Article pubs.acs.org/JAFC
Quantitative Trait Loci for Seed Isoflavone Contents in ‘MD96-5722’ by ‘Spencer’ Recombinant Inbred Lines of Soybean Masum Akond,† Shiming Liu,§ Stella K. Kantartzi,§ Khalid Meksem,§ Nacer Bellaloui,# David A. Lightfoot,§ Jiazheng Yuan,⊗ Dechun Wang,⊗ and My Abdelmajid Kassem*,† †
Plant Genomics and Biotechnology Laboratory, Department of Biological Sciences, Fayetteville State University, Fayetteville, North Carolina 28301-4298, United States § Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901-4415, United States # Crop Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 141 Experiment Station Road, P.O. Box 345, Stoneville, Mississippi 38776, United States ⊗ Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824-1325, United States ABSTRACT: Isoflavones from soybeans [Glycine max (L.) Merr.] have a significant impact on human health to reduce the risk of several major diseases. Breeding soybean for high isoflavone content in the seed is possible through marker-assisted selection (MAS) which can be based on quantitative trait loci (QTL). The objective of this study was to identify QTL controlling isoflavone content in a set of ‘MD96-5722’ by ‘Spencer’ recombinant inbred line (RIL) populations of soybean. Wide variations were found for seed concentrations of daidzein, glycitein, genistein, and total isoflavones among the RIL populations. Three QTL were identified on three different linkage groups (LG) represented by three different chromosomes (Chr). One QTL that controlled daidzein content was identified on LG A1 (Chr 5), and two QTL that underlay glycitein content were identified on LG K (Chr 9) and LG B2 (Chr 14). Identified QTL could be functional in developing soybean with preferable isoflavone concentrations in the seeds through MAS. KEYWORDS: soybean, SNP linkage map, QTL, RIL, daidzein, genistein, glycitein, isoflavones, ‘MD96-5722’, ‘Spencer’
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INTRODUCTION Dietetic phytoestrogens, popularly known as isoflavones, represent one of the most biologically active classes of flavonoids.1 Soybean [Glycine max (L.) Merr.] seeds are the major source of isoflavones, namely, daidzein, glycitein, and genistein. Isoflavones have antimutagenic activity,2 can reduce the risk of breast and prostate cancer3,4 and cardiovascular diseases,5,6 and can ameliorate the symptoms of menopause and osteoporosis in women. Isoflavones also play an important role in plant’s defense against pathogens and different types of stresses.7 However, the biological effects of these isoflavone components on animals depend on purity, dose, and dietary cofactors.8 Breeding soybean for high or low isoflavone content in the seed is possible through marker-assisted selection (MAS) and a method for MAS based on quantitative trait loci (QTL). Different studies reported isoflavone contents in soybean fluctuate among recombinant inbred lines and also cultivars,9,10 which allow breeders to identify QTL associated with isoflavone contents. To date, different types of molecular markers such as single nucleotide polymorphism (SNP), simple sequence repeat (SSR), amplified fragment length polymorphism (AFLP), restriction fragment length polymorphisms (RFLP), and random amplified polymorphic DNA (RAPD) were used to construct genetic and QTL maps in soybean.11−17 Large numbers of markers are necessary to cover the whole genome of soybean, which could identify most QTL and candidate genes for important agronomic traits. A universal linkage panel of soybean containing 1536 SNPs was developed by Hyten et © 2014 American Chemical Society
al. through the Illumina GoldenGate platform and is very efficient in construction of linkage maps subsequently identifying QTL.17 Large numbers of SNPs (>50000) were reported in maize and soybean developed through the Illumina Infinium platform using BeadChip.18,19 In this study, we analyzed the MD 96-5722 by Spencer recombinant inbred line (RIL) population using the Infinium BeadChip genotyping array of soybean on the Illumina platform. Molecular markers identified in the different populations did not cover the whole soybean genome, and none of the QTL have been further validated using other approaches.20 Thus, soybean breeders need more markers that control isoflavones. The first report of QTL underlying isoflvaone (phytoestrogen) content in the mapping population ‘Essex’ × ‘Forrest’21 and later on other groups used the same population14,22,23 and identified 25 QTL associated with isoflavones. In the population ‘AC756’ × ‘RCAT Angora’, Primomo et al.9 detected 17 QTL associated with daidzein, genistein, glycitein, and total isoflavone content. In 2009, Zeng et al.24 reported 11 QTL in a population of the cross ‘Zhongdou 27’ × ‘Jiunong 20’ associated with daidzein, genistein, glycitein, and total isoflavone content. We identified (unpublished data) 16 QTL for daidzein, genistein, and glycitein in the PI 438489B and ‘Hamilton’ RIL population, growing them in two environments. Received: Revised: Accepted: Published: 1464
September 11, 2013 January 21, 2014 January 29, 2014 January 29, 2014 dx.doi.org/10.1021/jf4040173 | J. Agric. Food Chem. 2014, 62, 1464−1468
Journal of Agricultural and Food Chemistry
Article
Table 1. Summary Statistics of Seed Isoflavone Concentrations (Values in μg/g) of MD96-5722 by Spencer RIL Population daidzein range mean SD skewness kurtosis variance CV
323−474 381.40 24.84 0.44 0.65 616.83 6.51
MD 96-5722 SD Spencer SD
376.75 13.45 388.75 42.93
glycitein RIL Values (n = 92) 417−693 547.69 58.47 0.11 −0.50 3418.85 10.68 Parents Mean Values (n = 4) 641.5 9.61 676.75 51.08
genistein
total isoflavones
499−671 592.37 36.76 −0.23 −0.20 1351.60 6.21
1,266−1,776 1,521.45 104.68 −0.03 −0.34 10958.23 6.88
555.5 13.82 585 26.65
1573.75 21.17 1650.5 44.86
Table 2. SNP Markers and Intervals Most Likely To Be Associated with the Isoflavone QTL for Mean Seed Daidzein and Glycitein Values across Two Environmentsa trait
QTL
Chr/LG
position
marker interval
LOD
additive
R2
daidzein glycitein glycitein
qDaid001 qGly001 qGly002
5/A1 9/K 14/B2
11.70 0.60 20.20
ss245748832−ss245762437 ss24687662−ss246876937 ss248275008−ss248278947
4.55 2.66 2.97
1.92 9.76 22.11
0.023 0.002 0.099
a
The chromosome numbers assignments to linkage group based on SoyBase and the Soybean Breeder’s Toolbox (http://soybase.org/LG2Xsome. php.
the 92 RILs (Table 1). Variations among RIL lines were 6.51, 10.68, 6.21, and 6.88% for daidzein, glycitein, genistein, and total isoflavones, respectively. Among the two parents, the mean values of genistein, glycitein, and total isoflavones were higher for Spencer than for MD 96-5722; however, the mean values were lower for daidzein. Individual or total isoflavone means of RILs suggested that the segregation of these traits fits a normal distribution model as both the skewness and kurtosis values for these traits were
Quantitative Trait Loci for Seed Isoflavone Contents in ‘MD96-5722’ by ‘Spencer’ Recombinant Inbred Lines of Soybean Masum Akond,† Shiming Liu,§ Stella K. Kantartzi,§ Khalid Meksem,§ Nacer Bellaloui,# David A. Lightfoot,§ Jiazheng Yuan,⊗ Dechun Wang,⊗ and My Abdelmajid Kassem*,† †
Plant Genomics and Biotechnology Laboratory, Department of Biological Sciences, Fayetteville State University, Fayetteville, North Carolina 28301-4298, United States § Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901-4415, United States # Crop Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 141 Experiment Station Road, P.O. Box 345, Stoneville, Mississippi 38776, United States ⊗ Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824-1325, United States ABSTRACT: Isoflavones from soybeans [Glycine max (L.) Merr.] have a significant impact on human health to reduce the risk of several major diseases. Breeding soybean for high isoflavone content in the seed is possible through marker-assisted selection (MAS) which can be based on quantitative trait loci (QTL). The objective of this study was to identify QTL controlling isoflavone content in a set of ‘MD96-5722’ by ‘Spencer’ recombinant inbred line (RIL) populations of soybean. Wide variations were found for seed concentrations of daidzein, glycitein, genistein, and total isoflavones among the RIL populations. Three QTL were identified on three different linkage groups (LG) represented by three different chromosomes (Chr). One QTL that controlled daidzein content was identified on LG A1 (Chr 5), and two QTL that underlay glycitein content were identified on LG K (Chr 9) and LG B2 (Chr 14). Identified QTL could be functional in developing soybean with preferable isoflavone concentrations in the seeds through MAS. KEYWORDS: soybean, SNP linkage map, QTL, RIL, daidzein, genistein, glycitein, isoflavones, ‘MD96-5722’, ‘Spencer’
■
INTRODUCTION Dietetic phytoestrogens, popularly known as isoflavones, represent one of the most biologically active classes of flavonoids.1 Soybean [Glycine max (L.) Merr.] seeds are the major source of isoflavones, namely, daidzein, glycitein, and genistein. Isoflavones have antimutagenic activity,2 can reduce the risk of breast and prostate cancer3,4 and cardiovascular diseases,5,6 and can ameliorate the symptoms of menopause and osteoporosis in women. Isoflavones also play an important role in plant’s defense against pathogens and different types of stresses.7 However, the biological effects of these isoflavone components on animals depend on purity, dose, and dietary cofactors.8 Breeding soybean for high or low isoflavone content in the seed is possible through marker-assisted selection (MAS) and a method for MAS based on quantitative trait loci (QTL). Different studies reported isoflavone contents in soybean fluctuate among recombinant inbred lines and also cultivars,9,10 which allow breeders to identify QTL associated with isoflavone contents. To date, different types of molecular markers such as single nucleotide polymorphism (SNP), simple sequence repeat (SSR), amplified fragment length polymorphism (AFLP), restriction fragment length polymorphisms (RFLP), and random amplified polymorphic DNA (RAPD) were used to construct genetic and QTL maps in soybean.11−17 Large numbers of markers are necessary to cover the whole genome of soybean, which could identify most QTL and candidate genes for important agronomic traits. A universal linkage panel of soybean containing 1536 SNPs was developed by Hyten et © 2014 American Chemical Society
al. through the Illumina GoldenGate platform and is very efficient in construction of linkage maps subsequently identifying QTL.17 Large numbers of SNPs (>50000) were reported in maize and soybean developed through the Illumina Infinium platform using BeadChip.18,19 In this study, we analyzed the MD 96-5722 by Spencer recombinant inbred line (RIL) population using the Infinium BeadChip genotyping array of soybean on the Illumina platform. Molecular markers identified in the different populations did not cover the whole soybean genome, and none of the QTL have been further validated using other approaches.20 Thus, soybean breeders need more markers that control isoflavones. The first report of QTL underlying isoflvaone (phytoestrogen) content in the mapping population ‘Essex’ × ‘Forrest’21 and later on other groups used the same population14,22,23 and identified 25 QTL associated with isoflavones. In the population ‘AC756’ × ‘RCAT Angora’, Primomo et al.9 detected 17 QTL associated with daidzein, genistein, glycitein, and total isoflavone content. In 2009, Zeng et al.24 reported 11 QTL in a population of the cross ‘Zhongdou 27’ × ‘Jiunong 20’ associated with daidzein, genistein, glycitein, and total isoflavone content. We identified (unpublished data) 16 QTL for daidzein, genistein, and glycitein in the PI 438489B and ‘Hamilton’ RIL population, growing them in two environments. Received: Revised: Accepted: Published: 1464
September 11, 2013 January 21, 2014 January 29, 2014 January 29, 2014 dx.doi.org/10.1021/jf4040173 | J. Agric. Food Chem. 2014, 62, 1464−1468
Journal of Agricultural and Food Chemistry
Article
Table 1. Summary Statistics of Seed Isoflavone Concentrations (Values in μg/g) of MD96-5722 by Spencer RIL Population daidzein range mean SD skewness kurtosis variance CV
323−474 381.40 24.84 0.44 0.65 616.83 6.51
MD 96-5722 SD Spencer SD
376.75 13.45 388.75 42.93
glycitein RIL Values (n = 92) 417−693 547.69 58.47 0.11 −0.50 3418.85 10.68 Parents Mean Values (n = 4) 641.5 9.61 676.75 51.08
genistein
total isoflavones
499−671 592.37 36.76 −0.23 −0.20 1351.60 6.21
1,266−1,776 1,521.45 104.68 −0.03 −0.34 10958.23 6.88
555.5 13.82 585 26.65
1573.75 21.17 1650.5 44.86
Table 2. SNP Markers and Intervals Most Likely To Be Associated with the Isoflavone QTL for Mean Seed Daidzein and Glycitein Values across Two Environmentsa trait
QTL
Chr/LG
position
marker interval
LOD
additive
R2
daidzein glycitein glycitein
qDaid001 qGly001 qGly002
5/A1 9/K 14/B2
11.70 0.60 20.20
ss245748832−ss245762437 ss24687662−ss246876937 ss248275008−ss248278947
4.55 2.66 2.97
1.92 9.76 22.11
0.023 0.002 0.099
a
The chromosome numbers assignments to linkage group based on SoyBase and the Soybean Breeder’s Toolbox (http://soybase.org/LG2Xsome. php.
the 92 RILs (Table 1). Variations among RIL lines were 6.51, 10.68, 6.21, and 6.88% for daidzein, glycitein, genistein, and total isoflavones, respectively. Among the two parents, the mean values of genistein, glycitein, and total isoflavones were higher for Spencer than for MD 96-5722; however, the mean values were lower for daidzein. Individual or total isoflavone means of RILs suggested that the segregation of these traits fits a normal distribution model as both the skewness and kurtosis values for these traits were
