Evolutionary history and rhizosphere microbial community composition in domesticated hops (Humulus lupulus L.) DOI Creative Commons

Alexandra McElwee‐Adame,

Raya Esplin‐Stout,

Trevor Mugoya

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 2, 2024

Abstract Humulus lupulus L. , commonly known as hops, is a perennial crop grown worldwide and well for its pharmacological, commercial, most importantly brewing applications. For hundreds of years, hops have undergone intense artificial selection with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such bitter acid concentrations, flavor aroma profiles, changes photoperiod, growth, pathogen/pest resistances. Previous studies individually explored between cultivars, aiming to identify markers that can quickly cost-effectively differentiate cultivars. However, little about their evolutionary history the variability associated rhizospheric microbial communities. Coupling phenotypic, genomic, soil metagenomic data, our study aims explore global population structure domestication 98 Additionally, we assessed growth rates, rates viral infection, usage dissolvable nitrogen, community compositions US non-US based Contrary previous studies, revealed hop cultivars cluster into four primary subpopulations; Central European, English, American ancestry previously reported, one new group, Nobles, revealing further substructure amongst European Modeling domesticated reveals an early divergence common ancestors modern around 2800 ybp, more recent divergences gene flow across Noble reconciled events human migrations. Furthermore, origin were shown overall outperform both nitrogen display novel composition.

Language: Английский

Solanum pan-genetics reveals paralogues as contingencies in crop engineering DOI Creative Commons
Matthias Benoit, Katharine M. Jenike, James W. Satterlee

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

Language: Английский

Citations

2
Abscission in plants: from mechanism to applications DOI Creative Commons

Jiahuizi Li,

Shihao Su

Advanced Biotechnology, Journal Year: 2024, Volume and Issue: 2(3)

Published: Aug. 9, 2024

Abscission refers to the natural separation of plant structures from their parent plants, regulated by external environmental signals or internal factors such as stress and aging. It is an advantageous process it enables plants shed unwanted organs, thereby regulating nutrient allocation ensuring dispersal fruits seeds parent. However, in agriculture horticulture, abscission can severely reduce crop quality yield. In this review, we summarize recent advances perspectives developmental molecular biology, emphasizing diverse regulatory networks across different lineages, model crops. The sophisticated involves several overlapping steps, including differentiation zone, activation abscission, tissue detachment, formation a protective layer. Finally, discuss potential applications physiological modifications genetic manipulations sustainable future.

Language: Английский

Citations

6
Genomic insights into genetic diversity and seed coat color change in common bean composite populations DOI Creative Commons
Eva Plestenjak, Mohamed Neji, Lovro Sinkovič

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 24, 2025

Introduction The color of the seed coat common bean ( Phaseolus vulgaris L.) is an important trait influencing marketability and consumer preferences. An understanding genetic mechanisms underlying variation can aid in breeding programs aimed at improving esthetic agronomic traits. This study investigates diversity molecular associated with change composite populations through phenotypic analysis whole genome sequencing (WGS). Methods Four two standard varieties were cultivated over a two-year period morphological traits assessed. WGS was performed on 19 phenotypes yielded 427 GB data average depth 30×. More than 8.6 million high-confidence single nucleotide polymorphisms (SNPs) identified. Genetic metrics such as (π), observed heterozygosity (Ho), expected (He) allelic richness (Ar) calculated. Population structure analyzed using Fst, principal component (PCA) clustering. Cross-population statistics (XP-CLR XP-EHH) used to identify selection signals change. Gene Ontology (GO) KEGG enrichment analyzes for candidate genomic regions. Results Phenotypic revealed significant differences among four populations, notable changes years. exhibited different growth habits plant types, especially KIS_Amand SRGB_00366, which showed highest color. identified SNPs, chromosomes 4 1 having SNP density (11% each), while 3 6 had lowest. (π = 0.222, Ar 1.380) SRGB_00189 lowest 0.067, 1.327). SRGB_00366 moderate 0.173, 1.338) INCBN_03048 medium 0.124, 1.047). Fst values indicated strong differentiation, between ETNA Golden_Gate (Fst 0.704) populations. Selective sweep XP-CLR XP-EHH 118 regions change, most located 4, 9, 10 11. Phosphatidylinositol signaling pathways highly enriched regions, indicating that cellular transport play critical role pigmentation. Key GO terms included phosphatidylinositol-biphosphate binding, exocytosis, vesicle-mediated transport, suggesting link pigment deposition coat. Discussion demonstrates within exhibiting variability. identification selective sweeps phosphatidylinositol-related provide new insights into controlling variation. differentiation highlights shaping landscape bean. results suggest controlled by both regulatory structural changes, providing valuable information programs. Conclusion provides detailed architecture key pigmentation improves our complex interactions this trait. These resources future efforts other

Language: Английский

Citations

0
Direct and interactive effects of crop domestication and mineral fertilization over leaf traits: insights from squash, maize, and beans DOI
Jorge Ruiz‐Arocho,

Nicholas Steinthal,

Eric von Wettberg

et al.

Genetic Resources and Crop Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: March 20, 2025

Language: Английский

Citations

0
Wild vs. cultivated strawberries: differential fruit quality traits and antioxidant properties in Fragaria chiloensis and Fragaria × ananassa DOI Creative Commons
Melina Fernanda Chamorro,

Ariel Omar Mazzoni,

María Natalia Lescano

et al.

Discover Food, Journal Year: 2025, Volume and Issue: 5(1)

Published: March 21, 2025

Language: Английский

Citations

0
Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.) DOI Creative Commons

Alexandra McElwee‐Adame,

Raya Esplin‐Stout,

Trevor Mugoya

et al.

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 24, 2025

ABSTRACT Humulus lupulus L ., commonly known as hop, is a perennial crop grown worldwide and well for its pharmacological, commercial, most importantly brewing applications. For hundreds of years, hop has undergone intense artificial selection, with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such bitter acid concentrations, flavour aroma profiles, changes photoperiod, growth, pathogen/pest resistances. Previous studies have individually explored between cultivars, aiming to identify markers that can quickly cost‐effectively differentiate cultivars. However, little about their evolutionary history the variability associated rhizospheric microbial communities. Coupling phenotypic, genomic, soil metagenomic data, our study explores global population structure domestication 98 We assessed growth rates, rates viral infection, usage dissolvable nitrogen, community compositions US non‐US based Our revealed cultivars cluster into four subpopulations: Central European, English, American ancestry previously reported, one new group, Nobles, revealing further substructure amongst European Modelling domesticated reveals divergence common ancestors modern around 2800 years before present (ybp), more recent divergences gene flow across Noble reconciled events human migrations. Furthermore, origin were shown overall outperform both nitrogen display novel composition under common‐garden settings United States.

Language: Английский

Citations

0
Independent domestication and cultivation histories of two West African indigenous fonio millet crops DOI Creative Commons
Thomas Kaczmarek, Philippe Cubry, Louis Champion

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 30, 2025

Crop evolutionary history and domestication processes are key issues for better conservation effective use of crop genetic diversity. Black white fonio (Digitaria iburua D. exilis, respectively) two small indigenous grain cereals grown in West Africa. The relationship between these cultivated crops wild Digitaria species is still unclear. Here, we analyse whole genome sequences 265 accessions comprising their close relatives. We show that black were the result independent domestications without gene flow. infer a cultivation expansion began at outset CE era, coinciding with earliest discovered archaeological remains Nigeria. Fonio population sizes declined few centuries ago, probably due to combination several factors, including major social agricultural changes, intensification slave trade introduction new, less labour-intensive crops. knowledge genomic resources outlined here will help promote conserve neglected climate-resilient thereby provide an opportunity tailor agriculture changing world.

Language: Английский

Citations

0
Current Insights into Weak Seed Dormancy and Pre-Harvest Sprouting in Crop Species DOI Creative Commons
Ángel J. Matilla

Plants, Journal Year: 2024, Volume and Issue: 13(18), P. 2559 - 2559

Published: Sept. 12, 2024

During the domestication of crops, seed dormancy has been reduced or eliminated to encourage faster and more consistent germination. This alteration makes cultivated crops particularly vulnerable pre-harvest sprouting, which occurs when mature are subjected adverse environmental conditions, such as excessive rainfall high humidity. Consequently, some seeds may bypass normal period begin germinate while still attached mother plant before harvest. Grains affected by sprouting characterized increased levels α-amylase activity, resulting in poor processing quality immediate grain downgrading. In agriculture industry, causes annual economic losses exceeding USD 1 billion worldwide. premature germination is influenced a complex interplay genetic, biochemical, molecular factors closely linked conditions like rainfall. However, exact mechanism behind this process unclear. Unlike vivipary refers activation during soft dough stage, grains immature. Mature with ABA impaired signaling (weak dormancy) susceptible sprouting. While can enhance resistance it lead undesirable outcomes for most non-uniform seedling establishment after sowing. Thus, crucial ensuring productivity sustainability an agronomically important trait affecting yield quality. On other hand, color resistance; however, genetic relationship between both characteristics remains unresolved. The identification mitogen-activated protein kinase kinase-3 (MKK3) gene responsible sprouting-1 (Phs-1) represents significant advancement our understanding how wheat controlled at levels. maturation, Viviparous-1 (Vp-1) plays role managing regulating maturation inhibiting through suppression proteases. Vp-1 key player essential program. Mutants exhibit unpigmented aleurone cell layer precocious due decreased sensitivity ABA. Recent research also revealed that TaSRO-1 interacts TaVp-1, contributing regulation wheat. goal review emphasize latest on suggest possible directions future studies.

Language: Английский

Citations

3
GENOMIC ANALYSES REVEAL A LACK OF WIDESPREAD STRONG SELECTION IN INDIGENOUS CHICKENS DOI Creative Commons
Zilong Wen, Xinyu Cai, Zexuan Liu

et al.

Poultry Science, Journal Year: 2025, Volume and Issue: unknown, P. 105081 - 105081

Published: March 1, 2025

The study of domestication has been revolutionized with the advent molecular genetics. Chickens, their clear history, emerge as an excellent model for into paths evolution in and improvement. Here we used genomic data from wild, indigenous, commercial chickens to better understand how genetic drift selection translate differentiations. Our investigation patterns allelic change divergence reveals a polygenic architecture governing differentiation during We uncover distinctive population-specific differentiations terms genes functions among chickens. Using Runs Of Homozygosity (ROH) based mixed approach developed this study, identified only directional signatures occurring wild Notably, our findings suggest that indigenous serve reservoirs diversity, necessary rapid adaptation new environments or subsequent modern breeding. This work provides unprecedented insights chicken improvement, it illuminates understanding other animal species.

Language: Английский

Citations

0
Cis-regulatory dynamics in plant domestication DOI
Xiang Li, Robert J. Schmitz

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

0