Characterization of the fan1 locus in soybean line A5 and development of molecular assays for high-throughput genotyping of FAD3 genes

Pham, Anh Van; Bilyeu, Kristin; Chen, Pengyin; Boerma, H. R.; Li, Zenglu

doi:10.1007/s11032-013-0003-1

Cited by 18 publications

(21 citation statements)

References 34 publications

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Section: Discussionmentioning

confidence: 99%

“…High oleic acid content in soybean seed is a key compositional trait that improves oxidative stability and increases oil functionality and shelf life. A study on characterization of the FAD3A gene in segregating populations byPham et al (2014) reported a correlation coefficient of .79 between oleic and linoleic acids in a population consisting of 300 F 2:3 seeds derived from R07-10231 9 IA30234 (high-yielding line 9 low linolenic line), and a correlation coefficient of .81 between oleic and linoleic acids in a second population consisting of 300 F 2:3 seeds derived from R05-1415 9 R07-167 (high protein line 9 high yield/low linolenic line).The reported results coincided with changes observed from this study in palmitic, linoleic and linolenic acids when oleic acid was I G U R E 1 Percent germination of high (left) vs. normal (right) oleic acid near-isogenic lines (NILs) derived from a G00-3213 BC 3 F 2:4 population across different temperatures (y-axis = percent germination; x-axis = temperature in degrees Celsius; coloured lines = percent germination obtained from the different time points after the seeds were plated [Colour figure can be viewed at wileyonlinelibrary.com]…”

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confidence: 99%

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Effects of high oleic acid soybean on seed yield, protein and oil contents, and seed germination revealed by near‐isogeneic lines

Bachleda

Grey

2017

Plant Breeding

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Typical soybean oil is composed of palmitic, stearic, oleic, linoleic and linolenic acids. High oleic acid content in soybean seed is a key compositional trait that improves oxidative stability and increases oil functionality and shelf life. Using a marker‐assisted selection method, near‐isogenic lines (NILs) of G00‐3213 for the high oleic trait were developed and yield tested. These NILs have various combinations of FAD2‐1A and FAD2‐1B alleles that were derived from the same backcrossing populations. The results indicated that G00‐3213 NILs with both homozygous mutant FAD2‐1A and FAD2‐1B alleles produced an average of 788 g/kg oleic acid content. The results also demonstrated that possessing these mutant alleles did not cause a yield reduction. Furthermore, seed germination tests across 12 temperatures (12.8–32.0°C) showed that modified seed composition for oleic acid in general did not have a major impact on seed germination. However, there was a possible reduction in seed germination vigour when high oleic seeds are planted in cold soil. The mutant FAD2‐1A and FAD2‐1B alleles did not hinder either seed or plant development.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Effects of high oleic acid soybean on seed yield, protein and oil contents, and seed germination revealed by near‐isogeneic lines

Bachleda

Grey

2017

Plant Breeding

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“…In addition, the genotyping procedures for both SSR and RFLP markers are labour-and time-consuming and cost-ineffective. In contrast, SNP markers have been used increasingly in genetic analyses, because of their high density on the whole genome and easy operation in a high-throughput setting (Tenaillon et al 2001, Song et al 2012, Pham et al 2014, Shi et al 2015, Tian et al 2015. The average density of SNP markers on the maize genome is one every 48-104 bp (Tenaillon et al 2001, Ching et al 2002.…”

Section: Discussionmentioning

confidence: 99%

Molecular mapping of quantitative trait loci for grain moisture at harvest in maize

et al. 2016

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In maize, high grain moisture (GM) at harvest causes problems in harvesting, threshing, artificial drying, storage, transportation and processing. Understanding the genetic basis of GM will be useful for breeding low‐GM varieties. A quantitative genetics approach was used to identify quantitative trait loci (QTL) related to GM at harvest in field‐grown maize. The GM of a double haploid population consisting of 240 lines derived from Xianyu335 was evaluated in three planting seasons and a high‐density genetic linkage map covering 1546.4 cM was constructed. The broad‐sense heritability of GM at harvest was 71.0%. Using composite interval mapping, six QTL for GM at harvest were identified on five chromosomes (Chr). Two QTL located on Chr1, qgm1‐1 and qgm1‐2, explained 5.0% and 10.8% of the phenotypic variation in GM at harvest, respectively. The QTL qgm2, qgm3, qgm4 and qgm5 accounted for 3.3%, 8.3%, 5.4% and 11.0% of the mean phenotypic variation, respectively. Because of their consistent detection over multiple planting seasons, the detected QTL appear to be robust and reliable for the breeding of low‐GM varieties.

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“…The clustering of data points from the assay makes the genotyping results straightforward and greatly benefits the SNP allele calling process. Moreover, it has been previously shown that the TaqMan assay is also powerful for detecting DNA deletions (Pham et al 2014;Fedick et al 2012).…”

Section: Resultsmentioning

confidence: 99%

“…Three versions of omega-3 fatty acid desaturase (FAD3) underlie the three fan loci and are responsible for the conversion of linoleate to linolenate: FAD3A (Glyma14g37350/fan1), FAD3B (Glyma02g39230/fan3), and FAD3C (Glyma18g06 950/fan2) (Bilyeu et al 2003Pham et al 2014). The mutant alleles of FAD3 have been identified from several sources with the reduced linolenic acid content (Table 1) (Chappell and Bilyeu 2006;Bilyeu et al 2005Bilyeu et al , 2006.…”

Section: Introductionmentioning

confidence: 99%

High-throughput and functional SNP detection assays for oleic and linolenic acids in soybean

et al. 2015

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Soybean is a primary source of vegetable oil, accounting for 53 % of the total vegetable oil consumption in the USA in 2013. Soybean oil with high oleic acid and low linolenic acid content is desired, because it not only improves the oxidative stability of the oil, but also reduces the amount of undesirable trans fat production by the hydrogenation processing. The mutant FAD2-1A and FAD2-1B alleles contribute to an elevated oleic acid level, while mutations in FAD3A and FAD3C lead to a reduction in linolenic acid levels of soybean seed oil. Although single nucleotide polymorphism (SNP) SimpleProbe assays have been developed for these genes, breederfriendly and high-throughput marker systems are needed for large-scale selections in soybean breeding programs. TaqMan or Kompetitive Allele Specific PCR assays were successfully developed to detect and discriminate mutant alleles of FAD2-1A (17D and PI 603452 sources) and FAD2-1B (PI 283327 source) for the high oleic acid trait, as well as those of FAD3A (CX1512-44 and C1640 sources) and FAD3C (CX1512-44 source) for low linolenic acid content soybean. The accuracy of the assays was validated using multiple populations as well as a panel of diverse soybean lines, and a perfect association was observed between the SNP alleles and their corresponding fatty acid phenotypes. These marker assays have been proven to be robust and reliable for detecting mutant and wild-type alleles and thus will assist forward and backcrossing breeding of soybean lines with desired oil profiles in an accurate and efficient manner.Electronic supplementary material The online version of this article (

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Characterization of the fan1 locus in soybean line A5 and development of molecular assays for high-throughput genotyping of FAD3 genes

Cited by 18 publications

References 34 publications

Effects of high oleic acid soybean on seed yield, protein and oil contents, and seed germination revealed by near‐isogeneic lines

Effects of high oleic acid soybean on seed yield, protein and oil contents, and seed germination revealed by near‐isogeneic lines

Molecular mapping of quantitative trait loci for grain moisture at harvest in maize

High-throughput and functional SNP detection assays for oleic and linolenic acids in soybean

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