scholarly journals The Ficus erecta genome to identify the Ceratocystis canker resistance gene for breeding programs in common fig (F. carica)

2019 ◽  
Author(s):  
Kenta Shirasawa ◽  
Hiroshi Yakushiji ◽  
Ryotaro Nishimura ◽  
Takeshige Morita ◽  
Shota Jikumaru ◽  
...  
Keyword(s):  
Single Molecule ◽  
Resistance Breeding ◽  
Nucleotide Polymorphisms ◽  
Donor Genome ◽  
Breeding Programs ◽  
Common Fig ◽  
Genome Wide ◽  
Resistance Trait ◽  
Whole Genome Resequencing ◽  
Recurrent Backcrossing

AbstractFicus erecta, a wild relative of common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programs. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig; however, this is time consuming and labor-intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programs. The genome sequence of F. erecta was determined using single-molecule real-time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51,806 high-confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double-digest restriction-site associated DNA sequencing. Subsequent linkage analysis and whole genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome-wide genotyping analysis enabled selection of female lines that possessed resistance and effective elimination of donor genome from progeny. The genome resources provided in this study will accelerate and enhance disease resistance breeding programs in fig.

scholarly journals Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261461
Author(s):  
Girma Mengistu ◽  
Hussein Shimelis ◽  
Ermias Assefa ◽  
Dagnachew Lule
Keyword(s):  
Sorghum Bicolor ◽  
Resistance Breeding ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Breeding Programs ◽  
Anthracnose Resistance ◽  
Progress Curve ◽  
Genome Wide ◽  
Population Structure Analysis

In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

scholarly journals Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation

2019 ◽  
Vol 48 (D1) ◽  
pp. D659-D667 ◽  
Author(s):  
Wenqian Yang ◽  
Yanbo Yang ◽  
Cecheng Zhao ◽  
Kun Yang ◽  
Dongyang Wang ◽  
...  
Keyword(s):  
Large Scale ◽  
Association Studies ◽  
Genotype Imputation ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Whole Genome Resequencing ◽  
Missing Genotypes

Abstract Animal-ImputeDB (http://gong_lab.hzau.edu.cn/Animal_ImputeDB/) is a public database with genomic reference panels of 13 animal species for online genotype imputation, genetic variant search, and free download. Genotype imputation is a process of estimating missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs) and thus can be widely used in large-scale genome-wide association studies (GWASs) using relatively inexpensive and low-density SNP arrays. However, most animals except humans lack high-quality reference panels, which greatly limits the application of genotype imputation in animals. To overcome this limitation, we developed Animal-ImputeDB, which is dedicated to collecting genotype data and whole-genome resequencing data of nonhuman animals from various studies and databases. A computational pipeline was developed to process different types of raw data to construct reference panels. Finally, 13 high-quality reference panels including ∼400 million SNPs from 2265 samples were constructed. In Animal-ImputeDB, an easy-to-use online tool consisting of two popular imputation tools was designed for the purpose of genotype imputation. Collectively, Animal-ImputeDB serves as an important resource for animal genotype imputation and will greatly facilitate research on animal genomic selection and genetic improvement.

scholarly journals Mapping of Diabetes Susceptibility Loci in a Domestic Cat Breed with an Unusually High Incidence of Diabetes Mellitus

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1369 ◽  
Author(s):  
Lois Balmer ◽  
Caroline Ann O’Leary ◽  
Marilyn Menotti-Raymond ◽  
Victor David ◽  
Stephen O’Brien ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Candidate Genes ◽  
The United States ◽  
Domestic Cat ◽  
Nucleotide Polymorphisms ◽  
Breeding Programs ◽  
Preventative Health ◽  
Genome Wide ◽  
A Genome

Genetic variants that are associated with susceptibility to type 2 diabetes (T2D) are important for identification of individuals at risk and can provide insights into the molecular basis of disease. Analysis of T2D in domestic animals provides both the opportunity to improve veterinary management and breeding programs as well as to identify novel T2D risk genes. Australian-bred Burmese (ABB) cats have a 4-fold increased incidence of type 2 diabetes (T2D) compared to Burmese cats bred in the United States. This is likely attributable to a genetic founder effect. We investigated this by performing a genome-wide association scan on ABB cats. Four SNPs were associated with the ABB T2D phenotype with p values <0.005. All exons and splice junctions of candidate genes near significant single-nucleotide polymorphisms (SNPs) were sequenced, including the genes DGKG, IFG2BP2, SLC8A1, E2F6, ETV5, TRA2B and LIPH. Six candidate polymorphisms were followed up in a larger cohort of ABB cats with or without T2D and also in Burmese cats bred in America, which exhibit low T2D incidence. The original SNPs were confirmed in this cohort as associated with the T2D phenotype, although no novel coding SNPs in any of the seven candidate genes showed association with T2D. The identification of genetic markers associated with T2D susceptibility in ABB cats will enable preventative health strategies and guide breeding programs to reduce the prevalence of T2D in these cats.

scholarly journals Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens

2014 ◽  
Vol 27 (3) ◽  
pp. 196-206 ◽  
Author(s):  
Vivianne G. A. A. Vleeshouwers ◽  
Richard P. Oliver
Keyword(s):  
Fungicide Resistance ◽  
Plant Pathogens ◽  
Functional Characterization ◽  
Resistance Breeding ◽  
World Population ◽  
Breeding Programs ◽  
Genome Wide ◽  
Disease Resistance Breeding ◽  
Pathogen Populations ◽  
New Strategies

One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. “Effectoromics” has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.

scholarly journals Extreme resistance to Potato Virus Y in potato carrying the Rysto gene is mediated by a TIR-NLR immune receptor

2018 ◽  
Author(s):  
Marta Grech-Baran ◽  
Kamil Witek ◽  
Katarzyna Szajko ◽  
Agnieszka I Witek ◽  
Karolina Morgiewicz ◽  
...  
Keyword(s):  
Single Molecule ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Resistance Breeding ◽  
Transgenic Potato ◽  
Extreme Resistance ◽  
Breeding Programs ◽  
Potato Plants ◽  
Gene Enrichment ◽  
Transgenic Potato Plants

ABSTRACTPotato virus Y (PVY) is a major potato pathogen that causes annual losses of billions of dollars. Control of its transmission requires extensive use of environmentally damaging insecticides. Rysto confers extreme resistance (ER) to PVY and is a valuable trait in resistance breeding programs. We isolated Rysto using Resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences Single-Molecule Real Time Sequencing). Rysto encodes a nucleotide binding-leucine rich repeat (NLR) protein with an N-terminal TIR domain, and is sufficient for PVY perception and extreme resistance in transgenic potato plants. We investigated the requirements for Rysto-dependent extreme resistance, and showed that Rysto function is temperature-independent and requires EDS1 and NRG1 proteins. Rysto may prove valuable for creating PVY-resistant cultivars of potato and other Solanaceae crops.

scholarly journals Characterization of Geminivirus Resistance in an Accession of Capsicum chinense Jacq.

2011 ◽  
Vol 24 (2) ◽  
pp. 172-182 ◽  
Author(s):  
Marco A. García-Neria ◽  
Rafael F. Rivera-Bustamante
Keyword(s):  
Systemic Acquired Resistance ◽  
Acquired Resistance ◽  
Resistance Breeding ◽  
Marker Genes ◽  
Oxygen Species ◽  
Breeding Programs ◽  
Viral Movement ◽  
Resistance Trait ◽  
Defensive Mechanism

Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV), members of the Geminiviridae family, are important pathogens of pepper (Capsicum annuum L.) and other solanaceous crops. Accession BG-3821 of C. chinense Jacq. was reported earlier as resistant to mixed infection with PepGMV and PHYVV. In this work, we characterized the Geminivirus resistance trait present in BG-3821. Segregation analysis suggested that resistance depends on two genes. Our data showed that PepGMV replication in protoplast of resistant plants is approximately 70% lower when compared with the levels observed in protoplasts from susceptible plants. Additionally, viral movement is less efficient in resistant plants. We also evaluated several characteristics commonly associated with systemic acquired resistance (SAR), which is a conserved defensive mechanism. The concentration of salicylic acid was higher in resistant plants inoculated with PepGMV than in susceptible plants. Marker genes for SAR were induced after inoculation with PepGMV in resistant leaves. Similarly, we found a higher accumulation of reactive oxygen species on resistant leaves compared with susceptible ones. A model for the mechanism acting in the Geminivirus resistance detected in BG-3821 is proposed. Finally, the importance of BG-3821 in Geminivirus resistance breeding programs is discussed.

scholarly journals Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Laura Iacolina ◽  
Astrid V. Stronen ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska ◽  
Louise S. Nørgaard ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Cattle Breed ◽  
European Bison ◽  
Nucleotide Polymorphisms ◽  
Runs Of Homozygosity ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Visual Identification ◽  
Genome Wide ◽  
Or Groups

Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.

scholarly journals Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon

Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 8
Author(s):  
Siyoung Lee ◽  
Girim Park ◽  
Yunseo Choi ◽  
Seoyeon Park ◽  
Hoytaek Kim ◽  
...  
Keyword(s):  
Genomic Region ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Genome Resequencing ◽  
Isogenic Lines ◽  
Genome Wide ◽  
Donor Parent ◽  
Caps Markers ◽  
Whole Genome Resequencing

Trans-lycopene is a functional phytochemical abundant in red-fleshed watermelons, and its contents vary among cultivars. In this study, the genetic basis of high trans-lycopene contents in scarlet red flesh was evaluated. Three near-isogenic lines (NILs) with high trans-lycopene contents were derived from the scarlet red-fleshed donor parent DRD and three coral red-fleshed (low trans-lycopene contents) recurrent parents. The lycopene contents of DRD (589.4 ± 71.8 µg/g) were two times higher than that of the recurrent parents, and values for NILs were intermediate between those of the parents. Coral red-fleshed lines and F1 cultivars showed low trans-lycopene contents (135.7 ± 18.0 µg/g to 213.7 ± 39.5 µg/g). Whole-genome resequencing of two NILs and their parents and an analysis of genome-wide single-nucleotide polymorphisms revealed three common introgressed regions (CIRs) on chromosomes 6, 9, and 10. Twenty-eight gene-based cleaved amplified polymorphic sequence (CAPS) markers were developed from the CIRs. The CAPS markers derived from CIR6 on chromosome 6, spanning approximately 1 Mb, were associated (R2 = 0.45–0.72) with the trans-lycopene contents, particularly CIR6-M1 and CIR6-M4. Our results imply that CIR6 is a major genomic region associated with variation in the trans-lycopene contents in red-fleshed watermelon, and CIR6-M1 and CIR6-M4 may be useful for marker-assisted selection.

scholarly journals Mapping of susceptible variants for cold medicine-related Stevens–Johnson syndrome by whole-genome resequencing

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Yosuke Kawai ◽  
Yuki Hitomi ◽  
Mayumi Ueta ◽  
Seik-Soon Khor ◽  
Ken Nakatani ◽  
...  
Keyword(s):  
Rare Variants ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Stevens Johnson Syndrome ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Severe Condition ◽  
Genome Wide ◽  
Johnson Syndrome ◽  
Whole Genome Resequencing

AbstractStevens–Johnson syndrome (SJS) and its severe condition with extensive skin detachment and a poor prognosis, toxic epidermal necrolysis (TEN), are immunologically mediated severe cutaneous reactions of the skin and mucous membranes such as the ocular surface. Genetic variations on theHLA-Aand other autosomal genes have been identified as risk factors for cold medicine-related SJS/TEN with severe ocular complications (CM-SJS/TEN with SOC). Using a whole-genome sequencing (WGS) approach, we explored other susceptible variants of CM-SJS/TEN with SOC, especially among rare variants and structural variants (SVs). WGS was performed on samples from 133 patients with CM-SJS/TEN with SOC and 418 healthy controls to obtain single nucleotide polymorphisms (SNPs) and SVs. Genome-wide association tests were performed with these variants. Our genome-wide association test reproduced the associations of the common variants ofHLA-Aand loci on chromosome 16q12.1. We also identified novel associations of SVs on these loci and an aggregation of rare coding variants on theTPRM8gene. In silico gene expression analysis on theHLA-Alocus revealed that the SNP (rs12202296), which was significantly associated with susceptibility to CM-SJS/TEN with SOC, was correlated to an increase inHLA-Aexpression levels in the whole blood (P = 2.9 × 10−17), from the GTEx database. The majority of variants that were significantly associated with CM-SJS/TEN with SOC were found in non-coding regions, indicating the regulatory role of genetic variations in the pathogenesis of CM-SJS/TEN with SOC.

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