Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies DOI Creative Commons
Soodeh Tirnaz, Jaco Zandberg, William J. W. Thomas

et al.

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Nov. 17, 2022

Global agricultural industries are under pressure to meet the future food demand; however, existing crop genetic diversity might not be sufficient this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals hidden wild relatives (CWRs), which could have significant impacts improvement. There many ex-situ in-situ resources around world holding rare valuable species, carry agronomically important traits it is crucial users aware their availability. Here we aim explore available ex-/in- situ such as genebanks, botanical gardens, national parks, conservation hotspots inventories CWR accessions. In addition highlight advances use genomic resources, contribution pangenome construction introducing novel genes into crops. We also discuss potential challenges modern breeding experimental approaches (e.g. de novo domestication, editing speed breeding) used CWRs computational machine learning) that up utilization programs towards adaptability yield

Language: Английский

Reap the crop wild relatives for breeding future crops DOI Creative Commons
Abhishek Bohra, Benjamin Kilian,

Shoba Sivasankar

et al.

Trends in biotechnology, Journal Year: 2021, Volume and Issue: 40(4), P. 412 - 431

Published: Oct. 9, 2021

Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that boosted crop resilience and global agricultural production. Advances in breeding genomics accelerated the identification of valuable CWRs for use improvement. The enhanced genetic diversity pools carrying optimum combinations favorable alleles targeted crop-growing regions is crucial to sustain gain. In parallel, growing sequence information on genomes combination precise gene-editing tools provide a fast-track route transform into ideal future crops. Data-informed germplasm collection management strategies together adequate policy support will be equally important improve access their sustainable meet food nutrition security targets.

Language: Английский

Citations

223
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber DOI Creative Commons
Hongbo Li, Shenhao Wang, Sen Chai

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Feb. 3, 2022

Abstract Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits evolutionary events; however, their comprehensive identification characterization in cucumber ( Cucumis sativus L.) have been hindered by the lack high-quality pan-genome. Here, we report graph-based pan-genome analyzing twelve chromosome-scale genome assemblies. Genotyping seven large chromosomal rearrangements based on provides useful information for use wild accessions breeding studies. A total ~4.3 million including 56,214 SVs identified leveraging chromosome-level The graph integrating both variant reference sequences aids associated with traits, warty fruits, flowering times root growth, enhances understanding trait evolution. provide rich resources future biological research genomics-assisted breeding.

Language: Английский

Citations

128
Breeding crops for drought-affected environments and improved climate resilience DOI Creative Commons
Mark Cooper, Carlos D. Messina

The Plant Cell, Journal Year: 2022, Volume and Issue: 35(1), P. 162 - 186

Published: Nov. 12, 2022

Abstract Breeding climate-resilient crops with improved levels of abiotic and biotic stress resistance as a response to climate change presents both opportunities challenges. Applying the framework “breeder’s equation,” which is used predict selection for breeding program cycle, we review methodologies strategies that have been successfully breed drought resistance, where target population environments (TPEs) spatially temporally heterogeneous mixture drought-affected favorable (water-sufficient) environments. Long-term improvement temperate maize US corn belt case study compared progress other geographies. Integration trait information across scales, from genomes ecosystems, needed accurately yield outcomes genotypes within current future TPEs. This will require transdisciplinary teams explore, identify, exploit novel accelerate outcomes; germplasm resources products (cultivars, hybrids, clones, populations) outperform replace in use by farmers, combination modified agronomic management suited their local

Language: Английский

Citations

91
Genotype–environment associations to reveal the molecular basis of environmental adaptation DOI Open Access
Jesse R. Lasky, Emily B. Josephs, Geoffrey P. Morris

et al.

The Plant Cell, Journal Year: 2022, Volume and Issue: 35(1), P. 125 - 138

Published: Aug. 25, 2022

A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation their environment. Climate change has given new urgency this goal, as society aims accelerate of ecologically important species, endangered crops hotter, less predictable climates. In pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, ecology. Now, rise genomics computational approaches may facilitate research. Genotype-environment associations (GEAs) use statistical between allele frequency environment origin test hypothesis that allelic at a gene adapted local environments. Researchers scan genome for GEAs generate hypotheses on genetic variants (environmental genome-wide association studies). Despite rapid adoption these methods, many questions remain about interpretation GEA findings, which arise from unanswered architecture limitations inherent association-based analyses. We outline strategies ground better GEA-generated using genetics ecophysiology. provide recommendations users who seek learn basis adaptation. When combined with rigorous testing framework, our understanding climate improvement.

Language: Английский

Citations

72
Plant pan-genomics and its applications DOI Creative Commons
Junpeng Shi, Zhixi Tian, Jinsheng Lai

et al.

Molecular Plant, Journal Year: 2022, Volume and Issue: 16(1), P. 168 - 186

Published: Dec. 15, 2022

Language: Английский

Citations

72
A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? DOI Creative Commons
Ying Gong, Yefang Li, Xuexue Liu

et al.

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 5, 2023

Abstract As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to complex routes of origin and migration, suggesting possible omission some population-specific sequences in current genome. Conversely, pangenome is collection all DNA contains shared by individuals (core genome) also able display sequence information unique each individual (variable genome). The progress research humans, plants proved missing components identification large structural variants (SVs) can be explored through pangenomic studies. Many specific shown related biological adaptability, phenotype important economic traits. maturity technologies methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic reference-free assembly will further promote development pangenome. In future, combined with long-read data multi-omics help resolve SVs their relationship main traits interest domesticated animals, providing better insights into animal domestication, evolution breeding. this review, we mainly discuss how analysis reveals variations (sheep, cattle, pigs, chickens) impacts on phenotypes contribute understanding diversity. Additionally, go potential issues future perspectives livestock poultry.

Language: Английский

Citations

46
Technology-enabled great leap in deciphering plant genomes DOI
Lingjuan Xie, Xiaojiao Gong, Kun Yang

et al.

Nature Plants, Journal Year: 2024, Volume and Issue: 10(4), P. 551 - 566

Published: March 20, 2024

Language: Английский

Citations

34
Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX DOI
Yupeng Wang, Haibao Tang, Xiyin Wang

et al.

Nature Protocols, Journal Year: 2024, Volume and Issue: 19(7), P. 2206 - 2229

Published: March 15, 2024

Language: Английский

Citations

31
Plant pangenomes for crop improvement, biodiversity and evolution DOI
Mona Schreiber, Murukarthick Jayakodi, Nils Stein

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(8), P. 563 - 577

Published: Feb. 20, 2024

Language: Английский

Citations

30
Population comparative genomics discovers gene gain and loss during grapevine domestication DOI Creative Commons
Qiming Long, Shuo Cao, Guizhou Huang

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(2), P. 1401 - 1413

Published: Jan. 29, 2024

Abstract Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors artificially selected for desired agronomic traits along with dramatic genomic variation in course of moderate to severe bottlenecks. However, previous investigations mainly focused on small-effect variants, while changes gene contents rarely investigated due lack population-level assemblies both and its relatives. Here, we applied comparative analyses discover gain loss grapevine using long-read representative population samples domesticated grapevines (V. vinifera ssp. vinifera) their sylvestris). Only ∼7% families were shared 16 Vitis genomes ∼8% specific each accession, suggesting variations genomes. Compared progenitors, accessions exhibited an increased presence genes associated asexual reproduction, showcased a higher abundance related pollination, revealing transition from sexual reproduction clonal propagation processes. Moreover, harbored fewer disease-resistance than progenitors. The SVs occurred frequently aroma between indicating rapid diversification these domestication. Our study provides insights resources biological studies breeding programs grapevine.

Language: Английский

Citations

18