scholarly journals Genome-wide Association for Plant Height and Flowering Time across 15 Tropical Maize Populations under Managed Drought Stress and Well-Watered Conditions in Sub-Saharan Africa

Crop Science ◽  
2016 ◽  
Vol 56 (5) ◽  
pp. 2365-2378 ◽  
Author(s):  
Jason G. Wallace ◽  
Xuecai Zhang ◽  
Yoseph Beyene ◽  
Kassa Semagn ◽  
Michael Olsen ◽  
...  
Keyword(s):  
Drought Stress ◽  
Flowering Time ◽  
Plant Height ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Tropical Maize ◽  
Maize Populations ◽  
Genome Wide ◽  
Sub Saharan

Molecular Improvement of Tropical Maize for Drought Stress Tolerance in Sub-Saharan Africa

2009 ◽  
Vol 28 (1-2) ◽  
pp. 16-35 ◽  
Author(s):  
Sylvester Anami ◽  
Marc De Block ◽  
Jesse Machuka ◽  
Mieke Van Lijsebettens
Keyword(s):  
Drought Stress ◽  
Stress Tolerance ◽  
Sub Saharan Africa ◽  
Tropical Maize ◽  
Drought Stress Tolerance ◽  
Sub Saharan

scholarly journals A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

2018 ◽  
Author(s):  
Veena Devi Ganeshan ◽  
Stephen O. Opiyo ◽  
Samuel K. Mutiga ◽  
Felix Rotich ◽  
David M. Thuranira ◽  
...  
Keyword(s):  
Association Study ◽  
Magnaporthe Oryzae ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Sub Saharan ◽  
Genomic Regions

ABSTRACTThe fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.

scholarly journals Genetic dissection of Striga hermonthica (Del.) Benth. resistance via genome-wide association and genomic prediction in tropical maize germplasm

2021 ◽  
Author(s):  
Manje Gowda ◽  
Dan Makumbi ◽  
Biswanath Das ◽  
Christine Nyaga ◽  
Titus Kosgei ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Genome Wide Association Study ◽  
Smallholder Farmers ◽  
Snp Markers ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Striga Hermonthica ◽  
Tropical Maize ◽  
Genome Wide ◽  
Indicator Traits

Abstract Key message Genome-wide association revealed that resistance to Striga hermonthica is influenced by multiple genomic regions with moderate effects. It is possible to increase genetic gains from selection for Striga resistance using genomic prediction. Abstract Striga hermonthica (Del.) Benth., commonly known as the purple witchweed or giant witchweed, is a serious problem for maize-dependent smallholder farmers in sub-Saharan Africa. Breeding for Striga resistance in maize is complicated due to limited genetic variation, complexity of resistance and challenges with phenotyping. This study was conducted to (i) evaluate a set of diverse tropical maize lines for their responses to Striga under artificial infestation in three environments in Kenya; (ii) detect quantitative trait loci associated with Striga resistance through genome-wide association study (GWAS); and (iii) evaluate the effectiveness of genomic prediction (GP) of Striga-related traits. An association mapping panel of 380 inbred lines was evaluated in three environments under artificial Striga infestation in replicated trials and genotyped with 278,810 single-nucleotide polymorphism (SNP) markers. Genotypic and genotype x environment variations were significant for measured traits associated with Striga resistance. Heritability estimates were moderate (0.42) to high (0.92) for measured traits. GWAS revealed 57 SNPs significantly associated with Striga resistance indicator traits and grain yield (GY) under artificial Striga infestation with low to moderate effect. A set of 32 candidate genes physically near the significant SNPs with roles in plant defense against biotic stresses were identified. GP with different cross-validations revealed that prediction of performance of lines in new environments is better than prediction of performance of new lines for all traits. Predictions across environments revealed high accuracy for all the traits, while inclusion of GWAS-detected SNPs led to slight increase in the accuracy. The item-based collaborative filtering approach that incorporates related traits evaluated in different environments to predict GY and Striga-related traits outperformed GP for Striga resistance indicator traits. The results demonstrated the polygenic nature of resistance to S. hermonthica, and that implementation of GP in Striga resistance breeding could potentially aid in increasing genetic gain for this important trait.

scholarly journals Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Javed Akhatar ◽  
Anna Goyal ◽  
Navneet Kaur ◽  
Chhaya Atri ◽  
Meenakshi Mittal ◽  
...  
Keyword(s):  
Plant Height ◽  
Indian Subcontinent ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Strong Interactions ◽  
N Availability ◽  
Oilseed Crop ◽  
Genome Wide Association Studies ◽  
Genome Wide

AbstractTimely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.

scholarly journals Methylome-wide analysis reveals epigenetic marks associated with resistance to tuberculosis in HIV-infected individuals from East Africa

2020 ◽  
Author(s):  
Catherine Stein ◽  
Penelope Bencheck ◽  
Jacquelaine Bartlett ◽  
Robert P Igo ◽  
Rafal S Sobota ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Sub Saharan Africa ◽  
Chromosome 1 ◽  
Chromosome 2 ◽  
Chromosome 5 ◽  
Epigenetic Marks ◽  
Genome Wide ◽  
A Genome ◽  
Immunodeficiency Virus ◽  
Sub Saharan

Background: Tuberculosis (TB) is the most deadly infectious disease globally and highly prevalent in the developing world, especially sub-Saharan Africa. Even though a third of humans are exposed to Myocbacterium tuberculosis (Mtb), most infected immunocompetent individuals do not develop active TB. In contrast, for individuals infected with both TB and the human immunodeficiency virus (HIV), the risk of active disease is 10% or more per year. Previously, we identified in a genome-wide association study a region on chromosome 5 that was associated with resistance to TB. This region included epigenetic marks that could influence gene regulation so we hypothesized that HIV-infected individuals exposed to Mtb, who remain disease free, carry epigenetic changes that strongly protect them from active TB. To test this hypothesis, we conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania. Results: In 221 HIV-infected adults from Uganda and Tanzania, we identified 3 regions of interest that included markers that were differentially methylated between TB cases and LTBI controls, that also included methylation QTLs and associated SNPs: chromosome 1 (RNF220, p=4x10-5), chromosome 2 (between COPS8 and COL6A3 genes, p=2.7x10-5), and chromosome 5 (CEP72, p=1.3x10-5). These methylation results colocalized with associated SNPs, methylation QTLs, and methylation x SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. Conclusion: Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.

scholarly journals Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

2019 ◽  
Author(s):  
Waltram Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Fengmin Wang ◽  
Yan Feng ◽  
...  
Keyword(s):  
Association Study ◽  
Genomic Selection ◽  
Candidate Genes ◽  
Plant Height ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide

Abstract Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

scholarly journals Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

2021 ◽  
Author(s):  
Dev Paudel ◽  
Rocheteau Dareus ◽  
Julia Rosenwald ◽  
Maria Munoz-Amatriain ◽  
Esteban Rios
Keyword(s):  
Flowering Time ◽  
Candidate Genes ◽  
Vigna Unguiculata ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Human Consumption ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Genome Wide

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

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