Response to water‐deficit following waterlogging varies among ecotypes of subterranean clover (Trifolium subterraneum ssp. yanninicum), a waterlogging‐tolerant annual pasture legume DOI Creative Commons
Gereltsetseg Enkhbat, Yoshiaki Inukai, P. G. H. Nichols

et al.

Annals of Applied Biology, Journal Year: 2023, Volume and Issue: 183(3), P. 287 - 301

Published: July 24, 2023

Abstract The pasture legume Trifolium subterraneum ssp. yanninicum L. is waterlogging tolerant, but water‐deficit (WD) susceptible. interactive effect of waterlogged (WL) and WD (soil moisture fluctuation [SMF]) results in a severe stress impact. We studied three diverse ecotypes to identify traits associated with adaptation SMF. Ecotypes were established glasshouse two treatments imposed at 21 days: well‐watered (WW–WW; 80% field capacity [FC]) WL (WL–WD). For WL–WD, pots for 28 days (Harvest I), then transitioned (drained 40% FC) maintained 10 II). shoot relative growth rates (RGR) Harvest I, had relatively little impact, although there was greater reduction Ecotype A (80% WW) than B (92%) C (87%). However, between Harvests I II, the impact WL–WD varied among being less affected (75% WW–WW) (57%) (63%). root RGR resulted (52% (77%) (74%), while showed large increase (117% compared (95%) In conclusion, response following ecotypes, which demonstrates contrasting responses SMF unrelated tolerance. High yield under together rapid post‐WL drying soil profile could enhance

Language: Английский

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

33
De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation DOI Creative Commons
Wen‐Hsi Kuo, Sara J. Wright,

Linda L. Small

et al.

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Aug. 7, 2024

White clover (Trifolium repens) is a globally important perennial forage legume. This species also serves as an eco-evolutionary model system for studying within-species chemical defense variation; it features well-studied polymorphism cyanogenesis (HCN release following tissue damage), with higher frequencies of cyanogenic plants favored in warmer locations worldwide. Using newly generated haplotype-resolved genome and two other long-read assemblies, we tested the hypothesis that copy number variants (CNVs) at genes play role ability white to rapidly adapt local environments. We examined questions on subgenome evolution this recently evolved allotetraploid chromosomal rearrangements broader IRLC legume clade.

Language: Английский

Citations

4
Haplotype-Resolved, Chromosome-Level Assembly of White Clover (Trifolium repens L., Fabaceae) DOI Creative Commons
James S. Santangelo, Paul Battlay, Brandon T. Hendrickson

et al.

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(8)

Published: Aug. 1, 2023

White clover (Trifolium repens L.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world increasingly used evolutionary ecology genetics to understand genetic basis of adaptation. Historically, improvements white breeding practices assessments variation nature have been hampered by a lack high-quality genomic resources for this species, owing part its high heterozygosity allotetraploid hybrid origin. Here, we use PacBio HiFi chromosome conformation capture (Omni-C) technologies generate chromosome-level, haplotype-resolved genome assembly totaling 998 Mbp (scaffold N50 = 59.3 Mbp) 1 Gbp 58.6 haplotypes 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide functionally annotated haploid mapping (968 Mbp, scaffold 59.9 Mbp), which drastically improves on existing reference both contiguity accuracy. 78,174 protein-coding genes, resulting protein BUSCO completeness scores 99.6% 99.3% against embryophyta_odb10 fabales_odb10 lineage datasets, respectively.

Language: Английский

Citations

10
Spain Germplasm Bank of Annual Forage Legumes Seeds at the Scientific and Technological Research Center of Extremadura (CICYTEX) DOI

Francisco Antonio Galea-Gragera,

Fernando Llera Cid

Published: Jan. 1, 2025

Language: Английский

Citations

0
De novo genome assembly of white clover (Trifolium repens L.) reveals the role of Copy Number Variation in rapid environmental adaptation DOI Creative Commons
Wen‐Hsi Kuo, Sara J. Wright,

Linda L. Small

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 17, 2024

Abstract Background White clover ( Trifolium repens ) is a globally important perennial forage legume. This species also serves as an eco-evolutionary model system for studying within-species chemical defense variation; it features well-studied polymorphism cyanogenesis (HCN release following tissue damage), with higher frequencies of cyanogenic plants favored in warmer locations worldwide. Using newly-generated haplotype-resolved genome and two other long-read assemblies, we tested the hypothesis that copy number variants (CNVs) at genes play role ability white to rapidly adapt local environments. We examined questions on subgenome evolution this recently evolved allotetraploid chromosomal rearrangements broader IRLC legume clade. Results Integration PacBio HiFi, Omni-C, Illumina linkage map data yielded first completely de novo assembly (created without priori sequence assignment subgenomes). find has undergone extensive transposon diversification since its origin but otherwise shows highly conserved organization composition diploid progenitors; unlike some species, structure legumes. further evidence CNVs major loci; these contribute quantitative variation phenotype adaptation across wild North American populations. Conclusions study among first, our knowledge, document plant highlights value pan-genome identifying contributions structural nature.

Language: Английский

Citations

2
Haplotype-resolved, chromosome-level assembly of white clover (Trifolium repensL., Fabaceae) DOI Creative Commons
James S. Santangelo, Paul Battlay, Brandon T. Hendrickson

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 8, 2023

Abstract Background White clover ( Trifolium repens L.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world, increasingly used evolutionary ecology genetics to understand genetic basis of adaptation. Historically, improvements white breeding practices assessments variation nature have been hampered by a lack high-quality genomic resources for this species, owing part its high heterozygosity allotetraploid hybrid origin. Findings Here, we use PacBio HiFi chromosome conformation capture (Omni-C) technologies generate chromosome-level, haplotype-resolved genome assembly totaling 998 Mbp (scaffold N50 = 59.3 Mbp) 1 Gbp 58.6 haplotypes 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide functionally annotated haploid mapping (968 Mbp, scaffold 59.9 Mbp), which drastically improves on existing reference both contiguity accuracy. 78,174 protein-coding genes, resulting protein BUSCO completeness scores 99.6% 99.3% against embryophyta_odb10 fabales_odb10 lineage datasets, respectively. Conclusions two assemblies as project: (1) haplotype-resolved, chromosome-level assembly, (2) assembly. These place among best sequenced legumes date, one plant recent polyploid origins. This work promises facilitate ongoing future agronomically ecologically species.

Language: Английский

Citations

1
Response to water‐deficit following waterlogging varies among ecotypes of subterranean clover (Trifolium subterraneum ssp. yanninicum), a waterlogging‐tolerant annual pasture legume DOI Creative Commons
Gereltsetseg Enkhbat, Yoshiaki Inukai, P. G. H. Nichols

et al.

Annals of Applied Biology, Journal Year: 2023, Volume and Issue: 183(3), P. 287 - 301

Published: July 24, 2023

Abstract The pasture legume Trifolium subterraneum ssp. yanninicum L. is waterlogging tolerant, but water‐deficit (WD) susceptible. interactive effect of waterlogged (WL) and WD (soil moisture fluctuation [SMF]) results in a severe stress impact. We studied three diverse ecotypes to identify traits associated with adaptation SMF. Ecotypes were established glasshouse two treatments imposed at 21 days: well‐watered (WW–WW; 80% field capacity [FC]) WL (WL–WD). For WL–WD, pots for 28 days (Harvest I), then transitioned (drained 40% FC) maintained 10 II). shoot relative growth rates (RGR) Harvest I, had relatively little impact, although there was greater reduction Ecotype A (80% WW) than B (92%) C (87%). However, between Harvests I II, the impact WL–WD varied among being less affected (75% WW–WW) (57%) (63%). root RGR resulted (52% (77%) (74%), while showed large increase (117% compared (95%) In conclusion, response following ecotypes, which demonstrates contrasting responses SMF unrelated tolerance. High yield under together rapid post‐WL drying soil profile could enhance

Language: Английский

Citations

0