Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties DOI Creative Commons
Clizia Villano, Silvia Procino, Giuseppe Blaiotta

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Sept. 13, 2023

Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence spontaneous somatic mutations played pivotal role shaping diverse landscape agrobiodiversity. These naturally occurring selections, termed 'clones,' represent vast reservoir potentially valuable traits and alleles that hold promise for enhancing grape quality bolstering plant resilience against environmental biotic challenges. Despite their potential, many these clones remain largely untapped.In light this context, study aims delve into population structure, genetic diversity, distinctive loci within collection 138 derived from six Campanian Apulian varieties, known desirable attributes viticulture winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis fixation index (FST) calculations were conducted both between populations at individual loci. Notably, varieties originating same geographical region exhibited pronounced similarity.The resulting SNP dataset facilitated identification approximately hundred featuring divergent markers (FST ≥ 0.80) annotated exons. Several associations with essential like phenotypic adaptability responsiveness, offering compelling opportunities breeding initiatives. By shedding on inherent treasured traditional grapevines, our contributes broader understanding potential. Importantly, it underscores urgency preserving characterizing resources safeguard intra-varietal diversity foster future advancements cultivation.

Language: Английский

Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity DOI Creative Commons
Manyi Sun, Mingyue Zhang, Xuening Chen

et al.

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: Aug. 19, 2022

Abstract Background The mitochondrion is an important cellular component in plants and that functions producing vital energy for the cell. However, evolution structure of mitochondrial genomes (mitogenomes) remain unclear Rosaceae family. In this study, we assembled 34 mitogenomes characterized genome variation, rearrangement rate, selection signal variation within these mitogenomes. Results Comparative analysis six genera from Amygdaloideae five Rosoideae subfamilies revealed three protein-coding genes were absent genera. Positive correlations between size repeat content identified 38 Twenty repeats with high recombination frequency (> 50%) provided evidence predominant substoichiometric conformation Variations rates eleven genera, Pyrus , Malus Prunus Fragaria Based on population data, phylogenetic inferences supported two distinct maternal lineages Asian cultivated pears. A -specific deletion (DEL-D) selective sweeps was based data. After DEL-D sequence fragments originally arose, they may have experienced a subsequent doubling event via homologous transfer Amygdaloideae; afterwards, variant significantly expanded to groups, thereby improving adaptation during domestication process. Conclusions This study characterizes variations gene content, size, impact provides insights into their structural patterns relationships.

Language: Английский

Citations

41
Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness DOI Creative Commons
Songtao Jiu,

Zhengxin Lv,

Moyang Liu

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(7)

Published: June 21, 2024

Chinese cherry (

Language: Английский

Citations

10
Unraveling the extensive phylogenetic discordance and evolutionary history of spurless taxa within the Aquilegia ecalcarata complex DOI Open Access
Huijie Liu,

Baocai Han,

Hong-Lin Mou

et al.

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Parallel evolution of the same, or at least very similar, phenotype(s) in different lineages is often interpreted as evidence for action natural selection. However, caution required when inferring parallel based on uncertain potentially incorrect phylogenetic frameworks. Here, by conducting extensive phylogenomic and population genetic analyses, we aim to clarify evolutionary history spurless taxa within Aquilegia ecalcarata complex. We observed substantial discordance patterns across entire genome, primarily attributed ancient introgression incomplete lineage sorting. Additionally, identified several whose positions were distorted admixture events. Using a backbone tree demographic modeling, determined that these independently originated twice this group. Intriguingly, our investigation revealed experienced expansion during global cooling, while their spurred sister groups underwent contraction. The losses petal spurs, therefore, may be linked adaptations low-temperature conditions. These findings emphasize importance comprehensive population-level analyses inference provide valuable insights into dynamics trait loss its implications adaptive strategies.

Language: Английский

Citations

1
Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe) DOI Creative Commons
Ticao Zhang, Qin Qiao, Xiao Du

et al.

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 64(8), P. 1487 - 1501

Published: June 24, 2022

Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide de novo chromosome-level genome sequence the cultivar "Qiu Jinxing." We assembled 823.41 Mb encoding 40 571 genes further anchored 779.24 into 17 pseudo-chromosomes, which account 94.64% genome. Phylogenomic analyses revealed that cultivated diverged from other species within Maleae (apple tribe) at approximately 35.4 Mya. Notably, involved flavonoid triterpenoid biosynthetic pathways have been significantly amplified In addition, our results indicated share unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected hawthorn. The amplification non-specific terminal repeat retrotransposons contributed most to expansion Furthermore, identified two paleo-sub-genomes extant found these sub-genomes showed different rearrangement mechanisms. also reconstructed ancestral chromosomes Rosaceae discussed possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) Maleae. Overall, study provides improved context understanding evolution species, this new high-quality reference useful resource horticultural improvement

Language: Английский

Citations

31
Multiomics analyses of the effects of LED white light on the ripening of apricot fruits DOI Creative Commons

Chunmei Bai,

Yanyan Zheng, Christopher B. Watkins

et al.

Journal of Advanced Research, Journal Year: 2024, Volume and Issue: 67, P. 1 - 13

Published: Jan. 9, 2024

Apricot (Prunus armeniaca L.) fruits are highly perishable and prone to quality deterioration during storage transportation. To investigate the effects of LED white light treatment on postharvest ripening using metabolomics, transcriptomics, ATAC-Seq analysis. Fruits were exposed 5 μmol m-2 s-1 for 12 hours followed by darkness at 20 °C daily days. The treatments physiological nutritional evaluated. These data combined with transcriptomic, metabolomic, from taken Day 8 provide insight into potential mechanism which delays ripening. activated pathways involved in ascorbate aldarate metabolism flavonoid phenylpropanoid biosynthesis. Specifically, increased expression UDP-sugar pyrophosphorylase (USP), L-ascorbate peroxidase (AO), dihydroflavonol 4-reductase (DFR), chalcone synthase (CHS), caffeoyl-CoA O-methyltransferase (CCOAOMT1), leading accumulation caffeoyl quinic acid, epigallocatechin, dihydroquercetin activation anthocyanin also affected genes associated plant hormone signal transduction, fruit texture color transformation, antioxidant activity. notable included 1-aminocyclopropane-1-carboxylate (ACS), oxidase (ACO), hexokinase (HK), lipoxygenase (LOX), malate dehydrogenase (MDH), endoglucanase (CEL), various transcription factors (TCP, MYB, EFR), (POD). analysis further revealed that primarily regulated results obtained this study insights exposure apricot LEDs offer a promising approach extending shelf life other vegetables.

Language: Английский

Citations

7
Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets DOI Creative Commons
Roberta Gargiulo, Véronique Decroocq, Santiago González

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(5)

Published: May 1, 2024

Abstract Effective population size ( N e ) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate have been preferred over demographic because they rely on genetic data rather than time‐consuming ecological monitoring. Methods based linkage disequilibrium (LD), particular, become popular as require single sampling provide estimates that refer recent generations. A software program the LD method, GONE, looks particularly promising contemporary recent‐historical (up 200 generations past). Genomic datasets from non‐model species, especially plants, may present some constraints use of maps reference genomes are seldom available, SNP genotyping usually reduced‐representation methods. In this study, we empirical four plant species explore limitations genomic when estimating using algorithm implemented addition exploring typical biological affect estimation such occurrence structure. We show how accuracy precision potentially change following factors: missing data, limited number SNPs/individuals sampled, lack information about location SNPs chromosomes, latter producing significant bias, previously unexplored data. finally compare obtained GONE for last programs currentNe NeEstimator.

Language: Английский

Citations

7
Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature DOI Creative Commons

Lian-Ying Shen,

Hang Luo,

Xiaoling Wang

et al.

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: Nov. 24, 2021

Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour (

Language: Английский

Citations

35
Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication DOI
Ya‐Mei Ding, Yu Cao, Wei‐Ping Zhang

et al.

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: July 4, 2022

Language: Английский

Citations

27
Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat DOI Creative Commons
Danlong Jing, Xinya Liu, Qiao He

et al.

Horticulture Research, Journal Year: 2022, Volume and Issue: 10(2)

Published: Dec. 2, 2022

Abstract Wild loquats (Eriobotrya japonica Lindl.) provide remarkable genetic resources for studying domestication and breeding improved varieties. Herein, we generate the first high-quality chromosome-level genome assembly of wild loquat, with 45 791 predicted protein-coding genes. Analysis comparative genomics indicated that loquat shares a common ancestor apple pear, recent whole-genome duplication event occurred in prior to its divergence. Genome resequencing showed germplasms can be distinctly classified into cultivated groups, commercial cultivars have experienced allelic admixture. Compared loquats, very few selected genomic regions had higher levels diversity. However, scans selective sweeps were mainly related fruit quality, size, flesh color during process. Large-scale transcriptome metabolome analyses further performed identify differentially expressed genes (DEGs) accumulated metabolites (DAMs) at various development stages. Unlike those key DEGs DAMs involved carbohydrate metabolism, plant hormone signal transduction, flavonoid biosynthesis, carotenoid biosynthesis significantly regulated development. These reference genome, resequencing, large-scale transcriptome/metabolome data valuable elucidating molecular loquat.

Language: Английский

Citations

27
The Domestication and Dispersal of Large-Fruiting Prunus spp.: A Metadata Analysis of Archaeobotanical Material DOI Creative Commons
Rita Dal Martello, Madelynn von Baeyer, Mark Hudson

et al.

Agronomy, Journal Year: 2023, Volume and Issue: 13(4), P. 1027 - 1027

Published: March 30, 2023

The Prunus genus contains many of the most economically significant arboreal crops, cultivated globally, today. Despite economic significance these domesticated species, pre-cultivation ranges, processes domestication, and routes prehistoric dispersal for all species remain unresolved. Among European plums, even taxonomic classification has been heavily debated over past several decades. In this manuscript, we compile archaeobotanical evidence prominent large-fruiting members Prunus, including peach, apricot, almonds, sloes, main plum types. By mapping out chronology geographic distributions are able to discuss aspects their domestication more clearly, as well identify gaps in data unanswered questions. We suggest that a clearer understanding will say lot about ancient peoples, cultivation delayed return crops is an indicator strong concept land tenure specialization strategies seems be tied urbanism reliable markets. Likewise, evolution traits long-generation perennials, especially within Rosaceae, represents awareness grafting cloning practices.

Language: Английский

Citations

16