Genome-wide introgression from a bread wheat × Lophopyrum elongatum amphiploid into wheat

2020 ◽  
Vol 133 (4) ◽  
pp. 1227-1241 ◽  
Author(s):  
Jiale Xu ◽  
Le Wang ◽  
Karin R. Deal ◽  
Tingting Zhu ◽  
Ramesh K. Ramasamy ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Lophopyrum Elongatum ◽  
Genome Wide

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

Plants ◽  
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.

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

Agronomy ◽  
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.

scholarly journals Variance heterogeneity genome‐wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Waseem Hussain ◽  
Malachy T. Campbell ◽  
Diego Jarquin ◽  
Harkamal Walia ◽  
Gota Morota
Keyword(s):  
Bread Wheat ◽  
Variance Heterogeneity ◽  
Epistatic Interactions ◽  
Genome Wide

Genome-wide association analysis of resistance to wheat spindle streak mosaic virus in bread wheat

2018 ◽  
Vol 68 (3) ◽  
pp. 609-616 ◽  
Author(s):  
D. Hourcade ◽  
M. Bogard ◽  
M. Bonnefoy ◽  
F. Savignard ◽  
F. Mohamadi ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Bread Wheat ◽  
Association Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yousef Rahimi ◽  
Mohammad Reza Bihamta ◽  
Alireza Taleei ◽  
Hadi Alipour ◽  
Pär K. Ingvarsson
Keyword(s):  
Bread Wheat ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Wheat Varieties ◽  
Data Set ◽  
Protein Coding ◽  
Genome Wide

Abstract Background Identification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). Genome-wide association studies (GWAS) have increasingly been used as potent tools in identifying marker-trait associations (MTAs). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Landraces collected from different climate zones can be an invaluable resource for such adaptive alleles. Results GWAS was performed using a collection of 298 Iranian bread wheat varieties and landraces to explore the genetic basis of agronomic traits during 2016–2018 cropping seasons under normal (well-watered) and stressed (rain-fed) conditions. A high-quality genotyping by sequencing (GBS) dataset was obtained using either all original single nucleotide polymorphism (SNP, 10938 SNPs) or with additional imputation (46,862 SNPs) based on W7984 reference genome. The results confirm that the B genome carries the highest number of significant marker pairs in both varieties (49,880, 27.37%) and landraces (55,086, 28.99%). The strongest linkage disequilibrium (LD) between pairs of markers was observed on chromosome 2D (0.296). LD decay was lower in the D genome, compared to the A and B genomes. Association mapping under two tested environments yielded a total of 313 and 394 significant (−log10P >3) MTAs for the original and imputed SNP data sets, respectively. Gene ontology results showed that 27 and 27.5% of MTAs of SNPs in the original set were located in protein-coding regions for well-watered and rain-fed conditions, respectively. While, for the imputed data set 22.6 and 16.6% of MTAs represented in protein-coding genes for the well-watered and rain-fed conditions, respectively. Conclusions Our finding suggests that Iranian bread wheat landraces harbor valuable alleles that are adaptive under drought stress conditions. MTAs located within coding genes can be utilized in genome-based breeding of new wheat varieties. Although imputation of missing data increased the number of MTAs, the fraction of these MTAs located in coding genes were decreased across the different sub-genomes.

scholarly journals The genome-wide transcriptional consequences of the nullisomic-tetrasomic stocks for homoeologous group 7 in bread wheat

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rongzhi Zhang ◽  
Shuaifeng Geng ◽  
Zhengrui Qin ◽  
Zongxiang Tang ◽  
Cheng Liu ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Homoeologous Group ◽  
Genome Wide

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

Agriculture ◽  
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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