Genome-wide association study identifies candidate genes related to oleic acid content in soybean seeds

Liu, Xiaoyi; Qin, Di; Piersanti, Angela; Zhang, Qi; Miceli, Cristina; Wang, Piwu

doi:10.1186/s12870-020-02607-w

Cited by 21 publications

(23 citation statements)

References 34 publications

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“… Population structure of 260 genotypes of spring soybean ( Liu et al, 2020 ): (A) Diagram showing the value of 260 samples based on clustering from 1 to 15; Cross validation error rate for each K -value of 1–15, X -axis is K -value 1–15, Y -axis is cross-validation errors. (B) Clustering analysis when the number of subgroups is in the range 2–15, the colors represent separate groups.…”

Section: Resultsmentioning

confidence: 99%

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Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean (Glycine max L.) at Seedling Stages Using SLAF-Seq

et al. 2021

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Root systems can display variable genetic architectures leading to nutrient foraging or improving abiotic stress tolerance. Breeding for new soybean varieties with efficient root systems has tremendous potential in enhancing resource use efficiency and plant adaptation for challenging climates. In this study, root related traits were analyzed in a panel of 260 spring soybean with genome-wide association study (GWAS). Genotyping was done with specific locus amplified fragment sequencing (SLAF-seq), and five GWAS models (GLM, MLM, CMLM, FaST-LMM, and EMMAX) were used for analysis. A total of 179,960 highly consistent SNP markers distributed over the entire genome with an inter-marker distance of 2.36 kb was used for GWAS analysis. Overall, 27 significant SNPs with a phenotypic contribution ranging from 20 to 72% and distributed on chromosomes 2, 6, 8, 9, 13, 16 and 18 were identified and two of them were found to be associated with multiple root-related traits. Based on the linkage disequilibrium (LD) distance of 9.5 kb for the different chromosomes, 11 root and shoot regulating genes were detected based on LD region of a maximum 55-bp and phenotypic contribution greater than 22%. Expression analysis revealed an association between expression levels of those genes and the degree of root branching number. The current study provides new insights into the genetic architecture of soybean roots, and the underlying SNPs/genes could be critical for future breeding of high-efficient root system in soybean.

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Section: Resultsmentioning

confidence: 99%

“…FIGURE 1 | Distribution of SNPs in 20 chromosomes of Soybean. Each color represents different densities(Liu et al, 2020).…”

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Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean (Glycine max L.) at Seedling Stages Using SLAF-Seq

et al. 2021

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“…Soybeans ( Glycine max (L.) Merrill) are a major oilseed crop that provides edible oil and protein in China [ 1 ]. Soybean oil is a complex mixture of five fatty acids: palmitic acid (C16:0), stearic acid (C18:0), oleic acid (C18:1), linoleic acid (LA) (C18:2), and linolenic acid (C18:3) [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study Identifies Candidate Genes Related to the Linoleic Acid Content in Soybean Seeds

Qin

Piersanti

Zhāng

et al. 2021

IJMS

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Soybean (Glycine max (L.) Merrill) oil is a complex mixture of five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic). The high content of linoleic acid (LA) contributes to the oil having poor oxidative stability. Therefore, soybean seed with a lower LA content is desirable. To investigate the genetic architecture of LA, we performed a genome-wide association study (GWAS) using 510 soybean cultivars collected from China. The phenotypic identification results showed that the content of LA varied from 36.22% to 72.18%. The GWAS analysis showed that there were 37 genes related to oleic acid content, with a contribution rate of 7%. The candidate gene Glyma.04G116500.1 (GmWRI14) on chromosome 4 was detected in three consecutive years. The GmWRI14 showed a negative correlation with the LA content and the correlation coefficient was −0.912. To test whether GmWRI14 can lead to a lower LA content in soybean, we introduced GmWRI14 into the soybean genome. Matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS) showed that the overexpression of GmWRI14 leads to a lower LA content in soybean seeds. Meanwhile, RNA-seq verified that GmWRI14-overexpressed soybean lines showed a lower accumulation of GmFAD2-1A and GmFAD2-1B than control lines. Our results indicate that the down-regulation of the FAD2 gene triggered by the transcription factor GmWRI14 is the underlying mechanism reducing the LA level of seed. Our results provide novel insights into the genetic architecture of LA and pinpoint potential candidate genes for further in-depth studies.

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“…Soybeans [Glycine max (L.) Merrill] is a major oilseed crop providing edible oil and protein in China (Liu et al, 2020). Soybean oil is a complex mixture of ve fatty acids, they are oleic acid (C18:1), linoleic acid (C18:2), linolenic acid (C18:3), stearic acid (C18:0) and palmitic acid (C16:0) (Zhao et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Soybean AP2-Domain Transcription Factor GmWRI4 Optimize Ratio of Oleic Acid to Linoleic Acid in Seed

Qin

Piersanti

Zhang

et al. 2021

Preprint

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Background: Soybean [Glycine max (L.) Merrill] oil is a complex mixture of five fatty acids (oleic, linoleic, linolenic, palmitic and stearic). As a vegetable oils, soybean oil has a less than desirable fatty acid composition. The high content of linoleic acid contributes to poor oil oxidative stability. Soybean oil with lower linoleic acid content is desirable. To investigate the genetic architecture of linoleic acid in soybean seed, 510 soybean germplasms from China were collected as natural populations. Results: Phenotypic identification results showed that the content of linoleic acid varied from 36.22% to 72.18%. After a total of 2,423,512 nucleotide polymorphism (SNP) were obtained, a new candidate gene Glyma.04G116500.1 (GmWRI14) related to linoleic acid was discovered by 3-year long Genome-wide association analysis (GWAS). GmWRI14 belongs to the plant WRI1 protein family. The GmWRI14 showed a negative correlation with the linoleic acid content and the correlation coefficient was -0.912. To test whether GmWRI14 can lead to lower linoleic acid content in soybean seed, we introduced GmWRI14 into the soybean genome. Overexpression of GmWRI14 leads to higher accumulation of oil with lower linoleic acid content in soybean seed. RNA-seq verified that GmWRI14-overexpressed lines showed lower accumulation of GmFAD2-1 and GmFAD2-2b than non-transgenic lines. Conclusions: These results indicate that the down-regulation of FAD2 gene triggered by the transcription factor WRI1 is the underlying mechanism reducing linoleic acid level of seed oil. GmWRI14 is a new key candidate gene related to linoleic acid. These results will significantly improve understanding of the transcriptional control exerted by GmWRI14.

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Genome-wide association study identifies candidate genes related to oleic acid content in soybean seeds

Cited by 21 publications

References 34 publications

Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean (Glycine max L.) at Seedling Stages Using SLAF-Seq

Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean (Glycine max L.) at Seedling Stages Using SLAF-Seq

Genome-Wide Association Study Identifies Candidate Genes Related to the Linoleic Acid Content in Soybean Seeds

Soybean AP2-Domain Transcription Factor GmWRI4 Optimize Ratio of Oleic Acid to Linoleic Acid in Seed

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