Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding DOI Creative Commons
Haifei Hu, Armin Scheben, Jian Wang

et al.

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 22(3), P. 544 - 554

Published: Nov. 14, 2023

Summary Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting expression recombination rates. However, compared with other variations, their roles in functional biology crop improvement remain largely unexplored. In this review, we highlight technological methodological advancements that have allowed comprehensive understanding inversion variants through the pangenome framework machine learning algorithms. Genome editing is an efficient method for inducing or reversing mutations plants, providing effective mechanism to modify local Given potential inversions breeding, anticipate increasing attention on from scientific community future research breeding applications.

Language: Английский

Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis DOI
Shuai Chen, Pengjie Wang, Weilong Kong

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(12), P. 1986 - 1999

Published: Nov. 27, 2023

Language: Английский

Citations

38
A chromosome‐level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation DOI Creative Commons
Liang Xu, Yan Wang,

Junhui Dong

et al.

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(5), P. 990 - 1004

Published: Jan. 17, 2023

Summary High‐quality radish ( Raphanus sativus ) genome represents a valuable resource for agronomical trait improvements and understanding evolution among Brassicaceae species. However, existing assembly remains fragmentary, which greatly hampered functional genomics research genome‐assisted breeding. Here, using NAU‐LB inbred line, we generated reference of 476.32 Mb with scaffold N50 56.88 by incorporating Illumina, PacBio BioNano optical mapping techniques. Utilizing Hi‐C data, 448.12 (94.08%) the assembled sequences were anchored to nine chromosomes 40 306 protein‐coding genes annotated. In total, 249.14 (52.31%) comprised repetitive sequences, long terminal repeats (LTRs, 30.31%) most abundant class. Beyond confirming whole‐genome triplication (WGT) event in R. lineage, found several tandem arrayed involved stress response process, may account distinctive phenotype high disease resistance . By comparing against Xin‐li‐mei genome, total 2 108 573 SNPs, 7740 large insertions, 7757 deletions 84 inversions identified. Interestingly, 647‐bp insertion promoter RsVRN1 gene can be directly bound DOF transcription repressor RsCDF3 , resulting into its low activity late‐bolting cultivar. Importantly, introgression this allele, In‐536 early‐bolting genotype could contribute delayed bolting time, indicating that it is potential genetic Together, provides information facilitate comparative genomic analysis accelerate genome‐guided breeding improvement radish.

Language: Английский

Citations

36
Allelic variation of terpene synthases drives terpene diversity in the wild species of the Freesia genus DOI
Tingting Bao, Shadrack Kimani, Yueqing Li

et al.

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 192(3), P. 2419 - 2435

Published: March 18, 2023

Abstract Terpene synthases (TPSs) play pivotal roles in conferring the structural diversity of terpenoids, which are mainly emitted from flowers, whereas genetic basis release floral volatile terpenes remains largely elusive. Though quite similar sequence, TPS allelic variants still function divergently, and how they drive terpene closely related species unknown. Here, TPSs responsible for scent wild Freesia were characterized, functions their natural variants, as well causal amino acid residues, investigated depth. Besides 8 previously reported modern cultivars, 7 additional functionally evaluated to contribute major volatiles species. Functional characterization demonstrated that TPS2 TPS10 changed enzymatic capacity while TPS6 drove products. Further residue substitution analysis revealed minor residues determining enzyme catalytic activity product specificity. The clarification reveals evolved differently determine interspecific genus might be used cultivar improvement.

Language: Английский

Citations

23
Molecular breakthroughs in modern plant breeding techniques DOI Creative Commons

Mughair Abdul Aziz,

Khaled Masmoudi

Horticultural Plant Journal, Journal Year: 2024, Volume and Issue: unknown

Published: March 1, 2024

Advancements in molecular approaches have been utilized to breed crops with a wide range of economically valuable traits develop superior cultivars. This review provides concise overview modern breakthroughs plant production. Genotyping and high-throughput phenotyping methods for predictive breeding are briefly discussed. In this study, we explore contemporary techniques producing desirable crop varieties. These include cisgenesis, clustered regularly interspaced short palindromic repeat (CRISPR/Cas9) gene editing, haploid induction, de novo domestication. We examine the speed approach—a strategy cultivating plants under controlled conditions. further highlight significance technologies efficiently utilizing agricultural resources production urban areas. The deciphering genomes has led development extensive DNA markers, quantitative trait loci (QTLs), pangenomes associated various traits. shift genotypic selection considerably expedites process. Based on population used, connection between phenotypic data several genetic elements, including genes, alleles that can be used genomic editing. integration genomic-assisted cutting-edge genome editing tools made it feasible rapidly manipulate generate multiple cycles accelerate Breakthroughs substantial improvements methods.

Language: Английский

Citations

17
The genomic route to tomato breeding: Past, present, and future DOI Creative Commons

Yan Wang,

Chuanlong Sun, Zhibiao Ye

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(4), P. 2500 - 2514

Published: April 30, 2024

Over the past 10,000 years, tomato species have undergone both unintentional and intentional selection to enhance their favorable traits for human consumption manufacturing. These processes significantly influenced genomes of played a critical role in improving varieties. In this review, we summarize recent advances genome sequencing, explore impact human-driven selection, recapitulate key genes associated with important agronomic breeding. We provide several examples genomics-guided breeding highlight potential resources facilitating improvement. Furthermore, elaborate progress strategies through design present how such efforts can help future enhancements align demands sustainability evolving societies.

Language: Английский

Citations

15
A near-complete cucumber reference genome assembly and Cucumber-DB, a multi-omics database DOI Creative Commons
Jiantao Guan,

Han Miao,

Zhonghua Zhang

et al.

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(8), P. 1178 - 1182

Published: June 20, 2024

Language: Английский

Citations

14
Improvement of crop production in controlled environment agriculture through breeding DOI Creative Commons
Krishna Bhattarai, Andrew B. Ogden, Sudeep Pandey

et al.

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

Published: Jan. 27, 2025

Controlled environment agriculture (CEA) represents one of the fastest-growing sectors horticulture. Production in controlled environments ranges from highly indoor with 100% artificial lighting (vertical farms or plant factories) to high-tech greenhouses without supplemental lighting, simpler and high tunnels. Although food production occurs soil inside tunnels, most CEA operations use various hydroponic systems meet crop irrigation fertility needs. The expansion offers promise as a tool for increasing near urban these do not rely on arable agricultural land. In addition, resilience climate instability by growing protective structures. Products harvested tend be quality, both internal external, are sought after consumers. Currently, producers cultivars bred open-field agriculture. Because energy other costs CEA, only limited number crops have proven themselves profitable produce. One factor contributing this situation may lack optimized cultivars. Indoor offer opportunities breeding that ideal systems. To facilitate specialized cultivars, wide range tools available breeders help speed process increase its efficiency. This review aims cover needs horticultural either already being produced potential production. It also reviews many including genomics-informed breeding, marker-assisted selection, precision high-throughput phenotyping, sources germplasm suitable breeding. availability published genomes trait-linked molecular markers should enable rapid progress CEA-specific will drive growth industry.

Language: Английский

Citations

1
Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication DOI Creative Commons
Ying Su, X Yang, Y. Wang

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(4), P. 2799 - 2814

Published: May 14, 2024

Abstract The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies breeding programs. In this study, we assembled haplotype-resolved telomere-to-telomere (T2T) genome for diploid cultivar Golden Delicious. Subsequently, constructed pangenome based on 12 assemblies from wild species to investigate dynamic changes functional genes. Our results revealed gene gain loss events during domestication. Compared with species, more families significantly enriched oxidative phosphorylation, pentose metabolic process, responses salt, abscisic acid biosynthesis process. analyses also demonstrated higher prevalence different types resistance analogs (RGAs) cultivars than their relatives, partially attributed segmental tandem duplication certain RGAs classes. Structural variations, mainly deletions insertions, have affected presence absence TIR-NB-ARC-LRR, NB-ARC-LRR, CC-NB-ARC-LRR Additionally, hybridization/introgression has contributed expansion genes domesticated apples. T2T provide important resources apples, emphasizing need study evolutionary mechanisms breeding.

Language: Английский

Citations

8
Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation DOI Creative Commons
Baopeng Ding, Haifei Hu, Yunpeng Cao

et al.

Horticultural Plant Journal, Journal Year: 2024, Volume and Issue: 10(6), P. 1274 - 1290

Published: Aug. 14, 2024

The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled annotated genomes of maternal (PsbM) paternal (PsbF) lines hybrid 'Yuluxiang' constructed pangenome 1.15 Gb by combining these two with five previously published representing cultivated wild germplasm. Using pangenome, identified 21 224 gene PAVs (Presence-absence variation) 1 158 812 SNPs (Single Nucleotide Polymorphism) in non-reference genome that were absent PsbM reference genome. Compared SNP markers, PAV-based analysis provides additional insights into population structure. In addition, some genes associated fruit quality traits have differential occurrence frequencies expression between Asian European populations. Moreover, our revealed a mutated an insertion promoter region PsbMGH3.1 potentially enhance sepal shedding 'Xuehuali' which vital quality. may play role IAA pathway, contributing to distinct low-auxin phenotype observed plants heterologously overexpressing this gene. This research helps capture populations genomic resources accelerating breeding.

Language: Английский

Citations

8
From Sequencing to Genome Editing in Cucurbitaceae: Application of Modern Genomic Techniques to Enhance Plant Traits DOI Creative Commons
Magdalena Pawełkowicz, Bartłomiej Zieniuk, Paweł Staszek

et al.

Agriculture, Journal Year: 2024, Volume and Issue: 14(1), P. 90 - 90

Published: Jan. 1, 2024

The availability of genome-sequencing and genome-editing techniques has increased the applicability innovative solutions, opening up revolutionary prospects for developments in horticultural plant breeding. Cucurbitaceae family is a group plants great importance horticulture due to their high nutritional economic value. These serve as important models elucidating principles development refining yield improvement strategies. While traditional breeding approaches have made significant contributions production cucurbits, they also been limited by reduced genetic diversity lower rates variation inherent these species. This comprehensive review summarises latest genome editing cucurbits. It covers various aspects enhancing traits resist biotic stresses such pathogenic fungi viruses, well abiotic adverse climate change, especially caused drought salinity. study focused on improvements quality optimisation architecture, sex determination flowers fruit features. provides insights that may hold promise future crop serves an reference advancement gene-editing technologies

Language: Английский

Citations

7