Genome wide association studies (GWAS) of element contents in grain with a special focus on zinc and iron in a world collection of barley (Hordeum vulgare L.)

Gyawali, Sanjaya; Otte, Marinus L.; Chao, Shiaoman; Jilal, Abderazzek; Jacob, Donna L.; Amezrou, Reda; Verma, Ramesh Pal Singh

doi:10.1016/j.jcs.2017.08.019

Cited by 42 publications

(26 citation statements)

References 30 publications

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“…The analyses of the tested populations helped to identify specific QTL for each of the studied indicators and map them on chromosomes. The QTL identified are valuable for the future development of barley cultivars with increased content of nutrients, especially Zn and Fe [35].…”

Section: Fe Mn Znmentioning

confidence: 99%

Wheat, Barley, and Oat Breeding for Health Benefit Components in Grain

Лоскутов

Khlestkina

2021

Plants

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Cereal grains provide half of the calories consumed by humans. In addition, they contain important compounds beneficial for health. During the last years, a broad spectrum of new cereal grain-derived products for dietary purposes emerged on the global food market. Special breeding programs aimed at cultivars utilizable for these new products have been launched for both the main sources of staple foods (such as rice, wheat, and maize) and other cereal crops (oat, barley, sorghum, millet, etc.). The breeding paradigm has been switched from traditional grain quality indicators (for example, high breadmaking quality and protein content for common wheat or content of protein, lysine, and starch for barley and oat) to more specialized ones (high content of bioactive compounds, vitamins, dietary fibers, and oils, etc.). To enrich cereal grain with functional components while growing plants in contrast to the post-harvesting improvement of staple foods with natural and synthetic additives, the new breeding programs need a source of genes for the improvement of the content of health benefit components in grain. The current review aims to consider current trends and achievements in wheat, barley, and oat breeding for health-benefiting components. The sources of these valuable genes are plant genetic resources deposited in genebanks: landraces, rare crop species, or even wild relatives of cultivated plants. Traditional plant breeding approaches supplemented with marker-assisted selection and genetic editing, as well as high-throughput chemotyping techniques, are exploited to speed up the breeding for the desired genotуpes. Biochemical and genetic bases for the enrichment of the grain of modern cereal crop cultivars with micronutrients, oils, phenolics, and other compounds are discussed, and certain cases of contributions to special health-improving diets are summarized. Correlations between the content of certain bioactive compounds and the resistance to diseases or tolerance to certain abiotic stressors suggest that breeding programs aimed at raising the levels of health-benefiting components in cereal grain might at the same time match the task of developing cultivars adapted to unfavorable environmental conditions.

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Section: Fe Mn Znmentioning

confidence: 99%

Wheat, Barley, and Oat Breeding for Health Benefit Components in Grain

Лоскутов

Khlestkina

2021

Plants

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“…In other studies, diverse barley lines from different regions, including the US (Zhou and Steffenson, 2013 ; Genievskaya et al, 2018 ), Europe (Xu et al, 2018 ), and India (Visioni et al, 2018 ), were used to identify the genetic architecture of complex traits (heading time, number of kernels per spike, grain yield) and disease resistance (durable spot, stripe rust) in barley. Although some studies used worldwide collections of barley germplasm, few have included barley varieties from Tibet (Pasam et al, 2012 ; Gyawali et al, 2017 ). Over the past decade, studies in barley (Cuesta-Marcos et al, 2008 ), wheat (Kiseleva et al, 2016 ), and rice (Yan et al, 2011 ) have shown that variations in heading date (HD), plant height (PH), and spike length (SL) contribute to environmental adaptation in cereal crops and also influence grain yield.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley (Hordeum Vulgare L.) in the Qinghai-Tibet Plateau

Lhundrup

Guo

et al. 2020

Front. Genet.

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Barley ( Hordeum vulgare L.) is one of the most important cereal crops worldwide. In the Qinghai-Tibet Plateau, six-rowed hulless (or naked) barley, called “qingke” in Chinese or “nas” in Tibetan, is produced mainly in Tibet. The complexity of the environment in the Qinghai-Tibet Plateau has provided unique opportunities for research on the breeding and adaptability of qingke barley. However, the genetic architecture of many important agronomic traits for qingke barley remains elusive. Heading date (HD), plant height (PH), and spike length (SL) are three prominent agronomic traits in barley. Here, we used genome-wide association (GWAS) mapping and GWAS with eigenvector decomposition (EigenGWAS) to detect quantitative trait loci (QTL) and selective signatures for HD, PH, and SL in a collection of 308 qingke barley accessions. The accessions were genotyped using a newly-developed, proprietary genotyping-by-sequencing (tGBS) technology, that yielded 14,970 high quality single nucleotide polymorphisms (SNPs). We found that the number of SNPs was higher in the varieties than in the landraces, which suggested that Tibetan varieties and varieties in the Tibetan area may have originated from different landraces in different areas. We have identified 62 QTLs associated with three important traits, and the observed phenotypic variation is well-explained by the identified QTLs. We mapped 114 known genes that include, but are not limited to, vernalization, and photoperiod genes. We found that 83.87% of the identified QTLs are located in the non-coding regulatory regions of annotated barley genes. Forty-eight of the QTLs are first reported here, 28 QTLs have pleotropic effects, and three QTL are located in the regions of the well-characterized genes HvVRN1, HvVRN3 , and PpD-H2 . EigenGWAS analysis revealed that multiple heading-date-related loci bear signatures of selection. Our results confirm that the barley panel used in this study is highly diverse, and showed a great promise for identifying the genetic basis of adaptive traits. This study should increase our understanding of complex traits in qingke barley, and should facilitate genome-assisted breeding for qingke barley improvement.

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“…Moreover, 14 QTLs for Fe and Zn as well as high-priority candidate genes were identified such as OsYSL1 and OsMTP1 for Fe and OsARD2, OsIRT1, OsNAS1 , and OsNAS2 for Zn in rice seeds ( Anuradha et al, 2012 ). GWAS approach has also been used to identify major loci for different elemental concentrations such as Ca, Fe, and Zn in wheat ( Velu et al, 2016 ; Alomari et al, 2017 ), Fe and Zn in barley ( Mamo et al, 2014 ; Gyawali et al, 2017 ), and Fe and Zn in maize ( Hindu et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification

et al. 2018

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The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P-value) ≥ 3.0. The PH1.1 and Zn7.1 were consistently identified in all the four environments, ten QTLs qDF3.1, qDF6.2 qDF9.1 qPH5.1 qGL3.1, qGW3.1, qGW11.1, and qZn6.2 were detected in two environments, while two major loci qBLB11.1 and qBLB5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t), and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1, and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.

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Genome wide association studies (GWAS) of element contents in grain with a special focus on zinc and iron in a world collection of barley (Hordeum vulgare L.)

Abstract: Genome wide association studies (GWAS) were carried out to map Quantitative Trait Loci (QTL) associated with element contents in the grain using 336 spring barley. Of the elements analyzed, Fe content ranged from 21.9 to 91.0 mg kg À1 , Zn from 10.4 to 54.5 mg kg À1 , Ba from 0.

Cited by 42 publications

References 30 publications

Wheat, Barley, and Oat Breeding for Health Benefit Components in Grain

Wheat, Barley, and Oat Breeding for Health Benefit Components in Grain

Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley (Hordeum Vulgare L.) in the Qinghai-Tibet Plateau

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification

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