scholarly journals Discovery and Validation of a Recessively Inherited Major-Effect QTL Conferring Resistance to Maize Lethal Necrosis (MLN) Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Ann Murithi ◽  
Michael S. Olsen ◽  
Daniel B. Kwemoi ◽  
Ogugo Veronica ◽  
Berhanu Tadesse Ertiro ◽  
...  
Keyword(s):  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Viral Disease ◽  
Major Effect ◽  
Eastern Africa ◽  
Source Population ◽  
Chromosome 6 ◽  
Maize Production ◽  
Breeding Populations ◽  
Progress Curve

Maize lethal necrosis (MLN) is a viral disease with a devastating effect on maize production. Developing and deploying improved varieties with resistance to the disease is important to effectively control MLN; however, little is known about the causal genes and molecular mechanism(s) underlying MLN resistance. Screening thousands of maize inbred lines revealed KS23-5 and KS23-6 as two of the most promising donors of MLN resistance alleles. KS23-5 and KS23-6 lines were earlier developed at the University of Hawaii, United States, on the basis of a source population constituted using germplasm from Kasetsart University, Thailand. Both linkage mapping and association mapping approaches were used to discover and validate genomic regions associated with MLN resistance. Selective genotyping of resistant and susceptible individuals within large F2 populations coupled with genome-wide association study identified a major-effect QTL (qMLN06_157) on chromosome 6 for MLN disease severity score and area under the disease progress curve values in all three F2 populations involving one of the KS23 lines as a parent. The major-effect QTL (qMLN06_157) is recessively inherited and explained 55%–70% of the phenotypic variation with an approximately 6 Mb confidence interval. Linkage mapping in three F3 populations and three F2 populations involving KS23-5 or KS23-6 as one of the parents confirmed the presence of this major-effect QTL on chromosome 6, demonstrating the efficacy of the KS23 allele at qMLN06.157 in varying populations. This QTL could not be identified in population that was not derived using KS23 lines. Validation of this QTL in six F2 populations with 20 SNPs closely linked with qMLN06.157 was further confirmed its consistent expression across populations and its recessive nature of inheritance. On the basis of the consistent and effective resistance afforded by the KS23 allele at qMLN06.157, the QTL can be used in both marker-assisted forward breeding and marker-assisted backcrossing schemes to improve MLN resistance of breeding populations and key lines for eastern Africa.

scholarly journals Genome‐Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High‐Quality Rice

2018 ◽  
Vol 11 (3) ◽  
pp. 170076 ◽  
Author(s):  
Gastón Quero ◽  
Lucía Gutiérrez ◽  
Eliana Monteverde ◽  
Pedro Blanco ◽  
Fernando Pérez de Vida ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
High Quality ◽  
Breeding Populations ◽  
Genome Wide ◽  
Genomic Regions

Linkage mapping and genome-wide association reveal candidate genes conferring thermotolerance of seed-set in maize

2019 ◽  
Vol 70 (18) ◽  
pp. 4849-4864 ◽  
Author(s):  
Jingyang Gao ◽  
Songfeng Wang ◽  
Zijian Zhou ◽  
Shiwei Wang ◽  
Chaopei Dong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Seed Set ◽  
Crop Yields ◽  
Expression Profiles ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

AbstractIt is predicted that high-temperature stress will increasingly affect crop yields worldwide as a result of climate change. In order to determine the genetic basis of thermotolerance of seed-set in maize under field conditions, we performed mapping of quantitative trait loci (QTLs) in a recombinant inbred line (RIL) population using a collection of 8329 specifically developed high-density single-nucleotide polymorphism (SNP) markers, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259 973 SNPs. In total, four QTLs and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified. Among them, four candidate genes were found in both linkage mapping and GWAS. Thermotolerance of seed-set was increased significantly in near-isogenic lines (NILs) that incorporated the four candidate genes in a susceptible parent background. The expression profiles of two of the four genes showed that they were induced by high temperatures in the maize tassel in a tolerant parent background. Our results indicate that thermotolerance of maize seed-set is regulated by multiple genes each of which has minor effects, with calcium signaling playing a central role. The genes identified may be exploited in breeding programs to improve seed-set and yield of maize under heat stress.

Genome-Wide Association Study of Piscine Myocarditis Virus (PMCV) Resistance in Atlantic Salmon (Salmo salar)

2019 ◽  
Vol 110 (6) ◽  
pp. 720-726 ◽  
Author(s):  
Borghild Hillestad ◽  
Hooman K Moghadam
Keyword(s):  
Genetic Variation ◽  
Atlantic Salmon ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Significant Quantitative Trait Locus ◽  
Viral Disease ◽  
Breeding Programs ◽  
Immunological Mechanisms ◽  
Trait Locus ◽  
Immune Related Genes

Abstract Cardiomyopathy syndrome is a severe, viral disease of Atlantic salmon that mostly affects farmed animals during their late production stage at sea. Caused by piscine myocarditis virus (PMCV), over the past few years outbreaks due to this disease have resulted in significant losses to the aquaculture industry. However, there is currently no vaccine that has proven effective against this virus. In this study, using a challenge model, we investigated the genetic variation for resistance to PMCV, by screening a large number of animals using a 55 K SNP array. In particular, we aimed to identify genetic markers that are tightly linked to higher disease resistance and can potentially be used in breeding programs. Using genomic information, we estimated a heritability of 0.51 ± 0.06, suggesting that resistance against this virus, to a great extent, is controlled by genetic factors. Through association analysis, we identified a significant quantitative trait locus (QTL) on chromosome 27, explaining approximately 57% of the total additive genetic variation. The region harboring this QTL contains various immune-related candidate genes, many of which have previously been shown to have a different expression profile between the naïve and infected animals. We also identified a suggestive association on chromosome 12, with the QTL linked markers located in 2 putatively immune-related genes. These results are of particular interest, as they can readily be implemented into breeding programs, can further assist in fine-mapping the causative mutations, and help in better understanding the biology of the disease and the immunological mechanisms underlying resistance against PMCV.

scholarly journals Phenotypic Stability and Genome-Wide Association Study of Late Blight Resistance in Potato Genotypes Adapted to the Tropical Highlands

2014 ◽  
Vol 104 (6) ◽  
pp. 624-633 ◽  
Author(s):  
Hannele Lindqvist-Kreuze ◽  
Manuel Gastelo ◽  
Willmer Perez ◽  
Gregory A. Forbes ◽  
David de Koeyer ◽  
...  
Keyword(s):  
Late Blight ◽  
Genome Wide Association Study ◽  
Principal Component ◽  
Late Blight Resistance ◽  
Breeding Population ◽  
Chromosome 9 ◽  
Blight Resistance ◽  
Tropical Highlands ◽  
Progress Curve ◽  
The Stability

Potato genotypes from a breeding population adapted to tropical highlands were analyzed for the stability of late blight resistance and also for marker-phenotype association. We harmonized the historical evaluation data, consisting of observations spanning 6 years from two field sites utilizing a resistance scale constructed by comparing the area under the disease progress curve (AUDPC) values of 172 genotypes with that of susceptible control ‘Yungay’. In total, 70 potato genotypes had a coefficient of variability <0.5 and were considered stable across the environments tested. A principal component analysis demonstrated that the ensemble of experiments formed two distinct groups that reflect the stability of genotype resistance to late blight. Phytophthora infestans isolates present in the experimental fields belonged to the EC-1 clonal lineage and showed variation in virulence beyond the concept of the avirulence determined by the conventionally used R1-R11 differential set. A single-nucleotide polymorphism (SNP) marker on chromosome 9 was associated with late blight resistance and linked to instability. Genotypes with either AACC or AAAC combinations for this SNP were highly resistant only in some environments, while the genotypes with the AAAA combination had more moderate levels of resistance but were stable across environments.

scholarly journals Gene duplication confers enhanced expression of 27-kDa γ-zein for endosperm modification in quality protein maize

2016 ◽  
Vol 113 (18) ◽  
pp. 4964-4969 ◽  
Author(s):  
Hongjun Liu ◽  
Junpeng Shi ◽  
Chuanlong Sun ◽  
Hao Gong ◽  
Xingming Fan ◽  
...  
Keyword(s):  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Genetic Selection ◽  
Quality Protein Maize ◽  
Genome Wide ◽  
Mapping Analysis ◽  
Enhanced Expression ◽  
Selection For ◽  
Trait Locus ◽  
Maize Domestication

The maize opaque2 (o2) mutant has a high nutritional value but it develops a chalky endosperm that limits its practical use. Genetic selection for o2 modifiers can convert the normally chalky endosperm of the mutant into a hard, vitreous phenotype, yielding what is known as quality protein maize (QPM). Previous studies have shown that enhanced expression of 27-kDa γ-zein in QPM is essential for endosperm modification. Taking advantage of genome-wide association study analysis of a natural population, linkage mapping analysis of a recombinant inbred line population, and map-based cloning, we identified a quantitative trait locus (qγ27) affecting expression of 27-kDa γ-zein. qγ27 was mapped to the same region as the major o2 modifier (o2 modifier1) on chromosome 7 near the 27-kDa γ-zein locus. qγ27 resulted from a 15.26-kb duplication at the 27-kDa γ-zein locus, which increases the level of gene expression. This duplication occurred before maize domestication; however, the gene structure of qγ27 appears to be unstable and the DNA rearrangement frequently occurs at this locus. Because enhanced expression of 27-kDa γ-zein is critical for endosperm modification in QPM, qγ27 is expected to be under artificial selection. This discovery provides a useful molecular marker that can be used to accelerate QPM breeding.

scholarly journals Conservation Genomics Reveals Low Connectivity Among Populations of Threatened Roseate Terns in the Atlantic Basin

2021 ◽  
Author(s):  
Paige Byerly ◽  
R. Terry Chesser ◽  
Robert Fleischer ◽  
Nancy McInerney ◽  
Natalia Przelomska ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Caribbean Region ◽  
Source Population ◽  
Population Declines ◽  
Conservation Genomics ◽  
Atlantic Basin ◽  
Seabird Species ◽  
Breeding Populations ◽  
The Caribbean ◽  
Roseate Tern

Abstract While the effects of barriers to dispersal such as population declines, habitat fragmentation, and geographic distance have been well-documented in terrestrial wildlife, factors impeding the dispersal of highly vagile taxa such as seabirds are less well understood. The roseate tern (Sterna dougallii) is a globally distributed seabird species, but populations tend to be both fragmented and small, and the species is declining across most of its range. Within the Atlantic Basin, past work has shown differentiation among roseate terns breeding on different continents, but these results were generated with a limited number of microsatellite markers. Relationships between breeding populations in the Northwestern Atlantic and the Caribbean have never been analyzed. We evaluated population structuring of roseate tern populations in North America and the Azores using both microsatellite markers and single-nucleotide polymorphisms generated through targeted sequencing of Ultra-conserved Elements. For both marker types, we found significant genetic differentiation among all 3 populations and evidence for moderate contemporary unidirectional gene flow from the Caribbean to the Azores, but not among other populations. Within the Caribbean metapopulation, we found high rates of unidirectional migration from the Virgin Islands to Florida, potentially indicative of movement from source population to sink or an artifact of dispersal among other unsampled populations in the Caribbean region. These observations have significance for species persistence in the Atlantic, as our results suggest that loss of genetic diversity within populations is unlikely to be buffered by inflow of new alleles from other breeding populations.

scholarly journals Identification and Validation of Genomic Regions Associated With Charcoal Rot Resistance in Tropical Maize by Genome-Wide Association and Linkage Mapping

2021 ◽  
Vol 12 ◽  
Author(s):  
Zerka Rashid ◽  
Harleen Kaur ◽  
Veerendra Babu ◽  
Pradeep Kumar Singh ◽  
Sharanappa I. Harlapur ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Macrophomina Phaseolina ◽  
Genome Wide Association ◽  
Common Disease ◽  
Chromosome 6 ◽  
Charcoal Rot ◽  
Stalk Rot ◽  
Genome Wide ◽  
A Genome ◽  
Mapping Populations

Charcoal rot is a post-flowering stalk rot (PFSR) disease of maize caused by the fungal pathogen, Macrophomina phaseolina. It is a serious concern for smallholder maize cultivation, due to significant yield loss and plant lodging at harvest, and this disease is expected to surge with climate change effects like drought and high soil temperature. For identification and validation of genomic variants associated with charcoal rot resistance, a genome-wide association study (GWAS) was conducted on CIMMYT Asia association mapping panel comprising 396 tropical-adapted lines, especially to Asian environments. The panel was phenotyped for disease severity across two locations with high disease prevalence in India. A subset of 296,497 high-quality SNPs filtered from genotyping by sequencing was correcting for population structure and kinship matrices for single locus mixed linear model (MLM) of GWAS analysis. A total of 19 SNPs were identified to be associated with charcoal rot resistance with P-value ranging from 5.88 × 10−06 to 4.80 × 10−05. Haplotype regression analysis identified 21 significant haplotypes for the trait with Bonferroni corrected P ≤ 0.05. For validating the associated variants and identifying novel QTLs, QTL mapping was conducted using two F2:3 populations. Two QTLs with overlapping physical intervals, qMSR6 and qFMSR6 on chromosome 6, identified from two different mapping populations and contributed by two different resistant parents, were co-located with the SNPs and haplotypes identified at 103.51 Mb on chromosome 6. Similarly, several SNPs/haplotypes identified on chromosomes 3, 6 and 8 were also found to be physically co-located within QTL intervals detected in one of the two mapping populations. The study also noted that several SNPs/haplotypes for resistance to charcoal rot were located within physical intervals of previously reported QTLs for Gibberella stalk rot resistance, which opens up a new possibility for common disease resistance mechanisms for multiple stalk rots.

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