Deciphering the evolution and complexity of wheat germplasm from a genomic perspective DOI Creative Commons
Zihao Wang, Ling-Feng Miao, Yongming Chen

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: 50(11), P. 846 - 860

Published: Aug. 21, 2023

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progresses in studying on genome are substantially trailed behind those other two major crops, rice maize, at least a decade. With rapid advances assembling reduced cost high-throughput sequencing, emerging de novo assemblies whole-genome sequencing data leading paradigm shift research. Here, we review recent progress dissecting germplasm evolution since release first high-quality genome. New insights have been gained during domestication modern breeding progress, genomic variations multiple scales contributing diversity germplasm, transcriptional epigenetic regulations functional genes polyploid wheat. Genomics databases bioinformatics tools meeting urgent needs genomics research also summarized. The ever-increasing omics data, along with advanced well-structured databases, expected accelerate deciphering gene resources future advances.

Language: Английский

Long-read sequence assembly: a technical evaluation in barley DOI Creative Commons
Martin Mascher, Thomas Wicker, Jerry Jenkins

et al.

The Plant Cell, Journal Year: 2021, Volume and Issue: 33(6), P. 1888 - 1906

Published: March 10, 2021

Abstract Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources often several complementary sequence genome mapping approaches. The recent development fast accurate long-read sequencing by circular consensus (CCS) on the PacBio platform may greatly increase scope pan-genome projects. Here, we compare current platforms regarding their ability to rapidly generate contiguous assemblies in studies barley (Hordeum vulgare). Most are clearly superior reference based short-reads. Assemblies derived from long reads excel most metrics, but CCS approach was cost-effective strategy for assembling tens genomes. A downsampling analysis indicated that 20-fold coverage can yield very good assemblies, while even five-fold data capture complete genes. We present an updated with near-complete representation intergenic space. Long-read underpin construction sequences multiple a species build infrastructures Triticeae crops wild relatives.

Language: Английский

Citations

274
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes DOI Creative Commons
Guangwei Li, Lijian Wang, Jianping Yang

et al.

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(4), P. 574 - 584

Published: March 18, 2021

Abstract Rye is a valuable food and forage crop, an important genetic resource for wheat triticale improvement indispensable material efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted 98.47% estimated size (7.86 Gb), with 93.67% (7.25 assigned to seven chromosomes. Repetitive elements constituted 90.31% genome. Compared previously Triticeae genomes, Daniela , Sumaya Sumana retrotransposons showed strong expansion rye. Further analyses assembly shed new light on genome-wide gene duplications their impact starch biosynthesis genes, physical organization complex prolamin loci, expression features underlying early heading trait putative domestication-associated chromosomal regions loci This sequence promises accelerate breeding related cereal crops.

Language: Английский

Citations

213
The mosaic oat genome gives insights into a uniquely healthy cereal crop DOI Creative Commons
Nadia Kamal, Nikos Tsardakas Renhuldt, Johan Bentzer

et al.

Nature, Journal Year: 2022, Volume and Issue: 606(7912), P. 113 - 119

Published: May 18, 2022

Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields Anatolia1,2. Oat has low carbon footprint, substantial health benefits the potential replace animal-based food products. However, lack of fully annotated reference genome hampered efforts deconvolute its complex evolutionary history functional gene dynamics. Here we present high-quality A. close relatives diploid longiglumis, AA, 14) tetraploid insularis, CCDD, 4x 28) progenitors. We reveal mosaic structure genome, trace large-scale genomic reorganizations polyploidization illustrate breeding barrier associated with architecture oat. showcase detailed analyses families implicated human nutrition, which adds evidence supporting safety gluten-free diets, perform mapping-by-sequencing agronomic trait related water-use efficiency. This resource for Avena genus will help leverage knowledge from other cereal genomes, improve understanding basic biology accelerate genomics-assisted reanalysis quantitative studies.

Language: Английский

Citations

138
Wheat genomic study for genetic improvement of traits in China DOI
Jun Xiao, Liu B, Yingyin Yao

et al.

Science China Life Sciences, Journal Year: 2022, Volume and Issue: 65(9), P. 1718 - 1775

Published: Aug. 24, 2022

Language: Английский

Citations

120
An unusual tandem kinase fusion protein confers leaf rust resistance in wheat DOI Creative Commons
Yajun Wang, Michaël Abrouk, Spyridon Gourdoupis

et al.

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(6), P. 914 - 920

Published: May 22, 2023

The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. Here we use mutagenesis and transcriptome sequencing clone the leaf rust resistance gene Lr9, which was introduced into bread wheat grass species Aegilops umbellulata2. We that Lr9 encodes unusual tandem kinase fusion protein. Long-read a line putative Ae. umbellulata donor enabled us assemble ~28.4-Mb translocation identify breakpoint. likewise cloned Lr58, reportedly introgressed triuncialis3, but has identical coding sequence compared Lr9. Cytogenetic haplotype analyses corroborate two genes originate same event. Our work sheds light on emerging role proteins in disease resistance, expanding repertoire for breeding.

Language: Английский

Citations

80
Genome-wide signatures of adaptation to extreme environments in red algae DOI Creative Commons
Chung Hyun Cho,

Seung In Park,

Tzu‐Yen Huang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Jan. 4, 2023

The high temperature, acidity, and heavy metal-rich environments associated with hot springs have a major impact on biological processes in resident cells. One group of photosynthetic eukaryotes, the Cyanidiophyceae (Rhodophyta), has successfully thrived sites worldwide for more than 1 billion years. Here, we analyze chromosome-level assemblies from three representative species to study environmental adaptation at genomic level. We find that subtelomeric gene duplication functional genes loss canonical eukaryotic traits played role adaptation, addition horizontal transfer events. Shared responses stress exist Cyanidiales Galdieriales, however, most adaptive (e.g., arsenic detoxification) evolved independently these lineages. Our results underline power local selection shape genomes may face vastly different stresses adjacent, extreme microhabitats.

Language: Английский

Citations

45
Genomics accelerated isolation of a new stem rust avirulence gene–wheat resistance gene pair DOI
Narayana M. Upadhyaya, Rohit Mago,

Vinay Panwar

et al.

Nature Plants, Journal Year: 2021, Volume and Issue: 7(9), P. 1220 - 1228

Published: July 22, 2021

Language: Английский

Citations

95
An efficient Oligo‐FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae DOI Open Access
Guangrong Li, Tao Zhang, Zhihui Yü

et al.

The Plant Journal, Journal Year: 2020, Volume and Issue: 105(4), P. 978 - 993

Published: Nov. 20, 2020

A chromosome-specific painting technique has been developed which combines the most recent approaches of companion disciplines molecular cytogenetics and genome research. We seven oligonucleotide (oligo) pools derivd from single-copy sequences on chromosomes 1 to 7 barley (Hordeum vulgare L.) corresponding collinear regions wheat (Triticum aestivum L.). The groups pooled oligos comprised between 10 986 12 496 45-bp monomers, these then produced stable fluorescence in situ hybridization (FISH) signals each linkage group barley. oligo probes were applied high-throughput karyotyping other Triticeae species genera Secale, Aegilops, Thinopyrum, Dasypyrum, study also extended some wheat-alien amphiploids derived lines. demonstrated that a complete set whole-chromosome facilitated inter-species chromosome homologous relationships visualized non-homologous chromosomal rearrangements derivatives. When combined with non-denaturing FISH procedures using tandem-repeat oligos, newly techniques provide an efficient tool for structure, organization, evolution among any wild non-sequenced genomes.

Language: Английский

Citations

81
The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding DOI Creative Commons
Liangliang Gao,

Dal-Hoe Koo,

Philomin Juliana

et al.

Theoretical and Applied Genetics, Journal Year: 2020, Volume and Issue: 134(2), P. 529 - 542

Published: Nov. 12, 2020

Abstract Key message The first cytological characterization of the 2N v S segment in hexaploid wheat; complete de novo assembly and annotation segment; frequency is increasing associated with higher yield. Aegilops ventricosa translocation has been utilized breeding disease-resistant wheat crops since early 1990s. This known to possess several important resistance genes against multiple diseases including root knot nematode, stripe rust, leaf rust stem rust. More recently, this blast, an emerging devastating disease South America Asia. To date, full its size, gene content association grain yield lacking. Here, we present a physical agronomically bread wheat. We assembled two varieties, ‘Jagger’ ‘CDC Stanley,’ delineated be approximately 33 Mb. A total 535 high-confidence were annotated within region, > 10% belonging nucleotide-binding leucine-rich repeat (NLR) families. Identification groups NLR that are potentially N genome-specific expressed specific tissues can fast-track testing candidate playing roles various resistances. also show among spring winter programs over half decades, positive impact on based historical datasets. significance due highlights importance understanding characterizing pan-genome for better insights into molecular improvement.

Language: Английский

Citations

73
GrainGenes: a data-rich repository for small grains genetics and genomics DOI Creative Commons
Eric Yao, Victoria Blake, Laurel Cooper

et al.

Database, Journal Year: 2022, Volume and Issue: 2022

Published: Jan. 1, 2022

Abstract As one of the US Department Agriculture—Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves data and community needs globally distributed small grains researchers for genetic improvement Triticeae family Avena species that include wheat, barley, rye oat. accomplishes its mission by continually enriching cross-linked content following findable, accessible, interoperable reusable principles, enhancing maintaining an intuitive web interface, creating tools to enable easy access establishing connections within between other biological databases facilitate knowledge discovery. operates database community, collaborates with curators genome sequencing groups contributes AgBioData Consortium International Wheat Initiative through Information System (WheatIS). Interactive linked is paramount successful now has 2917 manually curated gene records, including 289 genes 254 alleles from Gene Catalogue (WGC). There are >4.8 million models in 51 browser assemblies, 6273 quantitative trait loci >1.4 on 4756 physical maps contained 443 mapping sets, complete standardized metadata. Most notably, 50 new browsers outputs Barley PanGenome projects have been created. We provide example expression track Genome Sequencing Chinese Spring wheat demonstrate how tracks can be adapted different types. To help users benefit more data, created four tutorials available YouTube. executing vision service continuously responding global a centralized, long-term, interconnected repository. Database URL:https://wheat.pw.usda.gov

Language: Английский

Citations

56