic variance heterogeneity of oil concentration, 89% can be explained by additional linked mean-effects genetic variants. Furthermore, we demonstrated that gene × gene interactions play important roles in the formation of variance heterogeneity for fatty acid compositional traits. The interaction pattern was validated for one gene pair (GRMZM2G035341 and GRMZM2G152328) using yeast two-hybrid and bimolecular fluorescent complementation analyses. Our findings have implications for uncovering the genetic basis of hidden additive genetic effects and epistatic interaction effects, and we indicate opportunities to stabilize efficient breeding and selection of high-oil maize (Zea mays L.).

Three-dimensional genetic networks among seed oil-related traits, metabolites and genes reveal the genetic foundations of oil synthesis in soybean.

Although the biochemical and genetic basis of lipid metabolism is clear in Arabidopsis, there is limited information concerning the relevant genes in Glycine max (soybean). To address this issue, we constructed three-dimensional genetic networks using six seed oil-related traits, 52 lipid metabolism-related metabolites and 54 294 SNPs in 286 soybean accessions in total. As a result, 284 and 279 candidate genes were found to be significantly associated with seed oil-related traits and metabolites by phenotypic and metabolic genome-wide association studies and multi-omics analyses, respectively. Using minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) analyses, six seed oil-related traits were found to be significantly related to 31 metabolites. Among the above candidate genes, 36 genes were found to be associated with oil synthesis (27 genes), amino acid synthesis (four genes) and the tricarboxylic acid (TCA) cycle (five genes), and four genes (GmFATB1a, GmPDAT, GmPLDα1 and GmDAGAT1) are already known to be related to oil synthesis. Using this information, 133 three-dimensional genetic networks were constructed, 24 of which are known, e.g. pyruvate-GmPDAT-GmFATA2-oil content. Using these networks, GmPDAT, GmAGT and GmACP4 reveal the genetic relationships between pyruvate and the three major nutrients, and GmPDAT, GmZF351 and GmPgs1 reveal the genetic relationships between amino acids and seed oil content. In addition, GmCds1, along with average temperature in July and the rainfall from June to September, influence seed oil content across years. This study provides a new approach for the construction of three-dimensional genetic networks and reveals new information for soybean seed oil improvement and the identification of gene function.

Nutritional and antioxidant components and antioxidant capacity in green morph Amaranthus leafy vegetable.

Amaranth has two morphological types described as red and green morphs. Previous studies have extensively characterised red morph amaranth regarding both morphological and chemical properties including antioxidant activity, antioxidant phytochemical profile, mineral content and proximate composition. However, there is scarce information concerning green morph amaranth. Hence, the present study evaluated 12 green morph genotypes for proximate composition, antioxidant activity, antioxidant pigments, minerals, and phytochemicals. Green morph amaranth was found to contain abundant carbohydrates, dietary fiber and protein. We found notable levels of inorganic minerals including potassium, calcium, magnesium, iron, manganese, copper and zinc. Antioxidant capacity quantified as free radical quenching capacity varied between 27 and 48 µg g-1 Trolox equivalents. We additionally quantified antioxidants, including total phenolics, total flavonoid equivalents and vitamin C, as well as the antioxidant pigments carotenoids, chlorophylls and betalains. These data indicated that four green morph genotypes could be considered as enriched in their antioxidant profiles. Green morph amaranth could be a potential source of nutritional components and antioxidant phytochemicals in the human diet providing opportunities to address mineral nutrient deficiencies and provide an antioxidant rich food.

Nitrogen Fertilizer Levels Affect the Growth and Quality Parameters of Astragalus mongolica.

Owing to overexploitation, wild resources of Astragalus mongolica, a Chinese herbal plant that is widely distributed in the arid and semi-arid areas of Northern China, have gradually become exhausted, and therefore, commercial cultivation is increasingly important to meet the growing demand for astragalus and reduce the pressure on wild populations. Nitrogen level is an important factor that affects the yield and quality of A. mongolica. However, uniform standards for fertilization among production areas have not yet been determined. In this study, the effect of nitrogen fertilizer treatment on the yield and quality of A. mongolica in the Qinghai-Tibet Plateau was explored using a control treatment (no added nitrogen, N0) and five different nutrient levels: 37.5 kg/ha (N1), 75 kg/ha (N2), 112.5 kg/ha (N3), 150 kg/ha (N4), and 187.5 kg/ha (N5). According to grey relational analysis, the optimal nitrogen fertilizer treatment was the N4 level followed by the N5 and N2 levels. Nitrogen fertilizer significantly increased the root biomass, plant height, root length, and root diameter. However, nitrogen fertilization had no significant effect on the content of Astragaloside IV and mullein isoflavone glucoside. The content of ononin and calycosin continually accumulated throughout the growing period. The results showed that the ononin and calycosin content under N4 and N2 is higher than other levels and there is not significantly different between different nitrogen fertilizer levels about them. The content of formononetin decreased gradually with the progression of the growing season. The optimal nitrogen fertilizer treatment for A. mongolica is recommended to be 150 kg/ha and the content of active compounds and yield were observed to reach the maximum in October.

Quantile-Specific Heritability may Account for Gene-Environment Interactions Involving Coffee Consumption.

Estimated heritability of coffee intake ranges from 0.36 to 0.58, however, these point estimates assume that inherited effects are the same throughout the distribution of coffee intake, i.e., whether consumption is high or low relative to intake in the population. Quantile regression of 4788 child-parent pairs and 2380 siblings showed that offspring-parent and sibling concordance became progressively greater with increasing quantiles of coffee intake. Each cup/day increase in the parents' coffee intake was associated with an offspring increase of 0.020 ± 0.013 cup/day at the 10th percentile of the offsprings' coffee intake (slope ± SE, NS), 0.137 ± 0.034 cup/day at their 25th percentile (P = 5.2 × 10-5), 0.159 ± 0.029 cup/day at the 50th percentile (P = 5.8 × 10-8), 0.233 ± 0.049 cup/day at the 75th percentile (P = 1.8 × 10-6), and 0.284 ± 0.054 cup/day at the 90th percentile (P = 1.2 × 10-7). This quantile-specific heritability suggests that factors that distinguish heavier vs. lighter drinkers (smoking, male sex) will likely manifest differences in estimated heritability, as reported.

Polymorphisms of LAP3 gene and their association with the growth traits in the razor clam Sinonovacula constricta.

Leucine aminopeptidase 3 (LAP3) is an important proteolytic enzyme that catalyzes the hydrolysis of leucine residues from the amino termini of protein or peptide substrates and plays a critical role in protein metabolism and growth. In the present study, we investigated the full-length cDNA sequence of the LAP3 gene in Sinonovacula constricta (ScLAP3) using expressed sequence tags and rapid amplification of cDNA ends. The full-length ScLAP3 cDNA was 2885 bp, with a 1560 bp open reading frame encoding 519 amino acids. Sequence analysis revealed that ScLAP3 shared 70.9% identity with LAP3 from the blood clam Tegillarca granosa and 62.0-68.0% with other species. ScLAP3 was expressed in all six tested tissues, with significantly higher expression levels in the foot compared with mantle, adductor muscle, liver, gills, and siphon tissues in adults (P < 0.01). In the eight developmental stages, ScLAP3 expression gradually increased, with significantly higher levels in D-shaped larvae compared with other developmental stages (P < 0.01), suggesting that it may be involved in the formation of certain organs during early development. Association analysis identified three shared single nucleotide polymorphisms (SNPs), c.1073A > G, c.1139C > T and c.1154A > G in exons of ScLAP3 gene from 177 individuals of two groups, one selective strain and one wild population, which had significant effects on growth traits of S. constricta. The results provided candidate genetic markers to assist selective breeding of razor clams toward improved growth.

Natural Variation Reveals a Key Role for Rhamnogalacturonan I in Seed Outer Mucilage and Underlying Genes.

On imbibition, Arabidopsis (Arabidopsis thaliana) seeds release polysaccharides from their epidermal cells that form a two-layered hydrogel, termed mucilage. Analysis of a publicly available data set of outer seed mucilage traits of over 300 accessions showed little natural variation in composition. This mucilage is almost exclusively made up of rhamnogalacturonan I (RGI), highlighting the importance of this pectin for outer mucilage function. In a genome-wide association study, observed variations in polymer amount and macromolecular characteristics were linked to several genome polymorphisms, indicating the complexity of their genetic regulation. Natural variants with high molar mass were associated with a gene encoding a putative glycosyltransferase called MUCILAGE-RELATED70 (MUCI70). muci70 insertion mutants produced many short RGI polymers that were highly substituted with xylan, confirming that polymorphism in this gene can affect RGI polymer size. A second gene encoding a putative copper amine oxidase of clade 1a (CuAOα1) was associated with natural variation in the amount of RGI present in the outer mucilage layer; cuaoα1 mutants validated its role in pectin production. As the mutant phenotype is unique, with RGI production only impaired for outer mucilage, this indicates that CuAOα1 contributes to a further mechanism controlling mucilage synthesis.

The bracteatus pineapple genome and domestication of clonally propagated crops.

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding.

To obtain genetic information about the germplasm of tea (Camellia sinensis L.) in Japan, 167 accessions including 138 var. sinensis (96 Japanese var. sinensis and 42 exotic var. sinensis) and 29 Assam hybrids were analyzed using single nucleotide polymorphisms (SNPs) markers identified by double-digest restriction-site-associated DNA sequencing (ddRAD-seq) analysis. Approximately 10,000 SNPs were identified by ddRAD-seq and were mapped across the whole genome. The 167 tea accessions were classified into three genetic subgroups: (1) Japanese var. sinensis; (2) Japanese and exotic var. sinensis; (3) Assam hybrids and exotic var. sinensis. Leaf morphology varied widely within each genetic subgroups. The 96 Japanese var. sinensis were classified into four genetic subgroups as follows; two subgroups of Shizuoka (the largest tea production region) landraces, Uji (most ancient tea production region) landraces, and the pedigree of 'Yabukita', the leading green tea cultivar in Japan. These results indicated that the SNP markers obtained from ddRAD-seq are a useful tool to investigate the geographical background and breeding history of Japanese tea. This genetic information revealed the ancestral admixture situation of the 'Yabukita' pedigree, and showed that the genome structure of 'Yabukita' is clearly different from those of other Japanese accessions.