Genome-wide association mapping of genomic regions associated with phenotypic traits in Canadian western spring wheat

Grain protein content (GPC) is controlled by complex genetic systems and their interactions, and is an important quality determinant for hard spring wheat as it has a positive effect on bread and pasta quality. GPC is variable among genotypes and strongly influenced by environment. Thus, understanding the genetic control of wheat GPC and identifying genotypes with improved stability is an important breeding goal. The objectives of this research were to identify genetic backgrounds with less variation for GPC across environments and identify quantitative trait loci (QTLs) controlling the stability of GPC. A spring wheat nested association mapping (NAM) population of 650 recombinant inbred lines (RIL) derived from 26 diverse founder parents crossed to one common parent, 'Berkut', was phenotyped over three years of field trials (2014-2016). Genomic selection models were developed and compared based on prediction of GPC and GPC stability. After observing variable genetic control of GPC within the NAM population, seven RIL families displaying reduced marker-by-environment interaction were selected based on a stability index derived from Finlay-Wilkinson regression. A genome-wide association study identified seven significant QTLs for GPC stability with a Bonferroni-adjusted P value <0.05. This study also demonstrated that genome-wide prediction of GPC with ridge regression best linear unbiased estimates reached up to r = 0.69. Genomic selection can be used to apply selection pressure for GPC and improve genetic gain for GPC.

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Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

10.21203/rs.2.13122/v3 ◽

2019 ◽

Author(s):

Jaime Osorio ◽

Gina Garzón ◽

Paola Delgadillo ◽

Silvio Bastidas ◽

Leidy Moreno ◽

...

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Oil Palm ◽

Plant Architecture ◽

Elaeis Guineensis ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Elaeis Oleifera ◽

Genome Wide ◽

Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis , Elaeis oleifera , genotyping-by-sequencing, plant architecture, yield.

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Genomic Selection and Genome-Wide Association Studies for Grain Protein Content Stability in a Nested Association Mapping Population of Wheat

Agronomy ◽

10.3390/agronomy11122528 ◽

2021 ◽

Vol 11 (12) ◽

pp. 2528

Author(s):

Karansher S. Sandhu ◽

Paul D. Mihalyov ◽

Megan J. Lewien ◽

Michael O. Pumphrey ◽

Arron H. Carter

Keyword(s):

Association Mapping ◽

Protein Content ◽

Genomic Selection ◽

Genetic Control ◽

Spring Wheat ◽

Grain Protein Content ◽

Genome Wide Association ◽

Grain Protein ◽

Nested Association Mapping ◽

Genome Wide

Grain protein content (GPC) is controlled by complex genetic systems and their interactions and is an important quality determinant for hard spring wheat as it has a positive effect on bread and pasta quality. GPC is variable among genotypes and strongly influenced by the environment. Thus, understanding the genetic control of wheat GPC and identifying genotypes with improved stability is an important breeding goal. The objectives of this research were to identify genetic backgrounds with less variation for GPC across environments and identify quantitative trait loci (QTLs) controlling the stability of GPC. A spring wheat nested association mapping (NAM) population of 650 recombinant inbred lines (RIL) derived from 26 diverse founder parents crossed to one common parent, ‘Berkut’, was phenotyped over three years of field trials (2014–2016). Genomic selection models were developed and compared based on predictions of GPC and GPC stability. After observing variable genetic control of GPC within the NAM population, seven RIL families displaying reduced marker-by-environment interaction were selected based on a stability index derived from a Finlay–Wilkinson regression. A genome-wide association study identified eighteen significant QTLs for GPC stability with a Bonferroni-adjusted p-value < 0.05 using four different models and out of these eighteen QTLs eight were identified by two or more GWAS models simultaneously. This study also demonstrated that genome-wide prediction of GPC with ridge regression best linear unbiased estimates reached up to r = 0.69. Genomic selection can be used to apply selection pressure for GPC and improve genetic gain for GPC.

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Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping

Phytopathology ◽

10.1094/phyto-10-19-0372-r ◽

2020 ◽

Vol 110 (4) ◽

pp. 881-891 ◽

Cited By ~ 5

Author(s):

Anke Martin ◽

Paula Moolhuijzen ◽

Yongfu Tao ◽

Judy McIlroy ◽

Simon R. Ellwood ◽

...

Keyword(s):

Association Mapping ◽

Population Level ◽

Genome Wide Association ◽

Pyrenophora Teres ◽

Barley Cultivars ◽

Genome Wide ◽

A Genome ◽

Sexual Recombination ◽

Parastagonospora Nodorum ◽

Genomic Regions

Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.

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Genome-wide association analyses of common wheat (Triticum aestivum L.) germplasm identifies multiple loci for aluminium resistanceThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”

Genome ◽

10.1139/g10-058 ◽

2010 ◽

Vol 53 (11) ◽

pp. 957-966 ◽

Cited By ~ 45

Author(s):

Harsh Raman ◽

Benjamin Stodart ◽

Peter R. Ryan ◽

Emmanuel Delhaize ◽

Livinus Emebiri ◽

...

Keyword(s):

Triticum Aestivum ◽

Association Mapping ◽

Common Wheat ◽

Acid Soils ◽

Triticum Aestivum L ◽

Genome Wide Association ◽

Phenotypic Variance ◽

Association Analyses ◽

Genome Wide ◽

Genomic Regions

Aluminium (Al3+) toxicity restricts productivity and profitability of wheat ( Triticum aestivum L.) crops grown on acid soils worldwide. Continued gains will be obtained by identifying superior alleles and novel Al3+ resistance loci that can be incorporated into breeding programs. We used association mapping to identify genomic regions associated with Al3+ resistance using 1055 accessions of common wheat from different geographic regions of the world and 178 polymorphic diversity arrays technology (DArT) markers. Bayesian analyses based on genetic distance matrices classified these accessions into 12 subgroups. Genome-wide association analyses detected markers that were significantly associated with Al3+ resistance on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5B, 6A, 6B, 7A, and 7B. Some of these genomic regions correspond to previously identified loci for Al3+ resistance, whereas others appear to be novel. Among the markers targeting TaALMT1 (the major Al3+-resistance gene located on chromosome 4D), those that detected alleles in the promoter explained most of the phenotypic variance for Al3+ resistance, which is consistent with this region controlling the level of TaALMT1 expression. These results demonstrate that genome-wide association mapping cannot only confirm known Al3+-resistance loci, such as those on chromsomes 4D and 4B, but they also highlight the utility of this technique in identifying novel resistance loci.

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