Mapping of QTL Associated with Seed Amino Acids Content in “MD96-5722” by “Spencer” RIL Population of Soybean Using SNP Markers

Laila Khandaker; Masum Akond; Shiming Liu; Stella K. Kantartzi; Khalid Meksem; Nacer Bellaloui; David A. Lightfoot; My Abdelmajid Kassem

doi:10.4236/fns.2015.611101

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Food and Nutrition Sciences > Vol.6 No.11, August 2015

Mapping of QTL Associated with Seed Amino Acids Content in “MD96-5722” by “Spencer” RIL Population of Soybean Using SNP Markers ()

Laila Khandaker¹, Masum Akond¹, Shiming Liu², Stella K. Kantartzi², Khalid Meksem², Nacer Bellaloui³, David A. Lightfoot², My Abdelmajid Kassem^1,4*

¹Plant Genomics and Biotechnology Laboratory, Department of Biological Sciences, Fayetteville State University, Fayetteville, NC, USA.
²Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA.
³Crop Genetics Research Unit, Agricultural Research Service, USDA, Stoneville, MS, USA.
⁴The School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khiamah, United Arab Emirates.

DOI: 10.4236/fns.2015.611101 PDF HTML XML 2,710 Downloads 3,369 Views Citations

Abstract

Limited information is available on the genetic analysis of amino acid composition in soybean seeds. Previously, quantitative trait loci (QTLs) for seed isoflavones, protein, oil, and fatty acids were identified in the “MD96-5722” by “Spencer” and other RIL populations. There were wide variations for these seed constituents among the RIL populations. Therefore, the objective of this study was to identify QTLs controlling different amino acids content in soybean seeds. To achieve this objective, ninety-two F_5:7 recombinant inbred lines (RIL), developed from a cross of MD96-5722 and Spencer, using a total 5376 Single Nucleotide Polymorphism (SNPs) markers, were used. The RILs were genotyped by using 537 polymorphic, reliably segregating SNP markers, developed from the Illumina Infinium SoySNP6K BeadChip array. A total of 13 QTLs were identified with three QTLs for threonine on the linkage group (LG) A1, C2, and B2. Two QTLs were identified for each of the amino acids proline on LG D1a and B2, serine on LG A1 and C2, tryptophan on LG K and G, and cysteine on LG A1 and K. One QTL was identified for arginine on LG N and histidine on LG J. The new QTLs findings for seed amino acid will facilitate the development of soybean cultivars with higher protein and amino acid quality to help meet the industry and consumer needs.

Keywords

Soybean, Amino Acids, SNP, QTLs, Seed Composition, Constituents

Share and Cite:

Khandaker, L. , Akond, M. , Liu, S. , Kantartzi, S. , Meksem, K. , Bellaloui, N. , Lightfoot, D. and Kassem, M. (2015) Mapping of QTL Associated with Seed Amino Acids Content in “MD96-5722” by “Spencer” RIL Population of Soybean Using SNP Markers. Food and Nutrition Sciences, 6, 974-984. doi: 10.4236/fns.2015.611101.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Berk, Z. (1992) Technology of Production of Edible Flours and Protein Products from Soybeans. FAO Agricultural Services Bulletin No. 97, Rome, 178.
[2]	Ufaz, S. and Galili, G. (2008) Improving the Content of Essential Amino Acids in Crop Plants: Goals and Opportunities. Plant Physiology, 147, 954-961. http://dx.doi.org/10.1104/pp.108.118091
[3]	National Research Council (1998) Nutrient Requirements of Swine: 10th Revised Edition. Subcommittee on Swine Nutrition, Committee on Animal Nutrition, The National Academies Press, Washington DC, USA, 210.
[4]	Wilson, R.F. (1987) Seed Metabolism. In: Wilcox, J.R., Ed., Soybeans: Improvement, Production and Uses, 2nd Edition, American Society of Agronomy, Madison, 643-687.
[5]	Kwanyuen, P., Pantalone, V.R., Burton, J.W. and Wilson, R.F. (1997) A New Approach to Genetic Alteration of Soybean Protein Composition and Quality. Journal of the American Oil Chemists Society, 74, 983-987. http://dx.doi.org/10.1007/s11746-997-0015-2
[6]	Panthee, D.R., Pantalone, V.R., Saxton, A.M., West, D.R. and Sams, C.E. (2006) Genomic Regions Associated with Amino Acid Composition in Soybean. Molecular Breeding, 17, 79-89. http://dx.doi.org/10.1007/s11032-005-2519-5
[7]	Panthee, D.R., Pantalone, V.R., Saxton, A.M., West, D.R., Sams, C.E., Orf, J.H. and Killiam, A.S. (2006) Quantitative Trait Loci Controlling Sulfur Containing Amino Acids, Methionine and Cysteine, in Soybean Seeds. Theoretical and Applied Genetics, 112, 546-553. http://dx.doi.org/10.1007/s00122-005-0161-6
[8]	SoyBase (2014) SoyBase-A Genome Database for Glycine. Administered Online by USDA-ARS and Iowa State University. http://soybeanbreederstoolbox.org
[9]	Wang, X.L. and Larkins, B.A. (2001) Genetic Analysis of Amino Acid Accumulation in Opaque-2 Maize Endosperm. Plant Physiology, 125, 1766-1777. http://dx.doi.org/10.1104/pp.125.4.1766
[10]	Zhao, W.G., Park, E.J., Chung, J.W., Park, Y.J., Chung, I.M., Ahn, J.K. and Kim, G.H. (2009) Association Analysis of the Amino Acid Contents in Rice. Journal of Integrative Plant Biology, 51, 1126-1137. http://dx.doi.org/10.1111/j.1744-7909.2009.00883.x
[11]	Fallen, B.D., Hatcher, C.N., Allen, F.L., Kopsell, D.A., Saxton, A.M., Chen, P., Kantartzi, S.K., Cregan, P.B., Hyten, D.L. and Pantalone, V.R. (2013) Soybean Seed Amino Acid Content QTL Detected Using the Universal Soy Linkage Panel 1.0 of 1536 SNPs. Journal of Plant Genome Science, 1, 68-79.
[12]	Warrington, C.V. (2011) QTL Mapping and Optimum Resource Allocation for Enhancing Amino Acid Content in Soybean. Ph.D. Dissertation, University of Georgia, Athens, GA.
[13]	Akond, M., Kantartzi, S.K., Meksem, K., Song, Q., Wang, D., Wen, Z., Lightfoot, D.A. and Kassem, M.A. (2013) A SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array. Journal of Plant Genome Science, 1, 80-89.
[14]	Siehl, D.L. (1999) The Biosynthesis of Tryptophan, Tyrosine, and Phenylalanine from Chorismate. In: Singh, B.K., Ed., Plant Amino Acids: Biochemistry and Biotechnology, Marcel Dekker Inc., New York, 171-204.
[15]	Singh, B.K. (1999) Biosynthesis of Valine, Leucine, and Isoleucine. In: Singh, B.K., Ed., Plant Amino Acids: Biochemistry and Biotechnology, Marcel Dekker Inc., New York, 227-247.
[16]	Fontaine, J. (2003) Amino Acid Analysis of Feeds. In: D’Mello, J.P.F., Ed., Amino Acids in Animal Nutrition, 2nd Edition, CABI Publishing, Cambridge, MA, 15-40. http://dx.doi.org/10.1079/9780851996547.0015
[17]	AOAC (1990) Official Methods of Analysis of the Association of Official Analytical Chemists, 982.30E (a,b,c) Ch. 45.3.05. 15th Edition, AOAC International, Arlington, VA.
[18]	Ooijen, J.W.V. (2006) Join Map 4: Software for the Calculation of Genetic Linkage Maps in Experimental Populations. Kyazma, B.V., Wageningen.
[19]	Saito, K. (1999) Biosynthesis of Cysteine. In: Singh, B.K., Ed., Plant Amino Acids: Biochemistry and Biotechnology, Marcel Dekker Inc., New York, 267-291.
[20]	SAS (2002-2010) Statistical Analysis System, Cary, NC.
[21]	Matthews, B.F. (1999) Lysine, Threonine, and Methionine Biosynthesis. In: Singh, B.K., Ed., Plant Amino Acids: Biochemistry and Biotechnology, Marcel Dekker Inc., New York, 205-225.
[22]	Vaughn, J.N., Nelson, R.L., Song, O., Cregan, P.B. and Li, Z. (2014) The Genetic Architecture of Seed Composition in Soybean is Refined by Genome-Wide Association Scans across Multiple Populations. Genes, Genomes, Genetics, 4, 2283-2294. http://dx.doi.org/10.1534/g3.114.013433
[23]	Akond, M., Liu, S., Kantartzi, S.K., Khalid, M., Bellaloui, N., Lightfoot, D.A., Yuan, J., Wang, D. and Kassem, M.A. (2014) Quantitative Trait Loci for Seed Isoflavone Contents in “MD96-5722” by “Spencer” Recombinant Inbred Lines of Soybean. Journal of Agricultural and Food Chemistry, 62, 1464-1468. http://dx.doi.org/10.1021/jf4040173
[24]	Akond, M., Liu, S., Kantartzi, S.K., Meksem, K., Bellaloui, N., Lightfoot, D.A., Yuan, J., Wang, D. and Kassem, M.A. (2014) Identification of QTLs Controlling Protein, Oil and Fatty Acids’ Contents in Soybean. American Journal of Plant Sciences, 5, 158-167. http://dx.doi.org/10.4236/ajps.2014.51021