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Genome-Wide Association Mapping of Acid Soil Resistance in Barley (Hordeum vulgare L.).

Zhou G, Broughton S, Zhang XQ, Ma Y, Zhou M, Li C - Front Plant Sci (2016)

Bottom Line: GWAS for acid soil resistance were performed on the population using a general linkage model (GLM) and a mixed linkage model (MLM), respectively.A total of 22 QTLs (quantitative trait loci) were detected with the GLM and MLM analyses.The QTLs could be used in marker-assisted selection to identify and pyramid different loci for improved acid soil resistance in barley.

View Article: PubMed Central - PubMed

Affiliation: Western Barley Genetics Alliance, Department of Agriculture and Food, Government of Western Australia, PerthWA, Australia; Western Barley Genetics Alliance, Murdoch University, MurdochWA, Australia.

ABSTRACT
Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) have been used to detect QTLs underlying complex traits in major crops. In this study, we collected 218 barley (Hordeum vulgare L.) lines including wild barley and cultivated barley from China, Canada, Australia, and Europe. A total of 408 polymorphic markers were used for population structure and LD analysis. GWAS for acid soil resistance were performed on the population using a general linkage model (GLM) and a mixed linkage model (MLM), respectively. A total of 22 QTLs (quantitative trait loci) were detected with the GLM and MLM analyses. Two QTLs, close to markers bPb-1959 (133.1 cM) and bPb-8013 (86.7 cM), localized on chromosome 1H and 4H respectively, were consistently detected in two different trials with both the GLM and MLM analyses. Furthermore, bPb-8013, the closest marker to the major Al(3+) resistance gene HvAACT1 in barley, was identified to be QTL5. The QTLs could be used in marker-assisted selection to identify and pyramid different loci for improved acid soil resistance in barley.

No MeSH data available.


Related in: MedlinePlus

Estimation of the most probable number of clusters (k), based on nine independent runs and k ranging from 2 to 10.
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Figure 1: Estimation of the most probable number of clusters (k), based on nine independent runs and k ranging from 2 to 10.

Mentions: These 218 barley accessions were used to analyze population structure. The cluster parameter k was set from 2 to 10. To determine the number of clusters suitable for association mapping analysis, the parameter Δk was applied. When k = 6, Δk reached a top value of ∼3.0 (Figure 1). According to the explanation of Evanno et al. (2005), the appropriate number of clusters should be six. The compositions of each cluster are shown in Figure 2 and these clusters are represented by six different colors.


Genome-Wide Association Mapping of Acid Soil Resistance in Barley (Hordeum vulgare L.).

Zhou G, Broughton S, Zhang XQ, Ma Y, Zhou M, Li C - Front Plant Sci (2016)

Estimation of the most probable number of clusters (k), based on nine independent runs and k ranging from 2 to 10.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814478&req=5

Figure 1: Estimation of the most probable number of clusters (k), based on nine independent runs and k ranging from 2 to 10.
Mentions: These 218 barley accessions were used to analyze population structure. The cluster parameter k was set from 2 to 10. To determine the number of clusters suitable for association mapping analysis, the parameter Δk was applied. When k = 6, Δk reached a top value of ∼3.0 (Figure 1). According to the explanation of Evanno et al. (2005), the appropriate number of clusters should be six. The compositions of each cluster are shown in Figure 2 and these clusters are represented by six different colors.

Bottom Line: GWAS for acid soil resistance were performed on the population using a general linkage model (GLM) and a mixed linkage model (MLM), respectively.A total of 22 QTLs (quantitative trait loci) were detected with the GLM and MLM analyses.The QTLs could be used in marker-assisted selection to identify and pyramid different loci for improved acid soil resistance in barley.

View Article: PubMed Central - PubMed

Affiliation: Western Barley Genetics Alliance, Department of Agriculture and Food, Government of Western Australia, PerthWA, Australia; Western Barley Genetics Alliance, Murdoch University, MurdochWA, Australia.

ABSTRACT
Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) have been used to detect QTLs underlying complex traits in major crops. In this study, we collected 218 barley (Hordeum vulgare L.) lines including wild barley and cultivated barley from China, Canada, Australia, and Europe. A total of 408 polymorphic markers were used for population structure and LD analysis. GWAS for acid soil resistance were performed on the population using a general linkage model (GLM) and a mixed linkage model (MLM), respectively. A total of 22 QTLs (quantitative trait loci) were detected with the GLM and MLM analyses. Two QTLs, close to markers bPb-1959 (133.1 cM) and bPb-8013 (86.7 cM), localized on chromosome 1H and 4H respectively, were consistently detected in two different trials with both the GLM and MLM analyses. Furthermore, bPb-8013, the closest marker to the major Al(3+) resistance gene HvAACT1 in barley, was identified to be QTL5. The QTLs could be used in marker-assisted selection to identify and pyramid different loci for improved acid soil resistance in barley.

No MeSH data available.


Related in: MedlinePlus