Genome wide association studies (GWAS) of spot blotch resistance at the seedling and the adult plant stages in a collection of spring barley

Spot blotch is a severe biotic menace of wheat caused by Cochliobolus sativus (syn. Bipolaris sorokiniana). Spot blotch is liable to major yield losses in warm humid regions. A genome-wide association study using genotyping-by-sequencing (GBS) markers was conducted to identify genomic regions associated with spot blotch resistance in a diversity panel of 159 spring wheat genotypes. In total, 87,096 GBS markers covering the whole genome, with an average polymorphism information content value of 0.276, were applied. Linkage disequilibrium (LD) analysis indicated that the LD decay extent was approximately 100 Mbp. The panel was evaluated for disease severity (DS) and area under disease progress curve (AUDPC) for 2 years. In total, 24 marker-trait associations (MTA) were identified for DS and AUDPC of spot blotch, with 11 on chromosome 5B, 3 on 3A, 2 on 6B, and 1 each on 1A, 2A, 1D, 2D, 4B, 5A, 7A, and 7B. A marker on chromosome 7B significantly explained 14% of the phenotypic variation of spot blotch severity as well as 11% of AUDPC. Five markers—three on chromosome 5B, one on 3A, and one on 7B—were associated with both DS and AUDPC with R2 ranging from 8 to 12%. Significant MTA can be utilized to develop wheat germplasm with resistance to spot blotch.

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Genome‐wide association studies in a barley ( Hordeum vulgare ) diversity set reveal a limited number of loci for resistance to spot blotch ( Bipolaris sorokiniana )

Plant Breeding ◽

10.1111/pbr.12792 ◽

2019 ◽

Vol 139 (3) ◽

pp. 521-535 ◽

Cited By ~ 1

Author(s):

Fluturë Novakazi ◽

Olga Afanasenko ◽

Nina Lashina ◽

Gregory J. Platz ◽

Rod Snowdon ◽

...

Keyword(s):

Hordeum Vulgare ◽

Association Studies ◽

Bipolaris Sorokiniana ◽

Spot Blotch ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide

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New QTLs for Spot Blotch Disease Resistance in Wheat (Triticum aestivum L.) Using Genome-Wide Association Mapping

Frontiers in Genetics ◽

10.3389/fgene.2020.613217 ◽

2021 ◽

Vol 11 ◽

Author(s):

Vipin Tomar ◽

Daljit Singh ◽

Guriqbal Singh Dhillon ◽

Ravi Prakash Singh ◽

Jesse Poland ◽

...

Keyword(s):

Disease Resistance ◽

Association Studies ◽

Bipolaris Sorokiniana ◽

Spot Blotch ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Protein Families ◽

Wheat Production ◽

Genome Wide ◽

Diverse Field

Spot blotch disease caused by Bipolaris sorokiniana is a major constraint for wheat production in tropics and subtropics. The introgression of spot blotch resistance alleles to the disease susceptible lines is critical to securing the wheat production in these regions. Although genome-wide association studies (GWASs) for spot blotch were attempted earlier, the present study focused on identifying new quantitative trait loci (QTLs) for spot blotch under natural disease pressure in diverse field conditions. A total of 139 advanced spring wheat lines were evaluated in three environments (three years and two locations) in India and Bangladesh. The GWAS using 14,063 polymorphic genotyping-by-sequencing (GBS) markers identified eight QTLs associated with spot blotch disease resistance belonging to eight chromosomes across the wheat genome. Here, we report the identified marker–trait associations (MTAs), along with the allele effects associated with the disease. The functional annotation of the significant markers identified NBS-LRR, MADS-box transcription factor, and 34 other plant-related protein families across multiple chromosomal regions. The results indicate four promising new QTLs on chromosomes 1A (497.2 Mb), 1D (89.84 Mb), 2B (421.92 Mb), and 6D (6.84 Mb) associated with several disease resistance protein families. These results provide insights into new genomic regions associated with spot blotch disease, and with additional validation, could be utilized in disease resistance breeding efforts in wheat development.

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Genome-wide association studies uncover candidate genes for Zinc, Iron, and Selenium concentration in barley grains

10.21203/rs.3.rs-764366/v1 ◽

2021 ◽

Author(s):

Samar G. Thabet ◽

Dalia Z. Alomari ◽

Ahmad M. Alqudah

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Association Studies ◽

Spring Barley ◽

Genome Wide Association ◽

Human Consumption ◽

Genome Wide Association Studies ◽

Genome Wide ◽

A Genome ◽

Barley Grains

Abstract Background Barley (Hordeum vulgare L.) is one of the most important staple food crops worldwide. Mineral concentrations in cereals are important for human health; hence improving Zn, Fe and Se accumulation in grains is an imperative need. This study was designed to understand the genetic architecture of Zn, Fe and Se grain concentrations in barley grains. Results We performed a genome-wide association study (GWAS) for grain Zn, Fe and Se concentrations in 216 spring barley accessions, using field data from 2 years. All the accessions were genotyped with a high-density 9K SNPs array from IlluminaTM. The mean values of estimated BLUEs for Zn, Fe and Se were 38.37, 35.56 and 39.45 µg g− 1 dry weight, respectively. High heritability was equaled 75.65% for Fe across the two environments, while moderate heritability values were detected for Zn and Se. Notably, wide genetic variation was found among genotypes for Zn, Fe and Se concentrations. A total of 222 SNPs associated with Zn, Fe and Se were detected on all chromosomes, where the highest significant associations is linked to Fe accumulation. Three genomic regions include newly identified putative candidate genes, which are related to Zn uptake and transport or represent Homeobox leucine zipper protein. Additionally, several significant associations were physically located inside or near genes which are potentially involved in Zn and Fe homoeostasis of which two candidate genes at 5H (502,454,312–502,455,148 bp) and 7H (205,216,091–205,221,133 bp) were found to be involved in Basic helix loop helix (BHLH) family transcription factor and Squamosa promoter binding-like protein, respectively. Conclusions These findings provide new insights into the genetic basis of Zn, Fe and Se concentration in barley grains that in turn may help plant breeders to select high Zn, Fe and Se-containing genotypes to improve human consumption and grain quality.

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