Incorporating Genome-Wide Association Mapping Results Into Genomic Prediction Models for Grain Yield and Yield Stability in CIMMYT Spring Bread Wheat

AbstractCassava (Manihot esculenta Crantz), a key carbohydrate dietary source for millions of people in Africa, faces severe yield loses due to two viral diseases: cassava brown streak disease (CBSD) and cassava mosaic disease (CMD). The completion of the cassava genome sequence and the whole genome marker profiling of clones from African breeding programs (www.nextgencassava.org) provides cassava breeders the opportunity to deploy additional breeding strategies and develop superior varieties with both farmer and industry preferred traits. Here the identification of genomic segments associated with resistance to CBSD foliar symptoms and root necrosis as measured in two breeding panels at different growth stages and locations is reported. Using genome-wide association mapping and genomic prediction models we describe the genetic architecture for CBSD severity and identify loci strongly associated on chromosomes 4 and 11. Moreover, the significantly associated region on chromosome 4 colocalises with a Manihot glaziovii introgression segment and the significant SNP markers on chromosome 11 are situated within a cluster of nucleotide-binding site leucine-rich repeat (NBS-LRR) genes previously described in cassava. Overall, predictive accuracy values found in this study varied between CBSD severity traits and across GS models with Random Forest and RKHS showing the highest predictive accuracies for foliar and root CBSD severity scores.

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Genome-Wide Association Mapping and Genomic Prediction Analyses Reveal the Genetic Architecture of Grain Yield and Flowering Time Under Drought and Heat Stress Conditions in Maize

Frontiers in Plant Science ◽

10.3389/fpls.2018.01919 ◽

2019 ◽

Vol 9 ◽

Cited By ~ 23

Author(s):

Yibing Yuan ◽

Jill E. Cairns ◽

Raman Babu ◽

Manje Gowda ◽

Dan Makumbi ◽

...

Keyword(s):

Heat Stress ◽

Grain Yield ◽

Association Mapping ◽

Flowering Time ◽

Genomic Prediction ◽

Genetic Architecture ◽

Stress Conditions ◽

Genome Wide Association ◽

Genome Wide ◽

Drought And Heat Stress

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Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones

Scientific Reports ◽

10.1038/srep27312 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 31

Author(s):

C. Saint Pierre ◽

J. Burgueño ◽

J. Crossa ◽

G. Fuentes Dávila ◽

P. Figueroa López ◽

...

Keyword(s):

Grain Yield ◽

Bread Wheat ◽

Genomic Prediction ◽

Prediction Models ◽

Spring Bread Wheat ◽

Ecological Zones ◽

Agro Ecological Zones

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Genome-Wide Association and Prediction of Male and Female Floral Hybrid Potential Traits in Elite Spring Bread Wheat Genotypes

Plants ◽

10.3390/plants10050895 ◽

2021 ◽

Vol 10 (5) ◽

pp. 895

Author(s):

Samira El Hanafi ◽

Souad Cherkaoui ◽

Zakaria Kehel ◽

Ayed Al-Abdallat ◽

Wuletaw Tadesse

Keyword(s):

Genomic Selection ◽

Bread Wheat ◽

Genome Wide Association ◽

Hybrid Breeding ◽

Floral Traits ◽

Phenotypic Variance ◽

Spring Bread Wheat ◽

Genome Wide ◽

Anther Length ◽

Anther Extrusion

Hybrid wheat breeding is one of the most promising technologies for further sustainable yield increases. However, the cleistogamous nature of wheat displays a major bottleneck for a successful hybrid breeding program. Thus, an optimized breeding strategy by developing appropriate parental lines with favorable floral trait combinations is the best way to enhance the outcrossing ability. This study, therefore, aimed to dissect the genetic basis of various floral traits using genome-wide association study (GWAS) and to assess the potential of genome-wide prediction (GP) for anther extrusion (AE), visual anther extrusion (VAE), pollen mass (PM), pollen shedding (PSH), pollen viability (PV), anther length (AL), openness of the flower (OPF), duration of floret opening (DFO) and stigma length. To this end, we employed 196 ICARDA spring bread wheat lines evaluated for three years and genotyped with 10,477 polymorphic SNP. In total, 70 significant markers were identified associated to the various assessed traits at FDR ≤ 0.05 contributing a minor to large proportion of the phenotypic variance (8–26.9%), affecting the traits either positively or negatively. GWAS revealed multi-marker-based associations among AE, VAE, PM, OPF and DFO, most likely linked markers, suggesting a potential genomic region controlling the genetic association of these complex traits. Of these markers, Kukri_rep_c103359_233 and wsnp_Ex_rep_c107911_91350930 deserve particular attention. The consistently significant markers with large effect could be useful for marker-assisted selection. Genomic selection revealed medium to high prediction accuracy ranging between 52% and 92% for the assessed traits with the least and maximum value observed for stigma length and visual anther extrusion, respectively. This indicates the feasibility to implement genomic selection to predict the performance of hybrid floral traits with high reliability.

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Genome-Wide Association Mapping for Stomata and Yield Indices in Bread Wheat under Water Limited Conditions

Agronomy ◽

10.3390/agronomy11081646 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1646

Author(s):

Hafiz Ghulam Muhu-Din Ahmed ◽

Muhammad Nouman Iqbal ◽

Muhammad Arslan Iqbal ◽

Yawen Zeng ◽

Aziz Ullah ◽

...

Keyword(s):

Grain Yield ◽

Bread Wheat ◽

Significant Snps ◽

Water Shortage ◽

Genome Wide Association ◽

Yield Potential ◽

Strong Positive Correlation ◽

Leaf Venation ◽

Genome Wide ◽

Stomata Size

Genome-wide association study (GWAS) was performed for stomata- and yield-related attributes with high-density Illumina 90 K Infinium SNP (single nucleotide polymorphism) array in bread wheat to determine genetic potential of germplasm for scarce water resources with sustainable yield potential. Major yield and stomata attributes were phenotyped on a panel of Pakistani and foreign accessions grown in non-stressed and water shortage environments during two seasons. Highly significant variations were shown among accessions in both conditions for examined characteristics. Water shortage conditions reduced the overall wheat yield and strong positive correlation existed among stomatal frequency, leaf venation and grain yield per plant. Population structure analyses based on 90,000 SNP data classified the accessions into four sub-populations which indicated the presence of genetic variability. Marker-trait association (MTA) analyses revealed that 422 significant SNPs at p ≤ 10−3, after crossing the false discovery rate (FDR) <0.05 threshold, were linked with examined attributes. Pleiotropic loci (wsnp_Ex_c8913_14881924 and Tdurum_contig10598_304) were associated with flag leaf area (FLA), stomata size (SS), stomata frequency (SF), leaf venation (LV), number of grain per spike (NGS) and grain yield per plant (GYP), which were located on chromosome 4B and 6B at the positions 173.63cM and 229.64cM, respectively, under water shortage conditions. Pleotropic loci wsnp_Ex_c24167_33416760, wsnp_Ex_c5412_9564046 and Tdurum_contig81797_369 on chromosomes 7A, 2A and 4B at the positions 148.26cM, 261.05cM and 173.63cM, respectively, were significantly linked with stomata and yield indices such as FLA, SS, SF, LV, NGS and GYP under normal and water shortage conditions. The current experiment not only validated several MTAs for studied indices reported in other studies but also discovered novel MTAs significant under water shortage environments. Associated and significant SNPs will be useful in discovering novel genes underpinning water shortage tolerance in bread wheat for producing high-yielding and drought tolerant wheat varieties to fulfill the wheat demand for growing populations.

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Genome-wide association mapping and genomic prediction of yield-related traits and starch pasting properties in cassava

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03956-2 ◽

2021 ◽

Author(s):

Chalermpol Phumichai ◽

Pornsak Aiemnaka ◽

Piyaporn Nathaisong ◽

Sirikan Hunsawattanakul ◽

Phasakorn Fungfoo ◽

...

Keyword(s):

Association Mapping ◽

Genomic Prediction ◽

Pasting Properties ◽

Genome Wide Association ◽

Genome Wide

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Genetic architecture of grain yield in bread wheat based on genome-wide association studies

BMC Plant Biology ◽

10.1186/s12870-019-1781-3 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 29

Author(s):

Faji Li ◽

Weie Wen ◽

Jindong Liu ◽

Yong Zhang ◽

Shuanghe Cao ◽

...

Keyword(s):

Grain Yield ◽

Bread Wheat ◽

Genetic Architecture ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide

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Genome-Wide Association Mapping through 90K SNP Array for Quality and Yield Attributes in Bread Wheat against Water-Deficit Conditions

Agriculture ◽

10.3390/agriculture10090392 ◽

2020 ◽

Vol 10 (9) ◽

pp. 392

Author(s):

Hafiz Ghulam Muhu-Din Ahmed ◽

Muhammad Sajjad ◽

Yawen Zeng ◽

Muhammad Iqbal ◽

Sultan Habibullah Khan ◽

...

Keyword(s):

Grain Yield ◽

Candidate Genes ◽

Water Deficit ◽

Bread Wheat ◽

Genome Wide Association ◽

Water Deficit Stress ◽

Yield Attributes ◽

Yield And Quality ◽

Isolation And Characterization ◽

Genome Wide

The decrease in water resources is a serious threat to food security world-wide. In this regard, a genome-wide association study (GWAS) was conducted to identify grain yield and quality-related genes/loci under normal and water-deficit conditions. Highly significant differences were exhibited among genotypes under both conditions for all studied traits. Water-deficit stress caused a reduction in grains yield and an increase in grains protein contents (GPC) and gluten contents (GLC). Population structure divided the 96 genotypes into four sub-populations. Out of 72 significant marker-trait associations (MTAs), 28 and 44 were observed under normal and water-deficit stress conditions, respectively. Pleiotropic loci (RAC875_s117925_244, BobWhite_c23828_341 and wsnp_CAP8_c334_304253) for yield and quality traits were identified on chromosomes 5A, 6B and 7B, respectively, under normal conditions. Under a water-deficit condition, the pleiotropic loci (Excalibur_c48047_90, Tdurum_contig100702_265 and BobWhite_c19429_95) for grain yield per plant (GYP), GPC and GLC were identified on chromosomes 3A, 4A and 7B, respectively. The pleiotropic loci (BS00063551_51 and RAC875_c28721_290) for GPC and GLC on chromosome 1B and 3A, respectively, were found under both conditions. Besides the validation of previously reported MTAs, some new MTAs were identified for flag leaf area (FLA), thousand grain weight (TGW), GYP, GPC and GLC under normal and water-deficit conditions. Twenty SNPs associated with the traits were mapped in the coding DNA sequence (CDS) of the respective candidate genes. The protein functions of the identified candidate genes were predicted and discussed. Isolation and characterization of the candidate genes, wherein, SNPs were mapped in CDS will result in discovering novel genes underpinning water-deficit tolerance in bread wheat.

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