Identification of loci governing eight agronomic traits using a <scp>GBS</scp>‐<scp>GWAS</scp> approach and validation by <scp>QTL</scp> mapping in soya bean

Sonah, Humira; O’Donoughue, Louise S.; Cober, Elroy R.; Rajcan, Istvan; Belzile, François

doi:10.1111/pbi.12249

Cited by 311 publications

(307 citation statements)

References 50 publications

(81 reference statements)

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“…Note that LD decay varies across different chromosomes and even within heterochromatic and euchromatic chromosome regions. Sonah et al (2015) has shown LD for each of the chromosomes separately and observed range from 250 kb to 2.5 Mb. Hwang et al (2014) identified that the LD decay rate in heterochromatic and euchromatic chromosome regions was 360 and 9600 kb, respectively.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

Zhang

et al. 2017

Mol Breeding

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Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is a highly recalcitrant endoparasite of soybean roots, causing more yield loss than any other pest. To identify quantitative trait loci (QTL) controlling resistance to SCN (HG type 2.5.7, race 1), a genomewide association study (GWAS) was performed. The association panel, consisting of 120 Chinese soybean cultivars, was genotyped with 7189 single nucleotide polymorphism (SNPs). A total of 6204 SNPs with minor allele frequency >0.05 were used to estimate linkage disequilibrium (LD) and population structure. The mean level of LD measured by r 2 declined very rapidly to half its maximum value (0.51) at 220 kb. The overall population structure was approximately coincident with geographic origin. The GWAS results identified 13 SNPs in 7 different genomic regions significantly associated with SCN resistance. Of these, three SNPs were localized in previously mapped QTL intervals, including rhg1 and Rhg4. The GWAS results also detected 10 SNPs in 5 different genomic regions associated with SCN resistance. The identified loci explained an average of 95.5% of the phenotypic variance. The proportion of phenotypic variance was due to additive genetic variance of the validated SNPs. The present study identified multiple new loci and refined chromosomal regions of known loci associated with SCN resistance. The loci and trait-associated SNPs identified in this study can be used for developing soybean cultivars with durable resistance against SCN.

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Section: Discussionmentioning

confidence: 99%

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

Zhang

et al. 2017

Mol Breeding

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“…Conceptually, an increase in the compositional value of soybeans via altered carbon partitioning seems feasible, because a considerable portion of the soybean dry weight is composed of less valuable fiber and the poorly digestible oligosaccharides raffinose and stachyose (Padgette et al, 1996). However, neither conventional breeding nor quantitative trait locus mapping approaches for increasing soybean oil, while maintaining protein content, has been very successful, because increases in one of these components is usually associated with decreases in the other (Smith and Weber, 1968;Burton and Brim, 1981;Feng et al, 2004;Eskandari et al, 2013;Sonah et al, 2015). Consequently, the oil and protein contents of about 20% and 40% for commodity soybeans have changed little in the last several decades.…”

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confidence: 99%

An Improved Variant of Soybean Type 1 Diacylglycerol Acyltransferase Increases the Oil Content and Decreases the Soluble Carbohydrate Content of Soybeans

et al. 2016

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Kinetically improved diacylglycerol acyltransferase (DGAT) variants were created to favorably alter carbon partitioning in soybean (Glycine max) seeds. Initially, variants of a type 1 DGAT from a high-oil, high-oleic acid plant seed, Corylus americana, were screened for high oil content in Saccharomyces cerevisiae. Nearly all DGAT variants examined from high-oil strains had increased affinity for oleoyl-CoA, with S 0.5 values decreased as much as 4.7-fold compared with the wild-type value of 0.94 mM. Improved soybean DGAT variants were then designed to include amino acid substitutions observed in promising C. americana DGAT variants. The expression of soybean and C. americana DGAT variants in soybean somatic embryos resulted in oil contents as high as 10% and 12%, respectively, compared with only 5% and 7.6% oil achieved by overexpressing the corresponding wildtype DGATs. The affinity for oleoyl-CoA correlated strongly with oil content. The soybean DGAT variant that gave the greatest oil increase contained 14 amino acid substitutions out of a total of 504 (97% sequence identity with native). Seed-preferred expression of this soybean DGAT1 variant increased oil content of soybean seeds by an average of 3% (16% relative increase) in highly replicated, single-location field trials. The DGAT transgenes significantly reduced the soluble carbohydrate content of mature seeds and increased the seed protein content of some events. This study demonstrated that engineering of the native DGAT enzyme is an effective strategy to improve the oil content and value of soybeans.

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“…Significant natural variation for seed carotenoids also is present in diversity panels of maize (Zea mays), wheat (Triticum aestivum), Citrus spp., chickpea (Cicer arietinum), carrot (Daucus carota), pea (Pisum sativum), cassava (Manihot esculenta), and Arabidopsis (Abbo et al, 2010;Arango et al, 2010;Welsch et al, 2010;Yan et al, 2010;Blanco et al, 2011;Cook et al, 2012;Gonzalez-Jorge et al, 2013;Kandianis et al, 2013;Owens et al, 2014;Jourdan et al, 2015;Suwarno et al, 2015). Advances in high-throughput phenotyping and genotyping are allowing some of the genes underlying this natural variation to be identified through genome-wide association studies (GWAS; Harjes et al, 2008;Zhou et al, 2012;Gonzalez-Jorge et al, 2013;Owens et al, 2014;Wen et al, 2014;Sonah et al, 2015). In this study, we integrate GWAS, QTL analysis, and reverse genetics in the model plant Arabidopsis to functionally define the loci contributing to natural variation in seed carotenoid levels.…”

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confidence: 99%

ZEAXANTHIN EPOXIDASE Activity Potentiates Carotenoid Degradation in Maturing Seed

et al. 2016

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Elucidation of the carotenoid biosynthetic pathway has enabled altering the composition and content of carotenoids in various plants, but to achieve desired nutritional impacts, the genetic components regulating carotenoid homeostasis in seed, the plant organ consumed in greatest abundance, must be elucidated. We used a combination of linkage mapping, genome-wide association studies (GWAS), and pathway-level analysis to identify nine loci that impact the natural variation of seed carotenoids in Arabidopsis (Arabidopsis thaliana). ZEAXANTHIN EPOXIDASE (ZEP) was the major contributor to carotenoid composition, with mutants lacking ZEP activity showing a remarkable 6-fold increase in total seed carotenoids relative to the wild type. Natural variation in ZEP gene expression during seed development was identified as the underlying mechanism for fine-tuning carotenoid composition, stability, and ultimately content in Arabidopsis seed. We previously showed that two CAROTENOID CLEAVAGE DIOXYGENASE enzymes, CCD1 and CCD4, are the primary mediators of seed carotenoid degradation, and here we demonstrate that ZEP acts as an upstream control point of carotenoid homeostasis, with ZEPmediated epoxidation targeting carotenoids for degradation by CCD enzymes. Finally, four of the nine loci/enzymatic activities identified as underlying natural variation in Arabidopsis seed carotenoids also were identified in a recent GWAS of maize (Zea mays) kernel carotenoid variation. This first comparison of the natural variation in seed carotenoids in monocots and dicots suggests a surprising overlap in the genetic architecture of these traits between the two lineages and provides a list of likely candidates to target for selecting seed carotenoid variation in other species.

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Identification of loci governing eight agronomic traits using a GBS‐GWAS approach and validation by QTL mapping in soya bean

Cited by 311 publications

References 50 publications

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

An Improved Variant of Soybean Type 1 Diacylglycerol Acyltransferase Increases the Oil Content and Decreases the Soluble Carbohydrate Content of Soybeans

ZEAXANTHIN EPOXIDASE Activity Potentiates Carotenoid Degradation in Maturing Seed

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