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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 indicate epistatic interactions across 2 environments, red lines indicate epistatic interactions across 3 environments, black lines indicate epistatic interactions across 4 environments, green lines indicate epistatic interactions across 5 environments.
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pone.0163692.g002: The circle represented the whole soybean genome.Blue lines indicate epistatic interactions across 2 environments, red lines indicate epistatic interactions across 3 environments, black lines indicate epistatic interactions across 4 environments, green lines indicate epistatic interactions across 5 environments.

Mentions: The epistatic interaction values and their contribution to genetic values and variance were screened by the two way ANOVA test for each environment at significant level of p<0.01. In total, there were 560 of 1865 interaction pairs were screened, 4, 23, 99 and 344 SNP interaction pairs were detected as stable and effective interaction pairs across 5, 4, 3 and 2 environments respectively (Fig 2), which similar as the environment-universal QTLs, defined as QTLs associated with traits of interest in at least one macro-environment (i.e., year-location combination) [37, 38], here, it could be the environment-universal SNP interaction pairs, and there were no significance for the other SNP interaction pairs. Epistatic value and contribution rate data of stable interaction pairs across all environments are shown in S1 Table. Epistasis value was ranged from 0.01 to 0.89 at the p<0.01 level. Contribution rates of epistatic pairs were ranged from 0.01 to 0.85 at the p<0.01 level (S1 Table).


SNP-SNP Interaction Analysis on Soybean Oil Content under Multi-Environments
The circle represented the whole soybean genome.Blue lines indicate epistatic interactions across 2 environments, red lines indicate epistatic interactions across 3 environments, black lines indicate epistatic interactions across 4 environments, green lines indicate epistatic interactions across 5 environments.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163692.g002: The circle represented the whole soybean genome.Blue lines indicate epistatic interactions across 2 environments, red lines indicate epistatic interactions across 3 environments, black lines indicate epistatic interactions across 4 environments, green lines indicate epistatic interactions across 5 environments.
Mentions: The epistatic interaction values and their contribution to genetic values and variance were screened by the two way ANOVA test for each environment at significant level of p<0.01. In total, there were 560 of 1865 interaction pairs were screened, 4, 23, 99 and 344 SNP interaction pairs were detected as stable and effective interaction pairs across 5, 4, 3 and 2 environments respectively (Fig 2), which similar as the environment-universal QTLs, defined as QTLs associated with traits of interest in at least one macro-environment (i.e., year-location combination) [37, 38], here, it could be the environment-universal SNP interaction pairs, and there were no significance for the other SNP interaction pairs. Epistatic value and contribution rate data of stable interaction pairs across all environments are shown in S1 Table. Epistasis value was ranged from 0.01 to 0.89 at the p<0.01 level. Contribution rates of epistatic pairs were ranged from 0.01 to 0.85 at the p<0.01 level (S1 Table).

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)&mdash;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 &lt;3.55&times;10&minus;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.