Table_1_Genetic association of spikelet abortion with spike, grain, and shoot traits in highly-diverse six-rowed barley.xlsx

Spikelet abortion is a phenomenon where apical spikelet primordia on an immature spike abort. Regardless of the row-type, both apical and basal spikelet abortion occurs, and their extent decides the number of grain-bearing spikelets retained on the spike—thus, affecting the yield potential of barley. Reducing spikelet abortion, therefore, represents an opportunity to increase barley yields. Here, we investigated the variation for apical spikelet abortion along with 16 major spike, shoot, and grain traits in a panel of 417 six-rowed spring barleys. Our analyses showed a significantly large genotypic variation resulting in high heritability estimates for all the traits. Spikelet abortion (SA) varies from 13 to 51% depending on the genotype and its geographical origin. Among the seven spike traits, SA was negatively correlated with final spikelet number, spike length and density, while positively with awn length. This positive correlation suggests a plausible role of the rapidly growing awns during the spikelet abortion process, especially after Waddington stage 5. In addition, SA also showed a moderate positive correlation with grain length, grain area and thousand-grain weight. Our hierarchical clustering revealed distinct genetic underpinning of grain traits from the spike and shoot traits. Trait associations showed a geographical bias whereby European accessions displayed higher SA and grain and shoot trait values, whereas the trend was opposite for the Asian accessions. To study the observed phenotypic variation of SA explained by 16 other individual traits, we applied linear, quadratic, and generalized additive regression models (GAM). Our analyses of SA revealed that the GAM generally performed superior in comparison to the other models. The genetic interactions among traits suggest novel breeding targets and easy-to-phenotype “proxy-traits” for high throughput on-field selection for grain yield, especially in early generations of barley breeding programs.</p

DataSheet_1_Genetic association of spikelet abortion with spike, grain, and shoot traits in highly-diverse six-rowed barley.pdf

Spikelet abortion is a phenomenon where apical spikelet primordia on an immature spike abort. Regardless of the row-type, both apical and basal spikelet abortion occurs, and their extent decides the number of grain-bearing spikelets retained on the spike—thus, affecting the yield potential of barley. Reducing spikelet abortion, therefore, represents an opportunity to increase barley yields. Here, we investigated the variation for apical spikelet abortion along with 16 major spike, shoot, and grain traits in a panel of 417 six-rowed spring barleys. Our analyses showed a significantly large genotypic variation resulting in high heritability estimates for all the traits. Spikelet abortion (SA) varies from 13 to 51% depending on the genotype and its geographical origin. Among the seven spike traits, SA was negatively correlated with final spikelet number, spike length and density, while positively with awn length. This positive correlation suggests a plausible role of the rapidly growing awns during the spikelet abortion process, especially after Waddington stage 5. In addition, SA also showed a moderate positive correlation with grain length, grain area and thousand-grain weight. Our hierarchical clustering revealed distinct genetic underpinning of grain traits from the spike and shoot traits. Trait associations showed a geographical bias whereby European accessions displayed higher SA and grain and shoot trait values, whereas the trend was opposite for the Asian accessions. To study the observed phenotypic variation of SA explained by 16 other individual traits, we applied linear, quadratic, and generalized additive regression models (GAM). Our analyses of SA revealed that the GAM generally performed superior in comparison to the other models. The genetic interactions among traits suggest novel breeding targets and easy-to-phenotype “proxy-traits” for high throughput on-field selection for grain yield, especially in early generations of barley breeding programs.</p

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

Distribution of the best linear unbiased estimates (BLUEs) of the trait anther extrusion.

<p>Distribution of the best linear unbiased estimates (BLUEs) of the trait anther extrusion.</p

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

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

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

Significant markers based on BLUE values.

<p>Significant markers based on BLUE values.</p

Genome-Wide Association Mapping of Anther Extrusion in Hexaploid Spring Wheat

<div><p>In a number of crop species hybrids are able to outperform line varieties. The anthers of the autogamous bread wheat plant are normally extruded post anthesis, a trait which is unfavourable for the production of F1 hybrid grain. Higher anther extrusion (AE) promotes cross fertilization for more efficient hybrid seed production. Therefore, this study aimed at the genetic dissection of AE by genome wide association studies (GWAS) and determination of the main effect QTL. We applied GWAS approach to identify DArT markers potentially linked to AE to unfold its genetic basis in a panel of spring wheat accessions. Phenotypic data were collected for three years and best linear unbiased estimate (BLUE) values were calculated across all years. The extent of the AE correlation between growing years and BLUE values ranged from r = +0.56 (2013 <i>vs</i> 2015) to 0.91 (2014 <i>vs</i> BLUE values). The broad sense heritability was 0.84 across all years. Six accessions displayed stable AE >80% across all the years. Genotyping data included 2,575 DArT markers (with minimum of 0.05 minor allele frequency applied). AE was influenced both by genotype and by the growing environment. In all, 131 significant marker trait associations (MTAs) (|log₁₀ (<i>P</i>)| >FDR) were established for AE. AE behaved as a quantitative trait, with five consistently significant markers (significant across at least two years with a significant BLUE value) contributing a minor to modest proportion (4.29% to 8.61%) of the phenotypic variance and affecting the trait either positively or negatively. For this reason, there is potential for breeding for improved AE by gene pyramiding. The consistently significant markers linked to AE could be helpful for marker assisted selection to transfer AE to high yielding varieties allowing to promote the exploitation of hybrid-heterosis in the key crop wheat.</p></div

Summary of pleiotropic QTL detected in the spring wheat association mapping population exposed to independent and combined heat and drought stress.

<p>Summary of pleiotropic QTL detected in the spring wheat association mapping population exposed to independent and combined heat and drought stress.</p