Genomic insights into genetic diversity and seed coat color change in common bean composite populations

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

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Advances in Global Oyster Reef Restoration: Innovations and Sustainable Ecological Approaches

Sustainability, Journal Year: 2024, Volume and Issue: 16(22), P. 9795 - 9795

Published: Nov. 10, 2024

Oysters have been recognized as ecological engineers for aquatic ecosystems, oyster reefs provide critical habitats and foraging locations other marine species. In the past few decades, anthropogenic activities negatively impacted reef ecosystems across globe, resulting in a significant decline their population. This review critically examines causes extent of degradation, well effectiveness restoration initiatives employed to reverse this decline. Furthermore, evaluates strategies rehabilitate reefs. Different approaches, such genetic improvement, suitable site selection, seeding enhance restorations, are reviewed paper. some advanced approaches 3D printing, shell recycling, acoustics technologies also discussed paper, which opens new doors researchers field ecology. Challenges barriers hindering successful addressed, including financial constraints, regulatory complexities, public engagement. The findings insights presented herein contribute growing body knowledge on ecology serve valuable resource policymakers, scientists, conservation practitioners seeking effective restoring these vital coastal ecosystems.

Language: Английский

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CgPPOX and CgFECH Mediate Protoporphyrin IX Accumulation Predominantly in the Outer Mantle Fold of Pacific Oyster Crassostrea gigas

Marine Biotechnology, Journal Year: 2025, Volume and Issue: 27(1)

Published: Feb. 1, 2025

Language: Английский

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Correlation between SNPs in promoter region of gene, L-Type lectin (LvLTLC1) and the resistance trait of shrimp, Litopenaeus vannamei, against vibrios

Aquaculture Reports, Journal Year: 2025, Volume and Issue: 41, P. 102725 - 102725

Published: March 1, 2025

Language: Английский

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Identification of genes associated with pan-vibrios resistance (PVR) trait of shrimp Litopenaeus vannamei through Genome-wide association study

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 13, 2025

Vibriosis caused by various Vibrio species is the most serious bacterial disease of shrimp. Due to prevalence pathogenic vibrios, genetic breeding shrimps with pan-vibrios resistance (PVR) trait has more practical significance for successful shrimp farming. To explore loci associated PVR Litopenaeus vannamei, a genome-wide association study (GWAS) aiming at was conducted using 300 individuals from sources. After stringent screening, 243 single nucleotide polymorphisms (SNPs) corresponding selection threshold -log10(p) value ≥ 2.5 were evaluated their trait. Twenty candidate SNPs in genes and upstream region (≤ 5000 bp) screened out further validation association. The genotypes three (SNP15, SNP16, SNP17) different between G1 (uninfected) G4/G5 groups (seriously infected), among which GG genotype SNP15 significantly low vibrios load. combination GG-TT-AA linked, it strongest performance Notably, found located intron gene, LvCthrc1. can lead disappearance donor splicing site LvCthrc1, predictably generates novel transcript affecting gene function. highest expression level LvCthrc1 observed immune-related tissues such as hemocytes, gills, hepatopancreas. This first put forward concept provides valuable molecular markers on shrimp, L. vannamei.

Language: Английский

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Genomic prediction of growth traits in autotetraploid Pacific oyster (Crassostrea gigas) using whole-genome resequencing

Aquaculture, Journal Year: 2024, Volume and Issue: 593, P. 741259 - 741259

Published: June 21, 2024

Language: Английский

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