Shifting the limits in wheat research and breeding using a fully annotated reference genome

Science, Год журнала: 2018, Номер 361(6403)

Опубликована: Авг. 17, 2018

Insights from the annotated wheat genome Wheat is one of major sources food for much world. However, because bread wheat's a large hybrid mix three separate subgenomes, it has been difficult to produce high-quality reference sequence. Using recent advances in sequencing, International Genome Sequencing Consortium presents an with detailed analysis gene content among subgenomes and structural organization all chromosomes. Examples quantitative trait mapping CRISPR-based modification show potential using this agricultural research breeding. Ramírez-González et al. exploited fruits endeavor identify tissue-specific biased expression coexpression networks during development exposure stress. These resources will accelerate our understanding genetic basis wheat. Science , issue p. eaar7191 ; see also eaar6089

Язык: Английский

---

Plant pan-genomes are the new reference

Nature Plants, Год журнала: 2020, Номер 6(8), С. 914 - 920

Опубликована: Июль 20, 2020

Язык: Английский

---

Genome-edited powdery mildew resistance in wheat without growth penalties

Nature, Год журнала: 2022, Номер 602(7897), С. 455 - 460

Опубликована: Фев. 9, 2022

Язык: Английский

---

Impact of transposable elements on genome structure and evolution in bread wheat

Genome biology, Год журнала: 2018, Номер 19(1)

Опубликована: Авг. 3, 2018

Transposable elements (TEs) are major components of large plant genomes and main drivers genome evolution. The most recent assembly hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context enabled a detailed view into dynamics TEs A, B, D subgenomes. overall content is very similar between subgenomes, although we find no evidence for bursts amplification after polyploidization events. Despite near-complete turnover since subgenome lineages diverged from common ancestor, 76% families still present proportions each subgenome. Moreover, spacing syntenic genes also conserved, even though have been replaced by new insertions over time, suggesting that distances genes, but not sequences, under evolutionary constraints. composition immediate gene vicinity differs core intergenic regions. We same to be enriched or depleted near all three Evaluations at subfamily level timed long terminal repeat-retrotransposon highlight independent evolution diploid before cases concerted proliferation AB tetraploid. Even changed turnover, unexpected preservation observed subgenomes features like family proportions, spacing, enrichment genes.

Язык: Английский

---

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Genome biology, Год журнала: 2018, Номер 19(1)

Опубликована: Авг. 14, 2018

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access bread wheat reference genome sequence produced by International Wheat Genome Sequencing Consortium. browsers, BLAST, InterMine tools have established for in-depth exploration together additional linked datasets including physical maps, variations, gene expression, genetic phenomic data from other collaborative projects already stored in GnpIS information system. provides enhanced search browser features that will facilitate deployment latest genomics resources improvement.

Язык: Английский

---

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

The Plant Cell, Год журнала: 2021, Номер 34(2), С. 718 - 741

Опубликована: Ноя. 18, 2021

The identification and characterization of cis-regulatory DNA sequences how they function to coordinate responses developmental environmental cues is paramount importance plant biology. Key these regulatory processes are modules (CRMs), which include enhancers silencers. Despite the extraordinary advances in high-quality sequence assemblies genome annotations, understanding CRMs, regulate gene expression, lag significantly behind. This especially true for their distinguishing characteristics activity states. Here, we review current knowledge on CRMs breakthrough technologies enabling identification, characterization, validation CRMs; compare genomic distributions with respect target genes between different species, discuss role transposable elements harboring evolution expression. an exciting time study cis-regulomes plants; however, significant existing challenges need be overcome fully understand appreciate biology crop improvement.

Язык: Английский

---

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

New Phytologist, Год журнала: 2019, Номер 225(1), С. 511 - 529

Опубликована: Авг. 16, 2019

Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning traits great importance. MADS-box genes are prime candidates for this, as they involved in virtually all aspects plant development. Here, we present detailed overview phylogeny and expression 201 MIKC-type genes. Homoeolog retention significantly above average genome-wide rate genes, indicating that many homoeologs functionally not redundant. Gene generally agreement expected subfamily-specific pattern, broad conservation function during evolution. We also found extensive expansion some subfamilies, especially those potentially adaptation to different environmental conditions like flowering time Duplications prominent distal telomeric regions. A number show novel patterns respond, example, biotic stress, pointing towards neofunctionalization. speculate conserved, duplicated neofunctionalized may have played an role diversity hence contributing importance staple food.

Язык: Английский

---

Haplotype-resolved genome analyses of a heterozygous diploid potato

Nature Genetics, Год журнала: 2020, Номер 52(10), С. 1018 - 1023

Опубликована: Сен. 28, 2020

Abstract Potato ( Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform from a clonally propagated tetraploid into seed-propagated, inbred-line-based hybrid, but this process requires better understanding of potato genome. Here, we report 1.67-Gb haplotype-resolved assembly diploid potato, RH89-039-16, using combination multiple sequencing strategies, including circular consensus sequencing. Comparison two haplotypes revealed ~2.1% intragenomic diversity, 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs allelic genes, 16.6% and 30.8% exhibited differential expression methylation between alleles, respectively. Deleterious differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies eradicate or stack beneficial via meiotic recombination. This study offers holistic view genome organization species provides insights technological evolution resolving complex genomes.

Язык: Английский

---

Root Growth Adaptation to Climate Change in Crops

Frontiers in Plant Science, Год журнала: 2020, Номер 11

Опубликована: Май 8, 2020

Climate change is threatening crop productivity worldwide and new solutions to adapt crops these environmental changes are urgently needed. Elevated temperatures driven by climate affect developmental physiological plant processes that, ultimately, impact on yield quality. Plant roots responsible for water nutrients uptake, but in soil alter this process limiting growth. With the predicted variable climatic forecast, development of an efficient root system better adapted changing conditions crucial enhancing productivity. Root traits associated with improved adaptation rising increasingly being analysed obtain more suitable varieties. In review, we will summarize current knowledge about effect increasing growth their yield. First, describe main alterations architecture that different undergo response warmer soils. Then, outline coordinated metabolic taking place aerial parts modulate global increased temperatures. We discuss some regulatory mechanisms controlling soils, including activation heat oxidative pathways prevent damage cells disruption growth; interplay between hormonal gene expression protein homeostasis. also consider field, usually other abiotic biotic stresses such as drought, salinity, nutrient deficiencies, pathogen infections. present recent advances how able integrate respond complex stimuli order environment. Finally, prospects

Язык: Английский

---

How the pan-genome is changing crop genomics and improvement

Genome biology, Год журнала: 2021, Номер 22(1)

Опубликована: Янв. 4, 2021

Abstract Crop genomics has seen dramatic advances in recent years due to improvements sequencing technology, assembly methods, and computational resources. These have led the development of new tools facilitate crop improvement. The study structural variation within species characterization pan-genome revealed extensive genome content among individuals a that is paradigm shifting Here, we review how utilization these light pan-genomes are becoming available for many species.

Язык: Английский

---