Molecular Mechanisms of Heterosis and Its Applications in Tree Breeding: Progress and Perspectives DOI Open Access
Zeyu Li, Yan Zhao,

Keming Luo

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(22), P. 12344 - 12344

Published: Nov. 17, 2024

Heterosis, or hybrid vigor, refers to the phenomenon where progenies outperform their parents in traits such as yield and resistance. This has been widely applied plant breeding. Recent advances high-throughput genomics have significantly advanced our understanding of heterosis. review systematically summarizes genetic, molecular, epigenetic mechanisms underlying Furthermore, we discuss recent predictive methods for heterosis applications improving growth rate, resistance abiotic stresses, wood tree species. We also explore role unraveling heterosis, emphasizing potential integrating high-resolution genomics, single-cell sequencing, spatial transcriptomics achieve a comprehensive from molecular levels. Building on this, CRISPR-based gene-editing technologies can be employed precisely edit heterotic loci, enabling study allele function. Additionally, marker-assisted selection (MAS) utilized identify loci parental lines, facilitating optimal combinations reducing labor time costs Finally, utilization breeding provide forward-looking perspective future research directions, highlighting multi-omics approaches emerging tools revolutionize

Language: Английский

Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors DOI Creative Commons
Wenbo Chen, Qi Xie, Jia Fu

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 9, 2025

Abstract Background Fruit acidity and color are important quality attributes in peaches. Although there some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid regulation Results Here, we report peach graph-based pangenome constructed from sixteen individual genome assemblies, capturing abundant structural 82.3 Mb of sequences absent reference genome. Pangenome analysis reveals long terminal repeat retrotransposon insertion promoter NAC transcription factor (TF) PpBL peaches, which enhances expression . Genome-wide association study identifies significant between malate content. Silencing fruit ectopic overexpression tomatoes confirm that positive regulator accumulation. Furthermore, demonstrate works synergistically with another TF, PpNAC1, to activate aluminum-activated transporter PpALMT4 , leading increased Conclusions These findings, along previous research showing PpNAC1 also regulate anthocyanin accumulation, explain red coloration taste fruits.

Language: Английский

Citations

1
CentIER: accurate centromere identification for plant genome DOI Creative Commons
Dong Xu,

Jinbao Yang,

Huaming Wen

et al.

Plant Communications, Journal Year: 2024, Volume and Issue: 5(10), P. 101046 - 101046

Published: Aug. 8, 2024

This paper introduces CentIER, the first bioinformatic tool designed to detect complete centromeric regions without additional wet experiments. The accuracy of CentIER was validated on diverse plant genomes such as Arabidopsis, rice, maize and mulberry, results show that can perform significantly more accurate detection than existing tool.

Language: Английский

Citations

6
Chromosome-scale assembly of European flax (Linum usitatissimum L.) genotypes and pangenomic analysis provide genomic tools to improve breeding DOI
Boris B. Demenou,

Adama Ndar,

Christophe Pineau

et al.

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

Published: March 7, 2025

Abstract Decoding the genome of cultivated species is one key starting points for supporting marker-assisted selection to accelerate breeding programmes. To date, five six flax genotypes, including fiber flax, linseed and related wild mainly from Canada, China Russia, have been sequenced assembled. But no assembly was available Western European cultivar, although France world's leading producer (85% world production). The Canadian oilseed cultivars CDC Bethune used as reference studies activities. best date Chinese Yiya5 assembly, which had metric all assemblies available. Recent analyses shown that up 30% reads different origins do not map genome. Thus, much genetic information could be neglected using a reference. aim this study sequence, assemble annotate genomes four (two Bolchoï Idéo; two Marquise Attila) provide pangenome genotype characterization breeding. From 21 46 Gb ONT Minion long sequence data were -sequenced - assembled Flye, -polished, validated organised into hybrid scaffolds 100 197 optical (Bionano Genomics), finally anchored fifteen T2T pseudomolecules each assembly. final size reached 437, 441, 442 453 Mb Idéo, Marquise, Attila respectively. annotated ab initio predictions genomic sequences evidence transcriptomic data. A graph constructed ten cultivars, previous publicly (CDC Bethune, Longya10 Line 3896, Heiya-14, Atlant). total 835.77 Mbp (74,123 non-redundant orthologous proteins) with core 172.2 Mbp. resources generated development tools useful breeders improve efficiency variety evaluation.

Language: Английский

Citations

0
The Telomere-to-telomere genome of Pucai (蒲菜) (Typha angustifolia L.), a distinctive semi-aquatic vegetable with lignin and chlorophyll as quality characteristics DOI Creative Commons
Yapeng Li, Liyao Su, Ting Huang

et al.

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(7)

Published: March 11, 2025

Abstract Pucai () (Typha angustifolia L.), within the Typha spp., is a distinctive semiaquatic vegetable. Lignin and chlorophyll are two crucial traits quality indicators for Pucai. In this study, we assembled 207.00-Mb high-quality gapless genome of Pucai, telomere-to-telomere (T2T) level with contig N50 length 13.73 Mb. The most abundant type repetitive sequence, comprising 16.98% genome, long terminal repeat retrotransposons (LTR-RT). A total 30 telomeres 15 centromeric regions were predicted. Gene families related to lignin, biosynthesis, disease resistance greatly expanded, which played important roles in adaptation wetlands. slow evolution was indicated by σ whole-genome duplication (WGD)-associated Ks peaks from different Poales low activity recent LTR-RT Meanwhile, found unique WGD event Typhaceae. statistical analysis annotation genomic variations conducted interspecies intraspecies Typha. Based on T2T constructed lignin metabolic pathways Subsequently, candidate structural genes transcription factors that regulate biosynthesis identified. resources will provide molecular information accumulation help understand

Language: Английский

Citations

0
Telomere‐to‐telomere genome assembly reveals insights into the adaptive evolution of herbivore‐defense mediated by volatile terpenoids in Oenanthe javanica DOI Creative Commons
Kai Feng, Jialu Liu, Nan Sun

et al.

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: March 20, 2025

Releasing large quantities of volatiles is a defense strategy used by plants to resist herbivore attack. Oenanthe javanica, perennial herb the Apiaceae family, has distinctive aroma due volatile terpenoid accumulation. At present, complete genome and genetic characteristics terpenoids in O. javanica remain largely unclear. Here, telomere-to-telomere with size 1012.13 Mb contig N50 49.55 Mb, was established combining multiple sequencing technologies. Comparative analysis revealed that experienced recent species-specific whole-genome duplication event during evolutionary process. Numerous gene family expansions were significantly enriched biosynthesis process, monoterpenoid, diterpenoid pathways, which resulted abundant substance accumulation javanica. The showed repellent effects on herbivores. Terpenoid activated wounding signals under exogenous stimuli. TPS expanded compared those other species, members (OjTPS1, OjTPS3, OjTPS4, OjTPS5, OjTPS7, OjTPS16, OjTPS18, OjTPS30 OjTPS58) responsible for different functionally characterized. These results reveal evolution molecular process plant-herbivore interactions. This study also provides genomic resources biology research plants.

Language: Английский

Citations

0
Haplotype-resolved genome assembly provides insights into the genetic basis of green peach aphid resistance in peach DOI Creative Commons
Haixiang Yu, Jian Guo, Xuelian Wu

et al.

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Green peach aphid (GPA) is one of the most destructive pests peach, threatening both growth and fruit quality. However, mechanism underlying GPA resistance remains unclear. Here, we performed haplotype-resolved genome assembly a GPA-resistant cultivar identified an allele-specific expressed gene, PpNLR1, responsible for trait. A genome-wide association study (GWAS) revealed functional 20-bp insertion or deletion (indel) in PpNLR1 promoter, which co-segregated with trait directly influenced promoter activity. Furthermore, jasmonate (JA) signaling, activated during infestation, induced transcription PpERF109. This factor specifically bound to "CAAGT" motif within GWAS-identified resulting expression (ASE). Functional validation two alleles (PpNLR1-Hap1 PpNLR1-Hap2) Arabidopsis demonstrated their role resistance. Additionally, salivary proteins were as effectors, triggering reactive oxygen species (ROS) activating immune system conjunction protein. Comparative genomics phylogenetic analysis indicated that ∼53.6-kb genomic variation surrounding underwent negative selection evolution. In conclusion, JA-mediated PpERF109-PpNLR1 module effector significantly contribute peach. The novel key genes provide valuable resources future research breeding

Language: Английский

Citations

0
Comprehensive insights on association mapping in perennial fruit crops breeding - its implications, current status and future perspectives DOI
Ashwini Zadokar, Parul Sharma, Rajnish Sharma

et al.

Plant Science, Journal Year: 2024, Volume and Issue: unknown, P. 112281 - 112281

Published: Oct. 1, 2024

Language: Английский

Citations

0
Molecular Mechanisms of Heterosis and Its Applications in Tree Breeding: Progress and Perspectives DOI Open Access
Zeyu Li, Yan Zhao,

Keming Luo

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(22), P. 12344 - 12344

Published: Nov. 17, 2024

Heterosis, or hybrid vigor, refers to the phenomenon where progenies outperform their parents in traits such as yield and resistance. This has been widely applied plant breeding. Recent advances high-throughput genomics have significantly advanced our understanding of heterosis. review systematically summarizes genetic, molecular, epigenetic mechanisms underlying Furthermore, we discuss recent predictive methods for heterosis applications improving growth rate, resistance abiotic stresses, wood tree species. We also explore role unraveling heterosis, emphasizing potential integrating high-resolution genomics, single-cell sequencing, spatial transcriptomics achieve a comprehensive from molecular levels. Building on this, CRISPR-based gene-editing technologies can be employed precisely edit heterotic loci, enabling study allele function. Additionally, marker-assisted selection (MAS) utilized identify loci parental lines, facilitating optimal combinations reducing labor time costs Finally, utilization breeding provide forward-looking perspective future research directions, highlighting multi-omics approaches emerging tools revolutionize

Language: Английский

Citations

0