Identifying Candidate Genes for Enhancing Grain Zn Concentration in Wheat

Wheat (Triticum aestivum L.) is one of the major staple food crops worldwide. Despite efforts in improving wheat quality, micronutrient levels are still below the optimal range for human nutrition. In particular, zinc (Zn) deficiency is a widespread problem in human nutrition in countries relying mainly on a cereal diet; hence improving Zn accumulation in grains is an imperative need. This study was designed to understand the genetic architecture of Zn grain concentrations in wheat grains. We performed a genome-wide association study (GWAS) for grain Zn concentrations in 369 European wheat genotypes, using field data from 3 years. The complete wheat panel was genotyped by high-density arrays of single nucleotide polymorphic (SNP) markers (90k iSELECT Infinium and 35k Affymetrix arrays) resulting in 15,523 polymorphic markers. Additionally, a subpanel of 183 genotypes was analyzed with a novel 135k Affymetrix marker array resulting in 28,710 polymorphic SNPs for high-resolution mapping of the potential genomic regions. The mean grain Zn concentration of the genotypes ranged from 25.05–52.67 μg g-1 dry weight across years with a moderate heritability value. Notably, 40 marker-trait associations (MTAs) were detected in the complete panel of varieties on chromosomes 2A, 3A, 3B, 4A, 4D, 5A, 5B, 5D, 6D, 7A, 7B, and 7D. The number of MTAs in the subpanel was increased to 161 MTAs whereas the most significant and consistent associations were located on chromosomes 3B (723,504,241–723,611,488 bp) and 5A (462,763,758–466,582,184 bp) having major effects. These genomic regions include newly identified putative candidate genes, which are related to Zn uptake and transport or represent bZIP and mitogen-activated protein kinase genes. These findings provide the basis for understanding the genetic background of Zn concentration in wheat grains that in turn may help breeders to select high Zn-containing genotypes to improve human health and grain quality

A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development

Tobacco (Nicotiana tabacum L.) is a species in the large family of the Solanaceae and is important as an agronomic crop and as a model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available that can be used for genome analysis, genetic mapping and breeding. We report here on the development and characterization of 5,119 new and functional microsatellite markers and on the generation of a high-resolution genetic map for the tetraploid tobacco genome. The genetic map was generated using an F2 mapping population derived from the intervarietal cross of Hicks Broadleaf × Red Russian and merges the polymorphic markers from this new set with those from a smaller set previously used to produce a lower density map. The genetic map described here contains 2,317 microsatellite markers and 2,363 loci, resulting in an average distance between mapped microsatellite markers which is less than 2 million base pairs or 1.5 cM. With this new and expanded marker resource, a sufficient number of markers are now available for multiple applications ranging from tobacco breeding to comparative genome analysis. The genetic map of tobacco is now comparable in marker density and resolution with the best characterized genomes of the Solanaceae: tomato and potato

Genome-wide Association Mapping and Prediction of Adult Stage Septoria tritici Blotch Infection in European Winter Wheat via High-Density Marker Arrays

blotch (STB) caused by the fungus is a devastating foliar disease of wheat ( L.) that can lead to substantial yield losses. Quantitative genetic resistance has been proposed as a durable strategy for STB control. In this study, we dissected the genetic basis of STB infection in 371 European wheat varieties based on 35k and 90k single nucleotide polymorphism marker arrays. The phenotypic data analyses suggested that large genetic variance exists for STB infection with a broad-sense heritability of 0.78. Genome-wide association studies (GWAS) propose the highly quantitative nature of STB infection with potential associations on chromosomes 1A, 1B, 2D, 4A, 5A, 6A, 6D, 7A, and 7B. Increased marker density in GWAS by combining markers from both arrays helped to detect additional markers explaining increased genotypic variance. Linkage disequilibrium analyses revealed genes with a possible role in disease resistance. The potential of genomic prediction (GP) assessed via two models accounting for additive effects and additive plus epistatic interactions among the loci suggested the possibility of genomic selection for improved STB resistance. Genomic prediction results also indicated that the higher-order epistatic interactions are not abundant and that both marker platforms are equally suitable for GP of STB infection. Our results provide further understanding of the quantitative genetic nature of STB infection, serve as a resource for marker-assisted breeding, and highlight the potential of genomic selection for improved STB resistance

Genetic and physical mapping of anther extrusion in elite European winter wheat

<div><p>The production and cultivation of hybrid wheat is a possible strategy to close the yield gap in wheat. Efficient hybrid wheat seed production largely depends on high rates of cross-pollination which can be ensured through high anther extrusion (AE) by male parental lines. Here, we report the AE capacity and elucidate its genetics in 514 elite European winter wheat varieties via genome-wide association studies (GWAS). We observed a wide range of variation among genotypes and a high heritability (0.80) for AE. The whole panel was genotyped with the 35k Affymetrix and 90k iSELECT single nucleotide polymorphism (SNP) arrays plus <i>Ppd-D1</i>, <i>Rht-B1 and Rht-D1</i> candidate markers. GWAS revealed 51 marker-trait associations (MTAs) on chromosomes 1A, 1B, 2A, 4D and 5B, with <i>Rht-D1</i> (4D) being the most significant marker. Division of whole panel according to the <i>Rht-D1</i> genotype resulted in 212 and 294 varieties harboring <i>Rht-D1a</i> and <i>Rht-D1b</i> allele, respectively. The presence of <i>Rht-D1a</i> compared to <i>Rht-D1b</i> (mutant) allele had a large phenotypic influence on AE resulting in its ~17% increase. GWAS performed on the sub-panels detected novel MTAs on chromosomes 2D, 3B and 6A with increased phenotypic variance imparted by individual markers. Our study shows that AE is a highly quantitative trait and wild type <i>Rht-D1a</i> allele greatly improves AE. Moreover, demarcating the quantitative trait loci regions based on intra-chromosomal linkage disequilibrium revealed AE’s candidate genes/genomic regions. Understanding the genetics of AE in elite European wheat and utilizing the linked markers in breeding programs can help to enhance cross-pollination for better exploitation of heterosis.</p></div

Summary of genome-wide association studies (GWAS) for anther extrusion in different wheat panels.

<p><b>(A)</b> Manhattan plot based on linear mixed model using kinship matrix for correction of population stratification. <b>(B)</b> Quantile-quantile plot depicting expected <i>versus</i> observed <i>P</i> values at −log₁₀ scale. Full-set represents the GWAS results of varieties harboring both <i>Rht-D1a</i> and <i>Rht-D1b</i> alleles. <i>Rht-D1a</i> and <i>Rht-D1b</i> set represent the GWAS results in individual panels harboring either of the alleles. <i>n</i> denotes the total number of varieties used in GWAS panels.</p

List of most significant SNPs (MS-SNPs) representing QTLs on individual chromosomes.

<p>List of most significant SNPs (MS-SNPs) representing QTLs on individual chromosomes.</p

Identification and validation of QTL for spike fertile floret and fruiting efficiencies in hexaploid wheat (Triticum aestivum L.)

The spike fruiting efficiency (FE—grains per unit spike dry weight at anthesis, GN/SDW) is a promising trait to improve wheat yield potential. It depends on fertile floret efficiency (fertile florets per unit SDW—FFE, FF/SDW) and grain set (grains per fertile floret—GST). Given its difficult measurement, it is often estimated as the grains per unit of nongrain spike dry weight at maturity (FEm). In this study, quantitative trait loci (QTL) were mapped using a double haploid population (Baguette 19/BIOINTA 2002, with high and low FE, respectively) genotyped with the iSelect 90 K SNP array and evaluated in five environments. We identified 37 QTL, but two were major with an R2 > 10% and stable for being at least present in three environments: the QFEm.perg-3A (on Chr. 3A, 51.6 cM, 685.12 Mb) for FEm and the QFFE.perg-5A (on Chr. 5A, 42.1 cM, 461.49 Mb) for FFE, FE and FEm. Both QTL were validated using two independent F2 populations and KASP markers. For the most promising QTL, QFFE.perg-5A, the presence of the allele for high FFE resulted in + 4% FF, + 9% GN, + 13% GST, + 16% yield gSDW−1 and + 5% yield spike−1. QFEm.perg-3A and QFFE.perg-5A represent two new loci to use in MAS to improve wheat yield potential.EEA Marcos JuárezFil: Pretini, Nicole. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA). Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires; Argentina.Fil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Terrile, Ignacio Ismael. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina.Fil: Börner, Andreas. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Plieske, Jörg. Trait Genetics GmbH; AlemaniaFil: Ganal, Martin. Trait Genetics GmbH; AlemaniaFil: Röder, Marion. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: González, Fernanda Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA). Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina

Distribution of anther extrusion in wheat panels harboring both <i>Rht-D1a</i> and <i>Rht</i>-<i>D1b</i> alleles (full-set) and panels harboring only one of the alleles.

<p><i>n</i> denotes the number of varieties in individual panels.</p

Principal component analysis (PCA) of wheat varieties based on SNP genotype explains the absence of pronounced population structure.

<p>Full-set means that the varieties harbored both <i>Rht-D1a</i> and <i>Rht-D1b</i> alleles and <i>n</i> denotes the total number of varieties used.</p

Influence of the most significant SNPs (SNPs with the largest additive effect) on AE phenotype based on GWAS conducted on panels harboring full-set of varieties and varieties harboring only <i>Rht-D1a</i> and <i>Rht-D1b</i> alleles.

<p>Horizontal dotted line marks the mean of AE BLUEs. R and V denote the varieties harboring reference (major) and variant (minor) alleles, respectively.</p