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.)

TLDR: Genome wide association studies (GWAS) to map Quantitative Trait Loci (QTL) associated with element contents in the grain using 336 spring barley showed association with INTERMEDIUM-C, a modifier gene for lateral spikelet fertility in the 4H chromosome, validating current GWAS approach.

About: This article is published in Journal of Cereal Science.The article was published on 2017-09-01 and is currently open access. It has received 34 citations till now. The article focuses on the topics: Hordeum vulgare & Population.

Figures

Table 3 Significant SNP-element content association analyzed for barley grain in Jemma Shiam and Marchouch stations in Morocco.

Table 2 Genome wide association studies of row types 336 genotypes of barley, and gene annotation of significant SNP markers using BLAST search.

Table 3 Significant SNP-element content association analyzed for barley grain in Jemma Shiam and Marchouch stations in Morocco.

Fig. 3. Principal Coordinate Analysis (PCoA) based on genetic distance computed for 336 individuals (6-row ¼ 6-rowed barley, 2-row ¼ 2-rowed barley).

Fig. 2. Probabilities of 336 barley genotypes belonging to one of the two subpopulations indicated as the relative height of light bars (two-rowed barley) and dark bars (six-rowed barley).

Frequently asked questions

Q1. What contributions have the authors mentioned in the paper "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.)" ?

In this paper, the authors used a genome wide association study ( GWAS ) to map Quantitative Trait Loci ( QTL ) associated with element contents in the grain using 336 spring barley. 

Q2. What have the authors stated for future works in "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.)" ?

Currently, three crosses Rihane-03 x Zanbaka, Alanda-01 x Zanbaka, and Rihane-03 x Alanda-01, were made in ICARDA to study and map Zn and Fe contents in barley grains by utilizing information in genotypes identified in this study. 

Q3. What was the result of further filtering?

Further filtering for >10% missing data and <0.05 minor allele frequency resulted into 6519 SNPs which were used in further analysis (PCA and GWAS). 

Q4. What were the objectives of the current study?

The objectives of the current study were to (1) assess variability of element uptake in a world collection of cultivated barley germplasms at ICARDA and to (2) map QTL associated with element uptake in barley grain using the GWAS approach. 

Q5. What was the main goal of the study?

The major goal of their study was to identify and map QTL involved in uptake and translocation of elements in barley grains with, a focus on identifying Zn and Fe dense barley genotypes, so that this germplasmwould be available to barley researchers across the globe through ICARDA networks. 

Q6. What are the main causes of the deficiency of element?

Rapid changes in food habits and nutritive values of modern food in terms of micronutrients have contributed to element deficiency related problems. 

Q7. What are the major causes of over 65% of childhood deaths worldwide?

Deficiencies of elements, especially iron (Fe), zinc (Zn) magnesium (Mg), phosphorous (P), potassium (K), selenium (Se), and copper (C) are the major causes of over 65% of childhood deaths worldwide (Welch and Graham, 2004). 

Q8. What equipment was used for the analysis of a sample?

Digested samples and blanks were analyzed using Spectro Genesis SOP ICP-OES (Spectro Analytical Instrument GmbH, Germany) with SmartAnalyzer Vision software and Optimist nebulizer with a cyclonic spray chamber. 

Q9. How much of the barley produced is used as human food?

Around 3.7% of total barley production is used as human food annually worldwide, but in some countries, like in Morocco, Ethiopia and Eritrea, barley comprise as high as 60% of total food production (Newman and Newman, 2006). 

Q10. What is the first step towards exploitation of elements in barley?

The first step towards the exploitation of biofortification of elements in barley is to assess the status of element concentrations in the kernel and map Quantitative Trait Loci (QTL) associated with element uptake in plants. 

Q11. What is the role of Zn in the body's immune system?

Zn has important roles in several metabolic functions including accelerated growth, body's immune responses and synthesis of several enzymes such as DNA polymerases, carbonic anhydrases and alkaline phosphatases (Prasad, 1991). 

Q12. What is the significance of the QTL in barley?

information on barley genotypes capable of higher element uptake in the grain and the markers (SNPs) associated with the QTL is invaluable for future barley breeding programs. 

Q13. How many SNPs were significant for Fe?

Five SNPs with the unknown marker position were also significant for Fe. The R2 of these QTL ranged from 3.3 to 5.0% and additive effects from 12.9e6.15 mg kg 1. 

Q14. Why is barley less sensitive to Fe and Zn deficiencies?

Barley is less sensitive to both Fe and Zn deficiencies, because it has genes involved in the mobilization and uptake of Fe and Zn. 

Q15. How many SNPs were found in the 4HS chromosome?

In the current study, 3 SNPs, 11_20606, 11_21070, and 11_20422, were significantly (q < 0.05) correlated with row types (fertility of lateral spikelets), including three other SNPs in the 4HS chromosome at the span of 38.44e53.87 cM. 

Q16. What was the effect of the GLM models on the false positives?

Results showed that GLM models were not good enough to control the false positives (data not presented) while both MLM þ Q þ K and MLM þ PCA þ K were found effective for finding true associations. 

Q17. What was the pFDR used to test?

The pFDR (q < 0.05) was applied in order to test the statistical significance of multiple comparisons of all detected markers according to Storey (2002). 

Q18. How many genotypes were collected in the AM-2014 study?

The Genome Wide Association Study reported here, which the authors named Association Mapping panel 2014 (AM-2014) comprised a total of 336 genotypes. 

Q19. What is the role of QTL in barley?

They reported that QTL in 1HS, 2HL, and 5HL were responsible for Zn translocation in barley grain, which is confirmed by their study. 

Q20. What is the cheapest and accessible strategy for resolving nutritional deficiencies in food crops?

Of the three strategies for resolving nutritional deficiencies in food crops: biofortification, food fortification, and mineral supplement, biofortification is the cheapest and most accessible (Welch and Graham, 2004).