Nested association mapping-based GWAS for grain yield and related traits in wheat grown under diverse Australian environments

Chidzanga, Charity; Mullan, Daniel; Roy, Stuart J.; Baumann, Ute; Garcia, Melissa

doi:10.1007/s00122-022-04230-9

Cited by 13 publications

(9 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our analysis confirmed some known trait-associated genomic regions, or found associated markers in proximity (distance 0.1–6.5 Mbp) to previously described loci [ 21 , 23 , 33 , 34 , 35 , 36 , 37 , 38 ] ( Table 4 and Table 5 ). For example, the GPC-associated marker Tdurum_contig46670_911 on chromosome 6A (position 599,050,921 bp) has been reported as an environmentally specific one in a study on a Siberian wheat collection [ 23 ].…”

Section: Discussionsupporting

confidence: 89%

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

Kartseva,

Aleksandrov,

Alqudah

et al. 2024

Plants

View full text Add to dashboard Cite

Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits—grain protein content (GPC) and thousand kernel weight (TKW)—across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, and genotypic data from the 25K Infinium iSelect array. As a result, we detected 16 quantitative trait nucleotides (QTNs) associated with GPC and 15 associated with TKW, all of which passed the false discovery rate threshold. Seven loci favorably influenced GPC, resulting in an increase of 1.4% to 8.1%, while four loci had a positive impact on TKW with increases ranging from 1.9% to 8.4%. While some loci confirmed previously published associations, four QTNs linked to GPC on chromosomes 2A, 7A, and 7B, as well as two QTNs related to TKW on chromosomes 1B and 6A, may represent novel associations. Annotations for proteins involved in the senescence-associated nutrient remobilization and in the following buildup of resources required for seed germination have been found for selected putative candidate genes. These include genes coding for storage proteins, cysteine proteases, cellulose-synthase, alpha-amylase, transcriptional regulators, and F-box and RWP-RK family proteins. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content.

show abstract

Section: Discussionsupporting

confidence: 89%

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

Kartseva,

Aleksandrov,

Alqudah

et al. 2024

Plants

View full text Add to dashboard Cite

show abstract

“…The distribution of GY-related markers in different chromosomes has been observed before 29 , 80 . 4A was the chromosome that contained MTAs for GY in both environments; even SNP rs12851 on this chromosome showed its significant association in both environmental conditions.…”

Section: Discussionmentioning

confidence: 93%

Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS

Abdi

Alipour

Bernousi

et al. 2023

Sci Rep

View full text Add to dashboard Cite

Principal component analysis (PCA) is widely used in various genetics studies. In this study, the role of classical PCA (cPCA) and robust PCA (rPCA) was evaluated explicitly in genome-wide association studies (GWAS). We evaluated 294 wheat genotypes under well-watered and rain-fed, focusing on spike traits. First, we showed that some phenotypic and genotypic observations could be outliers based on cPCA and different rPCA algorithms (Proj, Grid, Hubert, and Locantore). Hubert’s method provided a better approach to identifying outliers, which helped to understand the nature of these samples. These outliers led to the deviation of the heritability of traits from the actual value. Then, we performed GWAS with 36,000 single nucleotide polymorphisms (SNPs) based on the traditional approach and two robust strategies. In the conventional approach and using the first three components of cPCA as population structure, 184 and 139 marker-trait associations (MTAs) were identified for five traits in well-watered and rain-fed environments, respectively. In the first robust strategy and when rPCA was used as population structure in GWAS, we observed that the Hubert and Grid methods identified new MTAs, especially for yield and spike weight on chromosomes 7A and 6B. In the second strategy, we followed the classical and robust principal component-based GWAS, where the first two PCs obtained from phenotypic variables were used instead of traits. In the recent strategy, despite the similarity between the methods, some new MTAs were identified that can be considered pleiotropic. Hubert's method provided a better linear combination of traits because it had the most MTAs in common with the traditional approach. Newly identified SNPs, including rs19833 (5B) and rs48316 (2B), were annotated with important genes with vital biological processes and molecular functions. The approaches presented in this study can reduce the misleading GWAS results caused by the adverse effect of outlier observations.

show abstract

“…In particular, the nested association mapping (NAM) approach relies on one (or more) recurrent parent that is recombined into several "donor" parents. The result is a balanced panel of progenies with several "donor" alleles contrasting the "recurrent" allele so that the effects of both can be identified via QTL analysis and GWAS (Alahmad et al, 2020;Alahmad et al, 2022;Chidzanga et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Trends and Perspectives for the Use of Crop Wild Relatives in Crop Breeding

2024

Frontiers Research Topics

View full text Add to dashboard Cite

Frontiers is more than just an open access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge. Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers journal seriesThe Frontiers journal series is a multi-tier and interdisciplinary set of openaccess, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing. All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community. At the same time, the Frontiers journal series operates on a revolutionary invention, the tiered publishing system, initially addressing specific communities of scholars, and gradually climbing up to broader public understanding, thus serving the interests of the lay society, too. Dedication to qualityEach Frontiers article is a landmark of the highest quality, thanks to genuinely collaborative interactions between authors and review editors, who include some of the world's best academicians. Research must be certified by peers before entering a stream of knowledge that may eventually reach the public -and shape society; therefore, Frontiers only applies the most rigorous and unbiased reviews. Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new generation. What are Frontiers Research Topics?Frontiers Research Topics are very popular trademarks of the Frontiers journals series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area.

show abstract

Nested association mapping-based GWAS for grain yield and related traits in wheat grown under diverse Australian environments

Cited by 13 publications

References 50 publications

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS

Trends and Perspectives for the Use of Crop Wild Relatives in Crop Breeding

Contact Info

Product

Resources

About