scholarly journals Genomic regions associated with resistance to Fusarium wilt in castor identified through linkage and association mapping approaches

Genome ◽  
2021 ◽  
Author(s):  
Ranjan K. Shaw ◽  
Mobeen Shaik ◽  
M. Santha Lakshmi Prasad ◽  
R.D. Prasad ◽  
manmode darpan mohanrao ◽  
...  
Keyword(s):  
Association Mapping ◽  
Fusarium Wilt ◽  
Gene Diversity ◽  
Snp Markers ◽  
Phenotypic Variance ◽  
Wilt Resistance ◽  
Individual Snps ◽  
Efficiency And Effectiveness ◽  
The Individual ◽  
Genomic Regions

Fusarium wilt caused by <i>Fusarium oxysporum</i> f. sp <i>ricini</i> is the most destructive disease in castor. Host plant resistance is the best strategy for management of wilt problem. Identification of molecular markers linked to wilt resistance will enhance the efficiency and effectiveness of breeding for wilt resistance. In the present study, mapping of genomic regions linked to wilt resistance was attempted using a bi-parental population of 185 F<sub>6</sub>- RILs and a genetically diverse panel of 300 germplasm accessions. Quantitative trait loci (QTL) analysis performed using a linkage map consisting of 1,090 SNP markers identified a major QTL on chromosome-7 with LOD score of 18.7, which explained 44 per cent of phenotypic variance. The association mapping performed using genotypic data from 3,465 SNP loci revealed 69 significant associations (p <1×10-4) for wilt resistance. The phenotypic variance explained by the individual SNPs ranged from 0.063 to 0.210. The QTL detected in the bi-parental mapping population was not identified in the association analysis. Thus, the results of this study indicate the possibility of vast gene diversity for Fusarium wilt resistance in castor.

scholarly journals Development of a low-density panel for genomic selection of pigs in Russia1

2019 ◽  
Vol 4 (1) ◽  
pp. 264-274
Author(s):  
Tatiana I Shashkova ◽  
Elena U Martynova ◽  
Asiya F Ayupova ◽  
Artemy A Shumskiy ◽  
Polina A Ogurtsova ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Reference Population ◽  
Snp Markers ◽  
Full Potential ◽  
Low Density ◽  
Single Chip ◽  
Large White ◽  
Pork Production ◽  
Individual Snps ◽  
The Individual

Abstract Genomic selection is routinely used worldwide in agricultural breeding. However, in Russia, it is still not used to its full potential partially due to high genotyping costs. The use of genotypes imputed from the low-density chips (LD-chip) provides a valuable opportunity for reducing the genotyping costs. Pork production in Russia is based on the conventional 3-tier pyramid involving 3 breeds; therefore, the best option would be the development of a single LD-chip that could be used for all of them. Here, we for the first time have analyzed genomic variability in 3 breeds of Russian pigs, namely, Landrace, Duroc, and Large White and generated the LD-chip that can be used in pig breeding with the negligible loss in genotyping quality. We have demonstrated that out of the 3 methods commonly used for LD-chip construction, the block method shows the best results. The imputation quality depends strongly on the presence of close ancestors in the reference population. We have demonstrated that for the animals with both parents genotyped using high-density panels high-quality genotypes (allelic discordance rate &lt; 0.05) could be obtained using a 300 single nucleotide polymorphism (SNP) chip, while in the absence of genotyped ancestors at least 2,000 SNP markers are required. We have shown that imputation quality varies between chromosomes, and it is lower near the chromosome ends and drops with the increase in minor allele frequency. Imputation quality of the individual SNPs correlated well across breeds. Using the same LD-chip, we were able to obtain comparable imputation quality in all 3 breeds, so it may be suggested that a single chip could be used for all of them. Our findings also suggest that the presence of markers with extremely low imputation quality is likely to be explained by wrong mapping of the markers to the chromosomal positions.

Evaluation of Brassica oleracea accessions for resistance to Plasmodiophora brassicae and identification of genomic regions associated with resistance

Genome ◽  
2020 ◽  
Vol 63 (2) ◽  
pp. 91-101 ◽  
Author(s):  
Mehdi Farid ◽  
Rong-Cai Yang ◽  
Berisso Kebede ◽  
Habibur Rahman
Keyword(s):  
Brassica Oleracea ◽  
Crop Production ◽  
Plasmodiophora Brassicae ◽  
Snp Markers ◽  
Phenotypic Variance ◽  
Clubroot Disease ◽  
Brassica Crop ◽  
A Genome ◽  
C Genome ◽  
Genomic Regions

Clubroot disease caused by Plasmodiophora brassicae is a challenge to Brassica crop production. Breakdown of resistance controlled by major genes of the Brassica A genome has been reported. Therefore, identification of resistance in the Brassica C genome is needed to broaden the genetic base of resistance in Brassica napus canola. In this study, we evaluated 135 Brassica oleracea accessions, belonging to eight variants of this species to identify resistant accessions as well as to identify the genomic regions associated with resistance to two recently evolved P. brassicae pathotypes, F3-14 (3A) and F-359-13 (5X L-G2). Resistance to these pathotypes was observed more frequently in var. acephala (kale) followed by var. capitata (cabbage); few accessions also carried resistance to both pathotypes. Association mapping using single nucleotide polymorphism (SNP) markers developed through genotyping by sequencing technique identified 10 quantitative trait loci (QTL) from six C-genome chromosomes to be associated with resistance to these pathotypes; among these, two QTL associated with resistance to 3A and one QTL associated with resistance to 5X L-G2 carried ≥3 SNP markers. The 10 QTL identified in this study individually accounted for 8%–18% of the total phenotypic variance. Thus, the results from this study can be used in molecular breeding of Brassica crops for resistance to this disease.

Genome-wide association analyses of common wheat (Triticum aestivum L.) germplasm identifies multiple loci for aluminium resistanceThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 957-966 ◽  
Author(s):  
Harsh Raman ◽  
Benjamin Stodart ◽  
Peter R. Ryan ◽  
Emmanuel Delhaize ◽  
Livinus Emebiri ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Association Mapping ◽  
Common Wheat ◽  
Acid Soils ◽  
Triticum Aestivum L ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Association Analyses ◽  
Genome Wide ◽  
Genomic Regions

Aluminium (Al3+) toxicity restricts productivity and profitability of wheat ( Triticum aestivum L.) crops grown on acid soils worldwide. Continued gains will be obtained by identifying superior alleles and novel Al3+ resistance loci that can be incorporated into breeding programs. We used association mapping to identify genomic regions associated with Al3+ resistance using 1055 accessions of common wheat from different geographic regions of the world and 178 polymorphic diversity arrays technology (DArT) markers. Bayesian analyses based on genetic distance matrices classified these accessions into 12 subgroups. Genome-wide association analyses detected markers that were significantly associated with Al3+ resistance on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5B, 6A, 6B, 7A, and 7B. Some of these genomic regions correspond to previously identified loci for Al3+ resistance, whereas others appear to be novel. Among the markers targeting TaALMT1 (the major Al3+-resistance gene located on chromosome 4D), those that detected alleles in the promoter explained most of the phenotypic variance for Al3+ resistance, which is consistent with this region controlling the level of TaALMT1 expression. These results demonstrate that genome-wide association mapping cannot only confirm known Al3+-resistance loci, such as those on chromsomes 4D and 4B, but they also highlight the utility of this technique in identifying novel resistance loci.

scholarly journals Association Mapping for Fusarium Wilt Resistance in Chinese Asparagus Bean Germplasm

2015 ◽  
Vol 8 (2) ◽  
Author(s):  
Xinyi Wu ◽  
Xiaohua Wu ◽  
Pei Xu ◽  
Baogen Wang ◽  
Zhongfu Lu ◽  
...  
Keyword(s):  
Association Mapping ◽  
Fusarium Wilt ◽  
Wilt Resistance ◽  
Asparagus Bean ◽  
Fusarium Wilt Resistance

Screening and Validation of Drought Tolerance and Fusarium Wilt Resistance in Advance Breeding Lines of Chickpea (Cicer arietinum L.)

2021 ◽  
Author(s):  
Yuvaraja Lambani ◽  
Laxuman . ◽  
R. Lokesha ◽  
Mahendar Thudi ◽  
Manish Roorkiwal ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Agricultural Research ◽  
Snp Markers ◽  
Research Station ◽  
Early Maturity ◽  
Wilt Resistance ◽  
Breeding Lines ◽  
Terminal Drought ◽  
Drought Tolerant ◽  
Fusarium Wilt Resistance

Background: Approximately 90% of the world’s chickpea is grown under rainfed conditions where terminal drought is one of the major constraints limiting productivity. The need of short-duration, Fusarium wilt tolerant cultivars/elite lines and able to escape drought due to early maturity were required. Methods: The present investigation was carried out using 54 genotypes, generated from six diverse crosses, along with ten checks (resistant/tolerance, susceptible) were screened against drought and Fusarium wilt at Zonal Agricultural Research Station, Kalaburagi, Karnataka (Latitude: 17.36 and Longitude: 76.82) during crop season 2018-19. Result: The results revealed that higher PCV, GCV, heritability, percent genetic advance were exhibited by number of pods per plant and seed yield per plot, whereas lower PCV, GCV recorded for days to 50% flowering and days to maturity in both normal and late sown conditions. The advanced breeding lines viz., KCD-8, KCD-24, KCD-28, KCD-32, KCD-37 and KCD-53 were identified as drought tolerant lines based on drought tolerant indices (viz., MP, YSI, DTE and DSI). The lines KCD-48 and KCD-32 were identified as Fusarium wilt resistance with lowest PDI of 1.47 and 2.46 respectively, as they were screened in wilt sick plot and further these were validated and confirmed the resistant alleles using two unpublished SNP markers (FW2_30366110 and FW2_30365816). The advanced breeding lines KCD-32 and KCD-37 were identified as drought tolerant and Fusarium wilt resistant.

scholarly journals Genomic regions associated with chocolate spot (Botrytis fabae Sard.) resistance in faba bean (Vicia faba L.)

2021 ◽  
Author(s):  
Tadesse S. Gela ◽  
Margaret Bruce ◽  
Wei Chang ◽  
Frederick L. Stoddard ◽  
Alan H. Schulman ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Faba Bean ◽  
Snp Markers ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Resistance Qtls ◽  
Climate Conditions ◽  
Botrytis Fabae ◽  
Chocolate Spot ◽  
Genomic Regions

Chocolate spot (CS), caused by Botrytis fabae Sard., is an important threat to global faba bean production. Growing resistant faba bean cultivars is, therefore, paramount to preventing yield loss. To date, there have been no reported quantitative trait loci (QTLs) associated with CS resistance in faba bean. The objective of this study was to identify genomic regions associated with CS resistance using a recombinant inbred line (RIL) population derived from resistant accession ILB 938. A total of 165 RILs from the cross between Melodie/2 and ILB 938/2 were genotyped and evaluated for CS reactions under replicated, controlled climate conditions. QTL analysis identified five loci contributing to CS resistance on faba bean chromosomes 1 and 6, accounting for 5.0-23.4% of the total phenotypic variance. The sequences of SNP markers linked to resistance QTLs on chromosome 1 that have the largest effects encode multiple classes of putative disease and/or defense-related genes. The results of this study not only provide insight into disease-resistance QTLs, but can also be used as potential targets for marker-assisted breeding in faba bean genetic improvement for CS resistance. Keywords: Botrytis fabae; chocolate spot; faba bean; disease resistance; QTL mapping; candidate gene

scholarly journals The Liability Threshold Model for Predicting the Risk of Cardiovascular Disease in Patients with Type 2 Diabetes: A Multi-Cohort Study of Korean Adults

Metabolites ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 6
Author(s):  
Eun Pyo Hong ◽  
Seong Gu Heo ◽  
Ji Wan Park
Keyword(s):  
Type 2 Diabetes ◽  
Cardiovascular Disease ◽  
Risk Prediction ◽  
Linear Mixed Model ◽  
Threshold Model ◽  
Snp Markers ◽  
Polygenic Risk Score ◽  
Phenotypic Variance ◽  
Prediction Approach

Personalized risk prediction for diabetic cardiovascular disease (DCVD) is at the core of precision medicine in type 2 diabetes (T2D). We first identified three marker sets consisting of 15, 47, and 231 tagging single nucleotide polymorphisms (tSNPs) associated with DCVD using a linear mixed model in 2378 T2D patients obtained from four population-based Korean cohorts. Using the genetic variants with even modest effects on phenotypic variance, we observed improved risk stratification accuracy beyond traditional risk factors (AUC, 0.63 to 0.97). With a cutoff point of 0.21, the discrete genetic liability threshold model consisting of 231 SNPs (GLT231) correctly classified 87.7% of 2378 T2D patients as high or low risk of DCVD. For the same set of SNP markers, the GLT and polygenic risk score (PRS) models showed similar predictive performance, and we observed consistency between the GLT and PRS models in that the model based on a larger number of SNP markers showed much-improved predictability. In silico gene expression analysis, additional information was provided on the functional role of the genes identified in this study. In particular, HDAC4, CDKN2B, CELSR2, and MRAS appear to be major hubs in the functional gene network for DCVD. The proposed risk prediction approach based on the liability threshold model may help identify T2D patients at high CVD risk in East Asian populations with further external validations.

Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 423-434
Author(s):  
Jan Dvorřák ◽  
Ming-Cheng Luo ◽  
Zu-Li Yang
Keyword(s):  
Related Species ◽  
Gene Diversity ◽  
Single Copy ◽  
Species Variation ◽  
Recombination Rates ◽  
Distal Chromosome ◽  
Phylogenetic Status ◽  
Average Gene ◽  
Genomic Regions ◽  
Chromosome Regions

Abstract RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.

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