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SNP-SNP Interaction Analysis on Soybean Oil Content under Multi-Environments

View Article: PubMed Central - PubMed

ABSTRACT

Soybean oil content is one of main quality traits. In this study, we used the multifactor dimensionality reduction (MDR) method and a soybean high-density genetic map including 5,308 markers to identify stable single nucleotide polymorphism (SNP)—SNP interactions controlling oil content in soybean across 23 environments. In total, 36,442,756 SNP-SNP interaction pairs were detected, 1865 of all interaction pairs associated with soybean oil content were identified under multiple environments by the Bonferroni correction with p <3.55×10−11. Two and 1863 SNP-SNP interaction pairs detected stable across 12 and 11 environments, respectively, which account around 50% of total environments. Epistasis values and contribution rates of stable interaction (the SNP interaction pairs were detected in more than 2 environments) pairs were detected by the two way ANOVA test, the available interaction pairs were ranged 0.01 to 0.89 and from 0.01 to 0.85, respectively. Some of one side of the interaction pairs were identified with previously research as a major QTL without epistasis effects. The results of this study provide insights into the genetic architecture of soybean oil content and can serve as a basis for marker-assisted selection breeding.

No MeSH data available.


The circle represented the whole soybean genome.Blue lines represented epistatic interactions between two markers across eleven environment, the black lines represented epistatic interactions between two markers across twelve environment.
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pone.0163692.g001: The circle represented the whole soybean genome.Blue lines represented epistatic interactions between two markers across eleven environment, the black lines represented epistatic interactions between two markers across twelve environment.

Mentions: There were two and 1863 SNP interaction pairs were identified under 12 and 11 environments which have been detected the available interaction pairs (Fig 1). Among the 20 linkage groups, most of stable interaction pairs were from Gm01 to others, including Gm01, Gm05, Gm06, Gm07, Gm08, Gm09, Gm10, Gm13, Gm18 and Gm20. Two SNP interaction pairs detected across 12 environments showed the interaction effect between Gm01 (Mark673223) and Gm05 (Mark310931, Mark312588), furthermore, 1863 SNP interaction pairs detected across 11 environments showed the strong interaction region at Gm01, Gm05, Gm06, Gm07, Gm09, Gm10, Gm13 and Gm18 (Fig 1). These 1865 SNP interaction pairs were detected stable across environments which almost 50% of all, so we saw them as the stable interaction pairs and used for next step calculation.


SNP-SNP Interaction Analysis on Soybean Oil Content under Multi-Environments
The circle represented the whole soybean genome.Blue lines represented epistatic interactions between two markers across eleven environment, the black lines represented epistatic interactions between two markers across twelve environment.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036806&req=5

pone.0163692.g001: The circle represented the whole soybean genome.Blue lines represented epistatic interactions between two markers across eleven environment, the black lines represented epistatic interactions between two markers across twelve environment.
Mentions: There were two and 1863 SNP interaction pairs were identified under 12 and 11 environments which have been detected the available interaction pairs (Fig 1). Among the 20 linkage groups, most of stable interaction pairs were from Gm01 to others, including Gm01, Gm05, Gm06, Gm07, Gm08, Gm09, Gm10, Gm13, Gm18 and Gm20. Two SNP interaction pairs detected across 12 environments showed the interaction effect between Gm01 (Mark673223) and Gm05 (Mark310931, Mark312588), furthermore, 1863 SNP interaction pairs detected across 11 environments showed the strong interaction region at Gm01, Gm05, Gm06, Gm07, Gm09, Gm10, Gm13 and Gm18 (Fig 1). These 1865 SNP interaction pairs were detected stable across environments which almost 50% of all, so we saw them as the stable interaction pairs and used for next step calculation.

View Article: PubMed Central - PubMed

ABSTRACT

Soybean oil content is one of main quality traits. In this study, we used the multifactor dimensionality reduction (MDR) method and a soybean high-density genetic map including 5,308 markers to identify stable single nucleotide polymorphism (SNP)—SNP interactions controlling oil content in soybean across 23 environments. In total, 36,442,756 SNP-SNP interaction pairs were detected, 1865 of all interaction pairs associated with soybean oil content were identified under multiple environments by the Bonferroni correction with p <3.55×10−11. Two and 1863 SNP-SNP interaction pairs detected stable across 12 and 11 environments, respectively, which account around 50% of total environments. Epistasis values and contribution rates of stable interaction (the SNP interaction pairs were detected in more than 2 environments) pairs were detected by the two way ANOVA test, the available interaction pairs were ranged 0.01 to 0.89 and from 0.01 to 0.85, respectively. Some of one side of the interaction pairs were identified with previously research as a major QTL without epistasis effects. The results of this study provide insights into the genetic architecture of soybean oil content and can serve as a basis for marker-assisted selection breeding.

No MeSH data available.