scholarly journals Genome-Wide Association Analysis for Stem Cross Section Properties, Height and Heading Date in a Collection of Spanish Durum Wheat Landraces

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1123
Author(s):  
Carmen M. Ávila ◽  
María Dolores Requena-Ramírez ◽  
Cristina Rodríguez-Suárez ◽  
Fernando Flores ◽  
Josefina C. Sillero ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Bread Wheat ◽  
Cross Section ◽  
Heading Date ◽  
Genome Wide Association ◽  
Plant Materials ◽  
Genome Wide ◽  
Culm Wall ◽  
Wheat Landraces ◽  
Durum Wheat Landraces

Durum wheat landraces have a high potential for breeding but they remain underexploited due to several factors, including the insufficient evaluation of these plant materials and the lack of efficient selection tools for transferring target traits into elite backgrounds. In this work, we characterized 150 accessions of the Spanish durum wheat collection for stem cross section, height and heading date. Continuous variation and high heritabilities were recorded for the stem area, pith area, pith diameter, culm wall thickness, height and heading date. The accessions were genotyped with DArTSeq markers, which were aligned to the durum wheat ‘Svevo’ genome. The markers corresponding to genes, with a minor allele frequency above 5% and less than 10% of missing data, were used for genome-wide association scan analysis. Twenty-nine marker-trait associations (MTAs) were identified and compared with the positions of previously known QTLs. MTAs for height and heading date co-localized with the QTLs for these traits. In addition, all the MTAs for stem traits in chromosome 2B were located in the corresponding synteny regions of the markers associated with lodging in bread wheat. Finally, several MTAs for stem traits co-located with the QTL for wheat stem sawfly (WSS) resistance. The results presented herein reveal the same genomic regions in chromosome 2B are involved in the genetic control of stem traits and lodging tolerance in both durum and bread wheat. In addition, these results suggest the importance of stem traits for WSS resistance and the potential of these landraces as donors for lodging tolerance and WSS resistance enhancement. In this context, the MTAs for stem-related traits identified in this work can serve as a reference for further development of markers for the introgression of target traits into elite material.

scholarly journals Exploring the Genetic Architecture of Root-Related Traits in Mediterranean Bread Wheat Landraces by Genome-Wide Association Analysis

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 613 ◽  
Author(s):  
Rubén Rufo ◽  
Silvio Salvi ◽  
Conxita Royo ◽  
Jose Soriano
Keyword(s):  
Molecular Markers ◽  
Bread Wheat ◽  
Root Development ◽  
Genome Wide Association Study ◽  
Abiotic Stress Tolerance ◽  
Genome Wide Association ◽  
Mediterranean Countries ◽  
Genome Wide ◽  
A Genome ◽  
Wheat Landraces

Background: Roots are essential for drought adaptation because of their involvement in water and nutrient uptake. As the study of the root system architecture (RSA) is costly and time-consuming, it is not generally considered in breeding programs. Thus, the identification of molecular markers linked to RSA traits is of special interest to the breeding community. The reported correlation between the RSA of seedlings and adult plants simplifies its assessment. Methods: In this study, a panel of 170 bread wheat landraces from 24 Mediterranean countries was used to identify molecular markers associated with the seminal RSA and related traits: seminal root angle, total root number, root dry weight, seed weight and shoot length, and grain yield (GY). Results: A genome-wide association study identified 135 marker-trait associations explaining 6% to 15% of the phenotypic variances for root related traits and 112 for GY. Fifteen QTL hotspots were identified as the most important for controlling root trait variation and were shown to include 31 candidate genes related to RSA traits, seed size, root development, and abiotic stress tolerance (mainly drought). Co-location for root related traits and GY was found in 17 genome regions. In addition, only four out of the fifteen QTL hotspots were reported previously. Conclusions: The variability found in the Mediterranean wheat landraces is a valuable source of root traits to introgress into adapted phenotypes through marker-assisted breeding. The study reveals new loci affecting root development in wheat.

scholarly journals Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

2020 ◽  
Author(s):  
Laura Pascual ◽  
Magdalena Ruiz ◽  
Matilde López-Fernández ◽  
Helena Pérez-Peña ◽  
Elena Benavente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Genome Wide Association Studies ◽  
Reference Set ◽  
Genome Wide ◽  
Wheat Landraces

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

scholarly journals Genome-wide association analysis of Mexican bread wheat landraces for resistance to yellow and stem rust

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0246015
Author(s):  
Prashant Vikram ◽  
Deepmala Sehgal ◽  
Achala Sharma ◽  
Sridhar Bhavani ◽  
Priyanka Gupta ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Association Analysis ◽  
Stem Rust ◽  
Principal Component ◽  
Genome Wide Association ◽  
Additive Interaction ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Core Set ◽  
Wheat Landraces

Deploying under-utilized landraces in wheat breeding has been advocated to accelerate genetic gains in current era of genomics assisted breeding. Mexican bread wheat landraces (Creole wheats) represent an important resource for the discovery of novel alleles including disease resistance. A core set of 1,098 Mexican landraces was subjected to multi-location testing for rust diseases in India, Mexico and Kenya. The landrace core set showed a continuous variation for yellow (YR) and stem rust (SR) disease severity. Principal component analysis differentiated Mexican landraces into three groups based on their respective collection sites. Linkage disequilibrium (LD) decay varied from 10 to 32 Mb across chromosomes with an averge of 23Mb across whole genome. Genome-wide association analysis revealed marker-trait associations for YR resistance in India and Mexico as well as for SR resistance in Kenya. In addition, significant additive-additive interaction effects were observed for both YR and SR resistance including genomic regions on chromosomes 1BL and 3BS, which co-locate with pleiotropic genes Yr29/Lr46/Sr58/Pm39/Ltn2 and Sr2/Yr30/Lr27, respectively. Study reports novel genomic associations for YR (chromosomes 1AL, 2BS, and 3BL) and SR (chromosomes 2AL, 4DS, and 5DS). The novel findings in Creole wheat landraces can be efficiently utilized for the wheat genetic improvement.

scholarly journals Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

2019 ◽  
Author(s):  
Laura Pascual ◽  
Magdalena Ruiz ◽  
Matilde López-Fernández ◽  
Helena Pérez-Peña ◽  
Elena Benavente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Genome Wide Association Studies ◽  
Reference Set ◽  
Genome Wide ◽  
Wheat Landraces

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were mapped against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

scholarly journals Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

2020 ◽  
Author(s):  
Laura Pascual ◽  
Magdalena Ruiz ◽  
Matilde López-Fernández ◽  
Helena Pérez-Peña ◽  
Elena Benavente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Genome Wide Association Studies ◽  
Reference Set ◽  
Genome Wide ◽  
Wheat Landraces

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

scholarly journals Unlocking the Patterns of the Tunisian Durum Wheat Landraces Genetic Structure Based on Phenotypic Characterization in Relation to Farmer’s Vernacular Name

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 634
Author(s):  
Cyrine Robbana ◽  
Zakaria Kehel ◽  
Karim Ammar ◽  
Carlos Guzmán ◽  
M’Barek Ben Naceur ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Durum Wheat ◽  
Smallholder Farmers ◽  
Phenotypic Variability ◽  
Phenotypic Characterization ◽  
Ecological Niches ◽  
Dry Conditions ◽  
New Gene ◽  
Wheat Landraces ◽  
Durum Wheat Landraces

During the 1970s, Tunisian durum wheat landraces were replaced progressively by modern cultivars. These landraces are nowadays maintained by smallholder farmers in some ecological niches and are threatened gradually by extinction resulting in the narrowing of the genetic diversity. This study aims to investigate patterns of phenotypic variability using twelve quantitative traits in a panel of 189 durum wheat landraces and seven checks, based on farmer’s population name attribution and genetic structure. Our results showed high phenotypic variability among and within landraces and checks for ten out of twelve studied traits. The principal components analysis showed similar grouping using farmers name attribution and genetic structure using K = 6. These results confirmed the identification of a new gene pool in the oases of Tunisia, represented by the sub-population Jenah Zarzoura and the robustness and high relationships between phenotypic and genome-wide genetic structure using DArTseq method. These findings will enhance the conservation efforts of these landraces and their use in breeding efforts at national and international levels to adapt to dry conditions.

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.

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