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Association mapping for kernel phytosterol content in almond.

Font I Forcada C, Velasco L, Socias I Company R, Fernández I Martí Á - Front Plant Sci (2015)

Bottom Line: The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations.Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome.These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

View Article: PubMed Central - PubMed

Affiliation: Genome Center, University of California, Davis Davis, CA, USA.

ABSTRACT
Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r(2) -value for all intra-chromosomal loci pairs was 0.040, whereas, the r(2) for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

No MeSH data available.


LD based on r2, averaged for map distance classes and germplasm groups based on population structure analysis in the STRUCTURE.
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Figure 4: LD based on r2, averaged for map distance classes and germplasm groups based on population structure analysis in the STRUCTURE.

Mentions: Extent of genome-wide LD was evaluated through pairwise comparisons among the 40 marker loci and the 71 almond germplasm accessions studied (Figures 3, 4). After removing low frequency alleles (MAF = 0.05), the results showed a high level of LD up to 20 cM, which dissipated at farther distances. The overall LD for all cultivars was 0.034 in the region from 0 to 10 cM, 0.079 from 10 to 20 cM, 0.036 from 20 to 30 cM, and 0.027 after 30 cM. These results were lower if the cultivars were separated in two different groups, Mediterranean and non-Mediterranean. Thus, the range of LD spaced every 10 cM was 0.061, 0.087, 0.045, and 0.032 for Mediterranean cultivars, and 0.058, 0.079, 0.039, and 0.028 for non-Mediterranean cultivars. A high level of LD up to 20 cM was observed for the whole ensemble of accessions when they were split in a Mediterranean and a non-Mediterranean group. The total r2-value for intra-chromosomal loci pairs was 0.040 and the unlinked markers pairs showed a similar percentage of significant LD in Mediterranean and non-Mediterranean cultivars (values of 0.091 and 0.073, respectively). Regarding the total r2-value for inter-chromosomal loci pairs was 0.036 for the whole ensemble, 0.082 for the Mediterranean accessions, and 0.062 for the non-Mediterranean accessions. The overall level of LD detected was low, which could be mostly likely due to poor marker coverage.


Association mapping for kernel phytosterol content in almond.

Font I Forcada C, Velasco L, Socias I Company R, Fernández I Martí Á - Front Plant Sci (2015)

LD based on r2, averaged for map distance classes and germplasm groups based on population structure analysis in the STRUCTURE.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4496553&req=5

Figure 4: LD based on r2, averaged for map distance classes and germplasm groups based on population structure analysis in the STRUCTURE.
Mentions: Extent of genome-wide LD was evaluated through pairwise comparisons among the 40 marker loci and the 71 almond germplasm accessions studied (Figures 3, 4). After removing low frequency alleles (MAF = 0.05), the results showed a high level of LD up to 20 cM, which dissipated at farther distances. The overall LD for all cultivars was 0.034 in the region from 0 to 10 cM, 0.079 from 10 to 20 cM, 0.036 from 20 to 30 cM, and 0.027 after 30 cM. These results were lower if the cultivars were separated in two different groups, Mediterranean and non-Mediterranean. Thus, the range of LD spaced every 10 cM was 0.061, 0.087, 0.045, and 0.032 for Mediterranean cultivars, and 0.058, 0.079, 0.039, and 0.028 for non-Mediterranean cultivars. A high level of LD up to 20 cM was observed for the whole ensemble of accessions when they were split in a Mediterranean and a non-Mediterranean group. The total r2-value for intra-chromosomal loci pairs was 0.040 and the unlinked markers pairs showed a similar percentage of significant LD in Mediterranean and non-Mediterranean cultivars (values of 0.091 and 0.073, respectively). Regarding the total r2-value for inter-chromosomal loci pairs was 0.036 for the whole ensemble, 0.082 for the Mediterranean accessions, and 0.062 for the non-Mediterranean accessions. The overall level of LD detected was low, which could be mostly likely due to poor marker coverage.

Bottom Line: The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations.Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome.These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

View Article: PubMed Central - PubMed

Affiliation: Genome Center, University of California, Davis Davis, CA, USA.

ABSTRACT
Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r(2) -value for all intra-chromosomal loci pairs was 0.040, whereas, the r(2) for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

No MeSH data available.