scholarly journals Detecting Major Introgressions in Wheat and their Putative Origins Using Coverage Analysis

2021 ◽  
Author(s):  
Jens Keilwagen ◽  
Heike Lehnert ◽  
Thomas Berner ◽  
Ekaterina Badaeva ◽  
Axel Himmelbach ◽  
...  
Keyword(s):  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Cultivated Plants ◽  
Wheat Cultivars ◽  
Nucleotide Polymorphism ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Coverage Analysis ◽  
Beneficial Traits ◽  
Donor Species

Abstract Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.

Diversity and conservation priorities of crop wild relatives in Mexico

2019 ◽  
Vol 17 (2) ◽  
pp. 140-150 ◽  
Author(s):  
Aremi R. Contreras-Toledo ◽  
Moisés Cortés-Cruz ◽  
Denise E. Costich ◽  
Ma. de Lourdes Rico-Arce ◽  
Joana Magos Brehm ◽  
...  
Keyword(s):  
Climate Change ◽  
Gap Analysis ◽  
Conservation Status ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Conservation Strategy ◽  
Ex Situ ◽  
Cultivated Plants ◽  
Conservation Priorities

AbstractCrop wild relatives (CWR) are valuable resources for crop breeding due to their close genetic relationship to the cultivated plants and their wide genetic variation, allowing the introgression of desirable traits into the crops, such as resistance to plant pests and diseases or adaptability to climate change. Mexico is a centre of agrobiodiversity, including CWR, but climate change, and other factors, are contributing to the loss of important Mexican CWR genetic diversity. The in situ and ex situ conservation status of Mexican priority CWR were assessed through a gap analysis as part of a national CWR conservation strategy for Mexico, to ensure the long-term preservation and improve the availability of these genetic resources. A set of 310 priority CWR taxa, previously identified as part of the national CWR inventory for Mexico, were analysed. Species distribution modelling and ecogeographic diversity analyses were used to detect gaps in in situ and ex situ conservation at taxon and ecogeographic levels. Priority target sites were identified throughout the country for complementary in situ and ex situ conservation of these taxa. The results obtained allow us to make recommendations for immediate conservation actions, thus helping to mitigate the threats to Mexican agrobiodiversity and enhance both national and global food security.

scholarly journals Crop wild relative materials from field research in the Yakutsk vicinity in 2020

VAVILOVIA ◽  
2021 ◽  
Vol 3 (4) ◽  
pp. 6-22
Author(s):  
G. V. Talovina
Keyword(s):  
Plant Genetic Resources ◽  
Field Research ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Cultivated Plants ◽  
Herbarium Specimens ◽  
Lena River ◽  
Forest Phytocenoses ◽  
The Republic ◽  
Floodplain Habitats

The N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) is working on replenishing seed and herbarium collections of cultivated plants and their wild relatives through collection missions in various regions of Russia. The collections are replenished with both live specimens (plantlets, runners, cuttings, bulbs, seeds, etc.), and with herbarium specimens of crop wild relatives (CWR). The Republic of Sakha (Yakutia) is characterized by a variety of natural conditions and resources, while many territories are difficult to reach by transport. Collection missions were carried out by VIR in the territory of Yakutia from 1972 to 1990. Field research in the territory of the republic is relevant to this day.In 2020, field research in the area of the projected bridge crossing over the Lena River near the city of Yakutsk resulted in collecting 18 samples of wild relatives of fruit, vegetable, essential oil, oil and fiber, forage legume, and cereals crops (live plants and seeds), as well as 45 CWR herbarium specimens. CWR (species of currants, onions, horseradish, water sorrel, tarragon wormwood, etc.) were found in floodplain habitats and on river banks, some were collected in ruderal biotopes, near settlements, less often in forest phytocenoses, and on steppe meadow slopes. All the samples were included in VIR collections. The phytocenoses from which CWR were collected, were comprehensively described.

scholarly journals (6) Highly Polymorphic Genesin Cultivated Tomato

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 999A-999
Author(s):  
Angela Baldo ◽  
Larry Robertson ◽  
Joanne Labate
Keyword(s):  
Amino Acid ◽  
Single Nucleotide Polymorphisms ◽  
Germplasm Conservation ◽  
Wild Relatives ◽  
Nonsynonymous Snps ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Tomato Genome ◽  
Single Nucleotide

Cultivated tomato varieties are genetically extremely similar. We identified 764 Unigenes with potential single nucleotide polymorphisms (SNPs) among more than 15 cultivars from public expressed tomato data. By sequencing regions from 53 of these Unigenes in two to three cultivars, we discovered an unexpected wealth of nucleotide polymorphism (62 SNPs and 12 indels in 21 Unigenes). This included a high proportion of predicted nonsynonymous nucleotide (17 of 33 SNPs in exons) and nonconservative amino acid (6 of 16 nonsynonymous SNPs) changes. We hypothesize that five of these regions are associated with introgressions from wild relatives. Identifying polymorphic, expressed genes in the tomato genome will be useful for both tomato improvement and germplasm conservation.

scholarly journals Draft Genome Sequences of Two Natural Isolates of the Yeast Barnettozyma californica from Ireland, UCD09 and UCD89

2018 ◽  
Vol 6 (25) ◽  
Author(s):  
Alisha A. Mullen ◽  
Ciara D. Lynch ◽  
Shannon M. Hill ◽  
Cian P. Holohan ◽  
Tadhg Ó Cróinín ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Draft Genome ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Genome Sequences ◽  
Yeast Genus ◽  
Single Nucleotide ◽  
Content Type ◽  
The Family ◽  
Natural Isolates

ABSTRACT No genome sequence of a species from Barnettozyma, a yeast genus in the family Phaffomycetaceae, is currently available. We isolated two B. californica strains from soils in Ireland and generated draft sequences of their 11.7-Mb genomes. Single nucleotide polymorphism (SNP) analysis showed 20,490 differences between the strains and suggests that B. californica is haploid.

scholarly journals Culture of Clinical Specimens Reveals Extensive Diversity ofLegionella pneumophilaStrains in Arizona

mSphere ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Brian H. Raphael ◽  
Trung Huynh ◽  
Ellen Brown ◽  
Jessica C. Smith ◽  
Irene Ruberto ◽  
...  
Keyword(s):  
Diagnostic Methods ◽  
Genomic Diversity ◽  
Source Attribution ◽  
Nucleotide Polymorphism ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Content Type ◽  
Clinical Specimens ◽  
Diagnostic Approaches ◽  
Legionnaires Disease

ABSTRACTBetween 2000 and 2017, a total of 236Legionellaspecies isolates from Arizona were submitted to the CDC for reference testing. Most of these isolates were recovered from bronchoalveolar lavage specimens. Although the incidence of legionellosis in Arizona is less than the overall U.S. incidence, Arizona submits the largest number of isolates to the CDC for testing compared to those from other states. In addition to a higher proportion of culture confirmation of legionellosis cases in Arizona than in other states, allLegionellapneumophilaisolates are forwarded to the CDC for confirmatory testing. Compared to that from other states, a higher proportion of isolates from Arizona were identified as belonging toL. pneumophilaserogroups 6 (28.2%) and 8 (8.9%). Genome sequencing was conducted on 113L. pneumophilaclinical isolates not known to be associated with outbreaks in order to understand the genomic diversity of strains causing legionellosis in Arizona. Whole-genome multilocus sequence typing (wgMLST) revealed 17 clusters of isolates sharing at least 99% identical allele content. Only two of these clusters contained isolates from more than one individual with exposure at the same facility. Additionally, wgMLST analysis revealed a group of 31 isolates predominantly belonging to serogroup 6 and containing isolates from three separate clusters. Single nucleotide polymorphism (SNP) and pangenome analysis were used to further resolve genome sequences belonging to a subset of isolates. This study demonstrates that culture of clinical specimens forLegionellaspp. reveals a highly diverse population of strains causing legionellosis in Arizona which could be underappreciated using other diagnostic approaches.IMPORTANCECulture of clinical specimens from patients with Legionnaires’ disease is rarely performed, restricting our understanding of the diversity and ecology ofLegionella. Culture ofLegionellafrom patient specimens in Arizona revealed a greater proportion of non-serogroup 1Legionellapneumophilaisolates than in other U.S. isolates examined. Disease caused by such isolates may go undetected using other diagnostic methods. Moreover, genome sequence analysis revealed that these isolates were genetically diverse, and understanding these populations may help in future environmental source attribution studies.

Priorities for enhancing the ex situ conservation and use of Australian crop wild relatives

2017 ◽  
Vol 65 (8) ◽  
pp. 638 ◽  
Author(s):  
Sally L. Norton ◽  
Colin K. Khoury ◽  
Chrystian C. Sosa ◽  
Nora P. Castañeda-Álvarez ◽  
Harold A. Achicanoy ◽  
...  
Keyword(s):  
Species Richness ◽  
Ex Situ Conservation ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Habitat Destruction ◽  
Food Plants ◽  
Ex Situ ◽  
Cultivated Plants ◽  
Food Crops ◽  
Major Food

Crop wild relatives – the wild cousins of cultivated plants – are increasingly recognised for their potential to contribute to the productivity, nutritional quality and sustainability of agricultural crops. However, the use of these genetic resources is dependent upon their conservation in genebanks and consequent availability to plant breeders, the status of which has not been comprehensively analysed in Australia. Such conservation assessments are given urgency by reports of increasing threats to natural populations due to habitat destruction, climate change, and invasive species, among other causes. Here we document Australian wild plants related to important food crops, and outline their priorities for ex situ conservation. Given that no major domesticated food plants originated in the country, Australia’s native flora of crop wild relatives is surprisingly rich, including potentially valuable cousins of banana, eggplant, melon, mung bean, pigeonpea, rice, sorghum, sweetpotato, soybean and yam. Species richness of the wild relatives of major food crops is concentrated in the northern and north-eastern tropical regions, in the Northern Territory, Western Australia, and Queensland. Geographic priorities for collecting of these taxa for ex situ conservation, due to the limited representation of their populations in genebanks, largely align with areas of high species richness. Proposed dam building and agricultural expansion in northern Australia make conservation action for these species more urgent. We outline key steps needed for enhancing the ex situ conservation of Australia’s heritage of major food crop wild relatives, and discuss the critical activities required to increase their use.

scholarly journals Fully Closed Genome Sequences of Five Type Strains of the Genus  Cronobacter and One Cronobacter sakazakii Strain: TABLE 1

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Deborah Moine ◽  
Mohamed Kassam ◽  
Leen Baert ◽  
Yanjie Tang ◽  
Caroline Barretto ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Source Tracking ◽  
Cronobacter Sakazakii ◽  
Nucleotide Polymorphism ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Next Generation Sequencing Ngs ◽  
Type Strains ◽  
Reference Genomes ◽  
Generation Sequencing

Cronobacter is associated with infant infections and the consumption of reconstituted infant formula. Here we sequenced and closed six genomes of C. condimenti T , C. muytjensii T , C. universalis T , C. malonaticus T , C. dublinensis T , and C. sakazakii that can be used as reference genomes in single nucleotide polymorphism (SNP)-based next-generation sequencing (NGS) analysis for source tracking investigations.

Phylogenetic analysis of wheat cultivars in Kazakhstan based on the wheat 90 K single nucleotide polymorphism array

2015 ◽  
Vol 15 (1) ◽  
pp. 29-35 ◽  
Author(s):  
Yerlan Turuspekov ◽  
Joerg Plieske ◽  
Martin Ganal ◽  
Eduard Akhunov ◽  
Saule Abugalieva
Keyword(s):  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphism ◽  
Single Nucleotide Polymorphism Array ◽  
Genetic Relationships ◽  
Snp Array ◽  
Geographic Origin ◽  
Wheat Cultivars ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The World

The recent introduction of Illumina single nucleotide polymorphism (SNP) arrays is an important step towards comprehensive genome-wide studies of genetic diversity in wheat. In this study, 90 cultivars of hexaploid spring wheat growing in Kazakhstan were genotyped using the high-density wheat 90 K Illumina SNP array. The analysis allowed the identification of 30,288 polymorphic SNPs. A subset of 3541 high-quality SNPs were used for a comparison of 690 wheat accessions representing landraces and varieties, including those from Asia, Australia, Canada, Europe, Kazakhstan, USA and other parts of the world. Phylogenetic analysis showed a clear separation of wheat cultivars according to their geographic origin. In the phylogenetic tree, accessions from Kazakhstan and the USA formed two neighbouring clusters with a common node, and they were distinct from accessions from other regions of the world, including Europe. The results provide important new insights into the genetic relationships between diverse wheat accessions.

scholarly journals Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives

2021 ◽  
Vol 12 ◽  
Author(s):  
Rowena Hill ◽  
Theo Llewellyn ◽  
Elizabeth Downes ◽  
Joseph Oddy ◽  
Catriona MacIntosh ◽  
...  
Keyword(s):  
Seed Banks ◽  
Crop Wild Relatives ◽  
Fungal Endophyte ◽  
Wild Relatives ◽  
Wild Plants ◽  
Plant Host ◽  
Seed Collection ◽  
Crop Genetic Diversity ◽  
Royal Botanic Gardens ◽  
Beneficial Traits

Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs–primarily Lasiodiplodia, Fusarium, and Aspergillus–while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant–of significance in light of Fusarium wilt, a disease threatening global banana crops–and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.

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