Identification of Selective Sweeps in the Domesticated Table and Wine Grape (Vitis vinifera L.)

Proteome-Wide Identification of Non-histone Lysine Methylation during Grape Berry Ripening

To gain a comprehensive understanding of non-histone methylation during berry ripening in grape (Vitis vinifera L.), the methylation of non-histone lysine residues was studied using a 4D label-free quantitative proteomics approach. In total, 822 methylation sites in 416 methylated proteins were identified, with xxExxx_K_xxxxxx as the conserved motif. Functional annotation of non-histone proteins with methylated lysine residues indicated that these proteins were mostly associated with "ripening and senescence", "energy metabolism", "oxidation-reduction process", and "stimulus response". Most of the genes encoding proteins subjected to methylation during grape berry ripening showed a significant increase in expression during maturation at least at one developmental stage. The correlation of methylated proteins with QTLs, SNPs, and selective regions associated with fruit quality and development was also investigated. This study reports the first proteomic analysis of non-histone lysine methylation in grape berry and indicates that non-histone methylation plays an important role in grape berry ripening.

Genomic and evolutionary relationships among wild and cultivated blueberry species

BACKGROUND

Blueberries (Vaccinium section Cyanococcus) are an economically important fruit crop in the United States. Understanding genetic structure and relationships in blueberries is essential to advance the genetic improvement of horticulturally important traits. In the present study, we investigated the genomic and evolutionary relationships in 195 blueberry accessions from five species (comprising 33 V. corymbosum, 14 V. boreale, 81 V. darrowii, 29 V. myrsinites, and 38 V. tenellum) using single nucleotide polymorphisms (SNPs) mined from genotyping-by-sequencing (GBS) data.

RESULTS

GBS generated ~ 751 million raw reads, of which 79.7% were mapped to the reference genome V. corymbosum cv. Draper v1.0. After filtering (read depth > 3, minor allele frequency > 0.05, and call rate > 0.9), 60,518 SNPs were identified and used in further analyses. The 195 blueberry accessions formed three major clusters on the principal component (PC) analysis plot, in which the first two PCs accounted for 29.2% of the total genetic variance. Nucleotide diversity (π) was highest for V. tenellum and V. boreale (0.023 each), and lowest for V. darrowii (0.012). Using TreeMix analysis, we identified four migration events and deciphered gene flow among the selected species. In addition, we detected a strong V. boreale lineage in cultivated blueberry species. Pairwise SweeD analysis identified a wide sweep (encompassing 32 genes) as a strong signature of domestication on the scaffold VaccDscaff 12. From this region, five genes encoded topoisomerases, six genes encoded CAP-gly domain linker (which regulates the dynamics of the microtubule cytoskeleton), and three genes coded for GSL8 (involved in the synthesis of the cell wall component callose). One of the genes, augustus_masked-VaccDscaff12-processed-gene-172.10, is a homolog of Arabidopsis AT2G25010 and encodes the protein MAINTENANCE OF MERISTEMS-like involved in root and shoot growth. Additional genomic stratification by admixture analysis identified genetic lineages and species boundaries in blueberry accessions. The results from this study indicate that V. boreale is a genetically distant outgroup, while V. darrowii, V. myrsinites, and V. tenellum are closely related.

CONCLUSION

Our study provides new insights into the evolution and genetic architecture of cultivated blueberries.

Genome-wide diversity analysis suggests divergence among Upper Guinea and the Dahomey Gap populations of the Sisrè berry (Syn: miracle fruit) plant (Synsepalum dulcificum [Schumach. & Thonn.] Daniell) in West Africa

Although Synsepalum dulcificum is viewed as one of the most economically promising orphan tree crops worldwide, its genetic improvement and sustainable conservation are hindered by a lack of understanding of its evolutionary history and current population structure. Here, we report for the first time the application of genome-wide single nucleotide polymorphism genotyping to a diverse panel of S. dulcificum accessions to depict the genetic diversity and population structure of the species in the Dahomey Gap (DG) and Upper Guinea (UG) regions to infer its evolutionary history. Our findings suggest low overall genetic diversity but strong population divergence within the species. Neighbor-joining analysis detected two genetic groups in the UG and DG regions, while STRUCTURE distinguished three genetic groups, corresponding to the UG, Western DG, and Central DG regions. Application of Monmonier's algorithm revealed the existence of a barrier disrupting connectivity between the UG and DG groups. The Western DG group consistently exhibited the highest levels of nucleotide and haplotype diversities, while that of the Central DG exhibited the lowest. Analyses of Tajima's D, Fu's Fs, and Achaz Y* statistics suggest that while both UG and Central DG groups likely experienced recent expansions, the Western DG group is at equilibrium. These findings suggest a geographical structuring of genetic variation which supports the conclusion of differential evolutionary histories among West African groups of S. dulcificum. These results provide foundational insights to guide informed breeding population development and design sustainable conservation strategies for this species.

Whole-genome re-sequencing, diversity analysis, and stress-resistance analysis of 77 grape rootstock genotypes

INTRODUCTION

Grape rootstocks play critical role in the development of the grape industry over the globe for their higher adaptability to various environments, and the evaluation of their genetic diversity among grape genotypes is necessary to the conservation and utility of genotypes.

METHODS

To analyze the genetic diversity of grape rootstocks for a better understanding multiple resistance traits, whole-genome re-sequencing of 77 common grape rootstock germplasms was conducted in the present study.

RESULTS

About 645 billion genome sequencing data were generated from the 77 grape rootstocks at an average depth of ~15.5×, based on which the phylogenic clusters were generated and the domestication of grapevine rootstocks was explored. The results indicated that the 77 rootstocks originated from five ancestral components. Through phylogenetic, principal components, and identity-by-descent (IBD) analyses, these 77 grape rootstocks were assembled into ten groups. It is noticed that the wild resources of V. amurensis and V. davidii, originating from China and being generally considered to have stronger resistance against biotic and abiotic stresses, were sub-divided from the other populations. Further analysis indicated that a high level of linkage disequilibrium was found among the 77 rootstock genotypes, and a total of 2,805,889 single nucleotide polymorphisms (SNPs) were excavated, GWAS analysis among the grape rootstocks located 631, 13, 9, 2, 810, and 44 SNP loci that were responsible to resistances to phylloxera, root-knot nematodes, salt, drought, cold and waterlogging traits.

DISCUSSION

This study generated a significant amount of genomic data from grape rootstocks, thus providing a theoretical basis for further research on the resistance mechanism of grape rootstocks and the breeding of resistant varieties. These findings also reveal that China originated V. amurensis and V. davidii could broaden the genetic background of grapevine rootstocks and be important germplasm used in breeding high stress-resistant grapevine rootstocks.

Effect of ultrasound assisted cleaning on pesticide removal and quality characteristics of Vitis vinifera leaves

In this study, the pesticide (acetamiprid, deltamethrin, and pyridaben) removal and physicochemical quality improvement of vine (Vitis vinifera) leaf were examined using ultrasonic and traditional cleaning for 5, 10, and 15 min. After an ultrasonic cleaning procedure at 37 kHz for 10 min, acetamiprid, deltamethrin, and pyridaben in vine leaf were reduced by 54.76, 58.22, and 54.55 %, respectively. Furthermore, the total phenolic content (TPC) in vine leaf increased to 13.45 mg GAE/g DW compared to that in control samples using traditional cleaning (10.37 mg GAE/g DW), but there were no significant differences in DPPH radical scavenging activity. After 15 min of conventional cleaning, the total chlorophyll and total carotenoid content of leaves were found to be lowest among all samples, at 6.52 mg/kg and 0.48 mg/kg, respectively. In conclusion, when compared to conventional cleaning methods, ultrasonic cleaning with no chemicals or heat treatment has proven to be a successful and environmentally friendly application in reducing commonly used pesticides and improving the physicochemical qualities of leaves.

Responses of soil respiration and microbial community structure to fertilizer and irrigation regimes over 2 years in temperate vineyards in North China

Fertilizer and irrigation regimes can profoundly affect soil carbon (C) emissions, which influence soil organic carbon (SOC) storage. However, information regarding the effects of fertilizer and irrigation management on the components of soil respiration (Rs) and the underlying microbial community characteristics in vineyard ecosystems remains limited. Therefore, a 2-year field experiment was conducted in a wine-grape vineyard (WGV) and a table-grape vineyard (TGV). Each vineyard included two fertilizer and irrigation regimes: farmers' practice (FP) and recommended practice (RP). The trenching method was employed to separate Rs into heterotrophic respiration (Rh) and autotrophic respiration (Ra). Additionally, the SOC storage and soil microbial community structure at 0-20 cm soil depth were determined after the 2-year experiment. The results showed that the fertilizer and irrigation regimes caused no effect on Ra. Compared with the FP treatment in WGV and TGV, the RP treatment significantly (P < 0.05) decreased the average daily Rh by 15.13 % and 17.11 %, which contributed to the annual Rs values at the whole-vineyard scale decreased by 8.93 % and 11.78 %, respectively. Besides, compared with the initial value, the SOC storage under RP treatment were effectively increased by 6.39 % and 6.33 % in WGV and TGV, respectively. Low annual total Rh was partially ascribed to the significant (P < 0.05) decline in Proteobacteria and Bacteroidetes relative abundance, thus reducing the decomposition rate of SOC. Compared with WGV, the fertilizer and water input was higher in the TGV, which resulted in the annual total Rs and Rh values at the whole-vineyard scale was increased by 11.53 % and 15.74 %, respectively, while the annual total Ra was decreased by 18.83 % due to the lower grapevine density and more frequent summer pruning. Overall, RP treatment was found to be a suitable strategy for reducing soil C emissions and benefiting SOC storage in vineyards around North China.

Large-scale discovery of non-conventional peptides in grape (Vitis vinifera L.) through peptidogenomics

Non-conventional peptides (NCPs), which are peptides derived from previously unannotated coding sequences, play important biological roles in plants. In this study, we used peptidogenomic methods that integrated mass spectrometry (MS) peptidomics and a six-frame translation database to extensively identify NCPs in grape. In total, 188 and 2021 non-redundant peptides from the Arabidopsis thaliana and Vitis vinifera L. protein database at Ensembl/URGI and an individualized peptidogenomic database were identified. Unlike conventional peptides, these NCPs derived mainly from intergenic, intronic, upstream ORF, 5'UTR, 3'UTR, and downstream ORF regions. These results show that unannotated regions are translated more broadly than we thought. We also found that most NCPs were derived from regions related to phenotypic variations, LTR retrotransposons, and domestication selection, indicating that the NCPs have an important function in complex biological processes. We also found that the NCPs were developmentally specific and had transient and specific functions in grape berry development. In summary, our study is the first to extensively identify NCPs in grape. It demonstrated that there was a large amount of translation in the genome. These results lay a foundation for studying the functions of NCPs and also provide a reference for the discovery of new functional genes in grape.

Pip shape echoes grapevine domestication history

The pip, as the most common grapevine archaeological remain, is extensively used to document past viticulture dynamics. This paper uses state of the art morphological analyses to analyse the largest reference collection of modern pips to date, representative of the present-day diversity of the domesticated grapevine from Western Eurasia. We tested for a costructure between the form of the modern pips and the: destination use (table/wine), geographical origins, and populational labels obtained through two molecular approaches. Significant structuring is demonstrated for each of these cofactors and for the first time it is possible to infer properties of varieties without going through the parallel with modern varieties. These results provide a unique tool that can be applied to archaeological pips in order to reconstruct the spatio-temporal dynamics of grape diversity on a large scale and to better understand viticulture history. The models obtained were then used to infer the affiliations with archaeobotanical remains recovered in Mas de Vignoles XIV (Nîmes, France). The results show a twofold shift between the Late Iron Age and the Middle Ages, from table to wine grape varieties and from eastern to western origins which correlates with previous palaeogenomic results.

Aerobic training, resistance training, or their combination as a means to fight against excess weight and metabolic syndrome in obese students - which is the most effective modality? A randomized controlled trial

This study aimed to determine the effects of either aerobic training (AT) or resistance training (RT) or both (A+RT) on obesity and its comorbidities in young adults. A total of 61 participants, aged 21.74 ± 1.42 years and with a body mass (BM) index (BMI) of 36.21 ± 2.43 kg/m², were randomized for 12 weeks into control (CONT, n = 15), AT (n = 15), RT (n = 16), and A+RT (n = 15) groups. BM, body composition, and cardiovascular disease risk factors were assessed before and after intervention. BM did not change in the CONT and RT groups but decreased significantly by 7.5 kg in the AT (p ≤ 0.05) and 8.82 kg in the A+RT (p ≤ 0.05) groups, respectively. Significant reductions were also noted in waist circumference, BMI, and body fat percentage in the exercising groups. The most significant variations were in the A+RT group. High-density lipoprotein cholesterol (HDL-C) concentrations were increased after A+RT by 2.39 mg/dL. Significant reductions were also noted in very-low-density lipoprotein cholesterol (VLDL-C) concentrations (-2.84 mg/dL) in the A+RT group. AT alone is effective in improving BM and body composition, while RT alone improves the body composition and A+RT ensures better outcomes concerning BM, body composition, HDL-C, and VLDL-C. Novelty: Aerobic training alone is effective in improving BM and body composition. Resistance training alone improves the body composition. The combination of aerobic and resistance exercises ensures better outcomes for BM, body composition, HDL-C, and VLDL-C.

High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)

Kochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (FST = 0.01) and no correlation between genetic and geographic distance (r2 = - 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species' genetic variation or limit the species' ability to respond to further selection pressure.