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2023 Vol.68, Issue 4 Preview Page
Development and Utilization of KASP Markers Targeting the Lipoxygenase Gene in Soybean
Seo-Young Shin12
,
Se-Hee Kang12
,
Byeong Hee Kang12
,
Sreeparna Chowdhury1
,
Won-Ho Lee12
,
Jeong-Dong Lee3
,
Sungwoo Lee4
,
Yu-Mi Choi5*
,
Bo-Keun Ha67
1Graduate Student, Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
2Graduate Student, BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
3Professor, Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
4Professor, Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
5Researcher, National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Republic of Korea
6Professor, Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
7Professor, BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
*Corresponding Author
1 December 2023. pp. 294-303
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Abstract

Lipoxygenase gives soybeans their grassy flavor, which can disrupt food processing efficiency. This study aimed to identify soybean genotypes with lipoxygenase deficiency among 1,001 soybean accessions and to develop kompetitive allele specific PCR (KASP) markers that can detect lipoxygenase mutations. Three lipoxygenase isozymes (Lox1, Lox2, and Lox3) were analyzed using a colorimetric assay based on a substrate-enzyme reaction. Among the 1,001 accessions examined, two (IT160160 and IT276392) exhibited a deficiency solely in Lox1, and one (IT269984) lacked both Lox1 and Lox2. IT160160 had a 74-bp deletion in exon 8 of Lox1 (Glyma13g347600), whereas IT276392 displayed a missense mutation involving the change of C to A at position 2,880 of Lox1. Moreover, we successfully developed four KASP markers that specifically target Lox1, Lox2, and Lox3 mutations. To validate the Lox1 KASP markers, we used two F2:3 populations generated through a cross between Daepung 2 (lipoxygenase wild type, maternal parent), IT160160, and IT276392 (null Lox1, paternal parent). The results revealed that the Daepung 2 × IT160160 group followed the expected 3:1 ratio according to Mendel’s law, whereas the Daepung 2 × IT276392 group did not. Furthermore, a comparison between the colorimetric and KASP marker analyses results revealed a high agreement rate of 96%. KASP markers offer a distinct advantage by allowing the distinction of heterozygous types independent of other variables. As a result, we present an opportunity to expedite the lipoxygenase-deficient cultivar development.

Keywords
KASP marker
lipoxygenase (Lox)
soybean
References
1
Arai, S., M. Noguchi, M. Kaji, H. Kato, and M. Fujimaki. 1970. n-Hexanal and some volatile alcohols: Their distribution in raw soybean tissues and formation in crude soy protein concentrate by lipoxygenase. Agricultural and Biological Chemistry. 34(9) : 1420-1423. 10.1080/00021369.1970.10859786
2
Axelrod, B. 1981. Lipoxygenase from soybeans. Methods Enzymol. 71 : 441-451. 10.1016/0076-6879(81)71055-3
3
Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15) : 2114-2120. 10.1093/bioinformatics/btu17024695404PMC4103590
4
Brash, A. R. 1999. Lipoxygenases: occurrence, functions, catalysis, and acquisition of substrate. Journal of Biological Chemistry. 274(34) : 23679-23682. 10.1074/jbc.274.34.2367910446122
5
Clemente, T. E. and E. B. Cahoon. 2009. Soybean oil: genetic approaches for modification of functionality and total content. Plant Physiology. 151(3) : 1030-1040. 10.1104/pp.109.14628219783644PMC2773065
6
Davies, C. and N. Nielsen. 1986. Genetic analysis of a null-allele for lipoxygenase-2 in soybean 1. Crop Science. 26(3) : 460-463. 10.2135/cropsci1986.0011183X002600030003x
7
Farhad, I., M. Islam, S. Hoque, and M. Bhuiyan. 2010. Role of potassium and sulphur on the growth, yield and oil content of soybean (Glycine max L.). An Academic Journal of Plant Sciences. 3(2) : 99-103.
8
Gerde, J. A. and P. J. White. 2008. Lipids. In Soybeans: Chemistry, Production, Processing, and Utilization. Elsevier. Amsterdam. The Netherlands, pp. 193-227. 10.1016/B978-1-893997-64-6.50010-X
9
Hajika, M., K. Kitamura, K. Igita, and Y. Nakazawa. 1992. Genetic relationships among the genes for lipoxygenase-1,-2 and-3 isozymes in soybean [Glycine max (L.) Merrill] seed. Japanese Journal of Breeding. 42(4) : 787-792. 10.1270/jsbbs1951.42.787
10
Hildebrand, D. and T. Hymowitz. 1982. Inheritance of Lipoxygenase-1 Activity in Soybean Seeds 1. Crop Science. 22(4) : 851-853. 10.2135/cropsci1982.0011183X002200040036x
11
Kim, S. D., Y. H. Kim, K. Y. Park, H. T. Yun, S. H. Lee, Y. H. Lee, Y. K. Seung, H. S. Kim, E. H. Hong, and Y. S. Kim. 1997. A new beany tasteless soybean variety "Jinpumkong 2" with good quality. Korean J. Breed. 29(4) : 502.
12
Kitamura, K. 1984. Biochemical characterization of lipoxygenase lacking mutants, Ll-less, L-2-less, and L-3-less soybeans. Agricultural and Biological Chemistry. 48(9) : 2339-2346. 10.1080/00021369.1984.10866488
13
Kitamura, K., C. Davies, N. Kaizuma, and N. Nielsen. 1983. Genetic Analysis of a Null‐Allele for Lipoxygenase-3 in Soybean Seeds 1. Crop Science. 23(5) : 924-927. 10.2135/cropsci1983.0011183X002300050026x
14
Kitamura, K., T. Kumagai, and A. Kikuchi. 1985. Inheritance of lipoxygenase-2 and genetic relationships among genes for lipoxygenase-1,-2 and-3 isozymes in soybean seeds. Japanese Journal of Breeding. 35(4) : 413-420. 10.1270/jsbbs1951.35.413
15
Lee, K. J., J. E. Hwang, V. Velusamy, B.-K. Ha, J.-B. Kim, S. H. Kim, J.-W. Ahn, S.-Y. Kang, and D. S. Kim. 2014. Selection and molecular characterization of a lipoxygenase-free soybean mutant line induced by gamma irradiation. Theoretical and Applied Genetics. 127 : 2405-2413. 10.1007/s00122-014-2385-925190478
16
Lenis, J. M., J. D. Gillman, J. D. Lee, J. G. Shannon, and K. D. Bilyeu. 2010. Soybean seed lipoxygenase genes: molecular characterization and development of molecular marker assays. Theoretical and Applied Genetics. 120 : 1139-1149. 10.1007/s00122-009-1241-920058147
17
Li, H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.
18
Mack, A., T. Peterman, and J. Siedow. 1987. Lipoxygenase isozymes in higher plants: biochemical properties and physiological role. Isozymes. 13 : 127-154.
19
Narvel, J. M., W. R. Fehr, and L. C. Weldon. 2000. Analysis of soybean seed lipoxygenases. Crop Science. 40(3) : 838-840. 10.2135/cropsci2000.403838x
20
Patil, G., J. Chaudhary, T. D. Vuong, B. Jenkins, D. Qiu, S. Kadam, G. J. Shannon, and H. T. Nguyen. 2017. Development of SNP genotyping assays for seed composition traits in soybean. International Journal of Plant Genomics. 2017 : 6572969. 10.1155/2017/657296928630621PMC5463095
21
Reinprecht, Y., S.-Y. Luk-Labey, K. Yu, V. W. Poysa, I. Rajcan, G. R. Ablett, and K. Peter Pauls. 2011. Molecular basis of seed lipoxygenase null traits in soybean line OX948. Theoretical and Applied Genetics. 122 : 1247-1264. 10.1007/s00122-011-1528-521243331
22
Sasaki, R. and H. Chiba. 1983. Enzymatic removal of flavor in soybean protein. Kagaku To Seibutsu. 21 : 536-543.
23
Schmutz, J., S. B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D. L. Hyten, Q. Song, J. J. Thelen, and J. Cheng. 2010. Genome sequence of the palaeopolyploid soybean. Nature. 463(7278) : 178-183. 10.1038/nature0867020075913
24
Siedow, J. N. 1991. Plant lipoxygenase: structure and function. Annual Review of Plant Biology. 42(1) : 145-188. 10.1146/annurev.pp.42.060191.001045
25
Suda, I., M. Hajika, Y. Nishiba, S. Furuta, and K. Igita. 1995. Simple and rapid method for the selective detection of individual lipoxygenase isoenzymes in soybean seeds. Journal of Agricultural and Food Chemistry. 43(3) : 742-747. 10.1021/jf00051a034
26
Wang, W. H., T. Takano, D. Shibata, K. Kitamura, and G. Takeda. 1994. Molecular basis of a null mutation in soybean lipoxygenase 2: substitution of glutamine for an iron-ligand histidine. Proceedings of the National Academy of Sciences. 91(13) : 5828-5832. 10.1073/pnas.91.13.58288016074PMC44090
27
Wolf, W. J. 1975. Lipoxygenase and flavor of soybean protein products. Journal of Agricultural and Food Chemistry. 23(2) : 136-141. 10.1021/jf60198a013
Information
  • Publisher :The Korean Society of Crop Science
  • Publisher(Ko) :한국작물학회
  • Journal Title :The Korean Journal of Crop Science
  • Journal Title(Ko) :한국작물학회지
  • Volume : 68
  • No :4
  • Pages :294-303
  • Received Date : 2023-10-16
  • Accepted Date : 2023-11-06
  • DOI :https://doi.org/10.7740/kjcs.2023.68.4.294
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