Identification of additive and epistatic effects QTLs for seed oil content in soybean based on an integrating map of two RIL populations

Abstract Background Soybean seed oil has been widely used in human consumption and industrial production. Results In order to identify the additive and epistatic effects QTLs and QTLs by environments interactions (AE and AAE) for seed oil content in soybean, an eight-environment conjoint analysis based on two populations RIL3613 and RIL6013 with an integrating map was conducted. An new high-density integrated genetic map containing 2212 SNP markers and covering 5718.01 cM with an average distance of 2.61 cM were constructed by the combination of two linkage maps of two associated recombinant inbred line (A-RIL) populations. A total of 64 additive effect and additive × environment interaction (AE) QTL were identified on 19 chromosomes by both ICIM and IM methods, and the proportion of phenotypic variations explained (PVE) range of QTL related to oil content was 1.29–10.75%, of which 19 QTLs had overlapping marker intervals, and qOil-5-1 was identified simultaneously in both RIL populations. Compared with previous SSR positioning results, it is found 8 SNP sites within the QTL physical interval located in the SSR sites. Among them, 4 QTLs were new found. Twelve pairs of epistatic QTLs (additive × additive, AA) and QTL interactions with environments (AAE) for oil content were identified by the ICIM method, of which 3 QTLs were new found, and 2 additive effect QTLs, qOil-9-2 and qOil-15-1, linked to the other two QTLs to produce epistatic effects. A total of 5 potential candidate genes were identified based on genetic ontology and annotated information showing the relationship with seed oil content and/or fatty acid biosynthesis and metabolism. Conclusion These QTLs with different effects provide the good basis for molecular-assisted breeding of soybean oil content-related traits and further fine mapping of related genes.

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Dynamic Transcriptome Changes Related to Oil Accumulation in Developing Soybean Seeds

International Journal of Molecular Sciences ◽

10.3390/ijms20092202 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2202 ◽

Cited By ~ 3

Author(s):

Songnan Yang ◽

Long Miao ◽

Jianbo He ◽

Kai Zhang ◽

Yan Li ◽

...

Keyword(s):

Fatty Acid ◽

Candidate Genes ◽

Molecular Basis ◽

Oil Content ◽

Seed Oil ◽

Soybean Seed ◽

Soybean Seeds ◽

Seed Oil Content ◽

Oil Accumulation ◽

Expression Levels

Soybean is one of the most important oil crops in the world. Revealing the molecular basis and exploring key candidate genes for seed oil synthesis has great significance for soybean improvement. In this study, we found that oil accumulation rates and gene expression levels changed dynamically during soybean seed development. The expression levels of genes in metabolic pathways such as carbon fixation, photosynthesis, glycolysis, and fatty acid biosynthesis were significantly up-regulated during the rapid accumulation of oil in developing soybean seeds. Through weighted correlation network analysis, we identified six co-expression modules associated with soybean seed oil content and the pink module was the most positively correlated (r = 0.83, p = 7 × 10−4) network. Through the integration of differential expression and co-expression analysis, we predicted 124 candidate genes potentially affecting soybean seed oil content, including seven genes in lipid metabolism pathway, two genes involved in glycolysis, one gene in sucrose metabolism, and 12 genes belonged to transcription factors as well as other categories. Among these, three genes (GmABI3b, GmNFYA and GmFAD2-1B) have been shown to control oil and fatty acid content in soybean seeds, and other newly identified candidate genes would broaden our knowledge to understand the molecular basis for oil accumulation in soybean seeds.

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Natural variation and selection in GmSWEET39 affect soybean seed oil content

New Phytologist ◽

10.1111/nph.16250 ◽

2019 ◽

Vol 225 (4) ◽

pp. 1651-1666 ◽

Cited By ~ 7

Author(s):

Long Miao ◽

Songnan Yang ◽

Kai Zhang ◽

Jianbo He ◽

Chunhua Wu ◽

...

Keyword(s):

Natural Variation ◽

Oil Content ◽

Seed Oil ◽

Soybean Seed ◽

Seed Oil Content ◽

Variation And Selection

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Elevation of soybean seed oil content through selection for seed coat shininess

Nature Plants ◽

10.1038/s41477-017-0084-7 ◽

2018 ◽

Vol 4 (1) ◽

pp. 30-35 ◽

Cited By ~ 16

Author(s):

Dajian Zhang ◽

Lianjun Sun ◽

Shuai Li ◽

Weidong Wang ◽

Yanhua Ding ◽

...

Keyword(s):

Seed Coat ◽

Oil Content ◽

Seed Oil ◽

Soybean Seed ◽

Seed Oil Content ◽

Selection For

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Soybean seed oil content: genetic control under different photoperiods

Genetics and Molecular Biology ◽

10.1590/s1415-47571998000300017 ◽

1998 ◽

Vol 21 (3) ◽

pp. 387-394 ◽

Cited By ~ 3

Author(s):

Zilda F.S. Miranda ◽

Carlos A. Arrabal Arias ◽

José Francisco Ferraz de Toledo ◽

Marcelo Fernandes de Oliveira

Keyword(s):

Oil Content ◽

Seed Oil ◽

Additive Genetic Variance ◽

Soybean Seed ◽

Sowing Date ◽

Inbred Lines ◽

Seed Oil Content ◽

Additive Interaction ◽

Additive Variance ◽

Sowing Dates

The oil content of soybean (Glycine max (L.) Merrill) seeds is a polygenic and complex trait that is responsive to environmental effects that occur during plant development. Our objective was to study the seed oil content of soybeans developed under diverse photoperiod and temperature conditions. Three parental inbred lines with classic (BR-13, FT-2 and BR85-29009) and one with long juvenile flowering type (OCEPAR 8) and the F2, F3, and F9 generations derived from all possible crosses between them (including reciprocals) were sowed in September 27th, October 20th and December 17th in 1993 in Londrina, Paraná State, Brazil (between 23o08'47" and 23o55'46" latitude S). The October and December sowing dates are within the period the varietal research personnel recommend for sowing soybeans in Paraná State. The analysis of variance indicated significant differences among sowing dates, among advanced inbred lines, and the sowing date x inbred line interaction. Seed oil content increased from September to October and decreased from October to December in all materials, but the reduction was greater in FT-2 and OCEPAR 8 among the parentals. The additive genetic variance (D) or additive variance among linked genes (D1) was significant for all crosses and sowing dates. Genotype x micro-environment interactions were important in some crosses. The additive [d] effects were greater in September and October, and the additive x additive interaction [i] was important in October among the mean genetic parameters. Significant dominance effects [h] were more frequent in December and October, often in direction of the increased seed oil content. The heritability estimates ranged from 15 to 43%, with the highest values obtained in September. The prediction of cross potential to generate higher seed oil inbred lines indicated that selection is likely to be successful in most crosses. The highest proportion of inbred lines with seed oil percentage above the standard (lines with more than 22% seed oil content) was for BR85-29009 x OCEPAR 8 in September, FT-2 x OCEPAR 8 in October, and in BR85-29009 x OCEPAR 8 and BR-13 x OCEPAR 8 in December.

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Diagnosis and recommendation integrated system (DRIS) of soybean seed oil content

Revista Brasileira de Ciência do Solo ◽

10.1590/s0100-06832012000600016 ◽

2012 ◽

Vol 36 (6) ◽

pp. 1820-1827 ◽

Cited By ~ 3

Author(s):

Alfredo Castamann ◽

Pedro Alexandre Varella Escosteguy ◽

Diego Berres ◽

Silas Zanella

Keyword(s):

Oil Content ◽

Seed Oil ◽

Soybean Seed ◽

Nutrient Status ◽

Integrated System ◽

Nutrient Ratios ◽

Seed Oil Content ◽

Leaf Analysis ◽

Full Flowering ◽

Soybean Leaves

The Diagnosis and Recommendation Integrated System (DRIS) can improve interpretations of leaf analysis to determine the nutrient status. Diagnoses by this method require DRIS norms, which are however not known for oil content of soybean seeds. The aims of this study were to establish and test the DRIS method for oil content of soybean seed (maturity group II cultivars). Soybean leaves (207 samples) in the full flowering stage were analyzed for macro and micro-nutrients, and the DRIS was applied to assess the relationship between nutrient ratios and the seed oil content. Samples from experimental and farm field sites of the southernmost Brazilian state Rio Grande do Sul (28° - 29° southern latitude; 52° -53° western longitude) were assessed in two growing seasons (2007/2008 and 2008/2009). The DRIS norms related to seed oil content differed between the studied years. A unique DRIS norm was established for seed oil content higher than 18.68 % based on data of the 2007/2008 growing season. Higher DRIS indices of B, Ca, Mg and S were associated with a higher oil content, while the opposite was found for K, N and P. The DRIS can be used to evaluate the leaf nutrient status of soybean to improve the seed oil content of the crop.

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Registration of ‘NC-Miller’ Soybean with High Yield and High Seed-Oil Content

Journal of Plant Registrations ◽

10.3198/jpr2012.01.0007crc ◽

2012 ◽

Vol 6 (3) ◽

pp. 294-297 ◽

Cited By ~ 2

Author(s):

J. W. Burton ◽

L. M. Miranda ◽

T. E. Carter ◽

D. T. Bowman

Keyword(s):

Oil Content ◽

Seed Oil ◽

High Yield ◽

Seed Oil Content

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Faculty Opinions recommendation of The homeobox gene GLABRA2 affects seed oil content in Arabidopsis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1031749.367855 ◽

2006 ◽

Author(s):

Erich Grotewold

Keyword(s):

Oil Content ◽

Seed Oil ◽

Homeobox Gene ◽

Seed Oil Content

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Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L.

International Journal of Molecular Sciences ◽

10.3390/ijms22031033 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1033

Author(s):

Abirami Rajavel ◽

Selina Klees ◽

Johanna-Sophie Schlüter ◽

Hendrik Bertram ◽

Kun Lu ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Brassica Napus ◽

Oil Content ◽

Seed Oil ◽

Seed Oil Content ◽

Complex Interplay ◽

Brassica Napus L ◽

Data Set ◽

Developmental Switches

Transcription factors (TFs) and their complex interplay are essential for directing specific genetic programs, such as responses to environmental stresses, tissue development, or cell differentiation by regulating gene expression. Knowledge regarding TF–TF cooperations could be promising in gaining insight into the developmental switches between the cultivars of Brassica napus L., namely Zhongshuang11 (ZS11), a double-low accession with high-oil- content, and Zhongyou821 (ZY821), a double-high accession with low-oil-content. In this regard, we analysed a time series RNA-seq data set of seed tissue from both of the cultivars by mainly focusing on the monotonically expressed genes (MEGs). The consideration of the MEGs enables the capturing of multi-stage progression processes that are orchestrated by the cooperative TFs and, thus, facilitates the understanding of the molecular mechanisms determining seed oil content. Our findings show that TF families, such as NAC, MYB, DOF, GATA, and HD-ZIP are highly involved in the seed developmental process. Particularly, their preferential partner choices as well as changes in their gene expression profiles seem to be strongly associated with the differentiation of the oil content between the two cultivars. These findings are essential in enhancing our understanding of the genetic programs in both cultivars and developing novel hypotheses for further experimental studies.

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