Molecular marker utilization in oilseed crop breeding: a review

Document Type : Review paper

Authors
1 Department of Plant Science and Medicinal Plants, Agriculture faculty of Meshghin Shahr, University of Mohaghegh Ardabili.
2 Department of Crop Production and Genetics, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
Abstract
It has been observed that molecular markers are one of the most important tools in the advancement of oilseed crops and in developing varieties capable of withstanding drought, salinity, and high-temperature stresses. The present review focuses on the use of DNA-based molecular markers such as SSRs and SNPs in oilseed crop breeding. These markers, in addition to being able to identify and locate QTLs associated with stress tolerance, by using Marker-Assisted Selection (MAS) will aid in accelerating selection. Although the oilseed crops, including canola, soybean, and sunflower, have achieved certain levels of environmental stress tolerance, their inability to overcome abiotic stresses such as drought, salinity, and temperature extremes further dampens growth and productivity to contribute to the existing yield gap. However, the integration of molecular markers into breeding programs saves not only genetic diversity but also contributes to the quicker release of high-yielding varieties under extreme conditions. This review, therefore, enumerates examples of successful applications and emphasizes the future research needs of using molecular markers in breeding these under-investigated oilseed crops to build more robust world food systems resilient to global warming.
Keywords
Subjects

Abdi, G., Tarighat, M.A., Jain, M., Tendulkar, R., Tendulkar, M., and Barwant, M. (2024). "Revolutionizing Genomics: Exploring the Potential of Next-Generation Sequencing," in Advances in Bioinformatics. Springer), 1-33.
Adje, C., Missihoun, A.A., Sedah, P., Adoukonou Sagbadja, H., Achigan Dako, E., and Agbangla, C. (2023). Genetic diversity and structure of Benin pineapple (Ananas comosus (L) Merr.) germplasm collection using Simple Sequence Repeat (SSR) markers. J Plant Mol Breed. 11(2): 94-106.
Aguet, F., Alasoo, K., Li, Y.I., Battle, A., Im, H.K., Montgomery, S.B., and Lappalainen, T. (2023). Molecular quantitative trait loci. Nat. Rev. Methods Primers. 3(1): 4.
Akacin, I., Ersoy, Ş., Doluca, O., and Güngörmüşler, M. (2022). Comparing the significance of the utilization of next generation and third generation sequencing technologies in microbial metagenomics. Microbiological Research 264: 127154.
Akbari, N., and Darvishzadeh, R. (2024). Identification of REAMP markers related to morpho-phisiological and agronomic traits in oilseed sunflower (Helianthus annuus L.) under normal and limited irrigation conditions. Cro Sci Res Arid Reg 6(2): 245-260.
Ali, M.A., Azeem, F., Abbas, A., Joyia, F.A., Li, H., and Dababat, A.A. (2017). Transgenic strategies for enhancement of nematode resistance in plants. Front. Plant Sci. 8: 750.
Allen, A.M., Winfield, M.O., Burridge, A.J., Downie, R.C., Benbow, H.R., Barker, G.L., Wilkinson, P.A., Coghill, J., Waterfall, C., and Davassi, A. (2017). Characterization of a Wheat Breeders’ Array suitable for high‐throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). j. Plant Biotech. 15(3): 390-401.
Baba Nitsa, M., Odiyi, A.C., Akinyele, B.O., Aiyelari, O.P., and Fayeun, L.S. (2023). Genetic diversity assessment of thirty nine Coffea canephora accessions using EST-SSR markers. J Plant Mol Breed. 11(1): 17-27.
Bhatnagar, S., King, C.A., Purcell, L., and Ray, J.D. (Year). "Identification and mapping of quantitative trait loci associated with crop responses to water-deficit stress in soybean [Glycine max (L.) Merr.]", in: The ASACSSA-SSSA International annual meeting poster abstract).
Bhattacharjee, M., Prakash, S., Roy, S., Soumen, S., Begum, T., and Dasgupta, T. (2020). SSR-based DNA fingerprinting of 18 elite Indian varieties of sesame (Sesamum indicum L.). The Nucleus 63: 67-73.
Chao, H., Kilaru, A., and Liu, L. (2023). Editorial: Genetics, breeding and engineering to enhance oil quality and yield. Front. Plant Sci. 14. doi: 10.3389/fpls.2023.1265897.
Chen, H., Cui, S., Fu, S., Gai, J., and Yu, D. (2008). Identification of quantitative trait loci associated with salt tolerance during seedling growth in soybean (Glycine max L.). Aust. J. Agric. Res. 59(12): 1086-1091.
Chen, H., Kumawat, G., Yan, Y., Fan, B., and Xu, D. (2021). Mapping and validation of a major QTL for primary root length of soybean seedlings grown in hydroponic conditions. BMC genom. 22: 1-9.
Cornelious, B., Chen, P., Chen, Y., De Leon, N., Shannon, J., and Wang, D. (2005). Identification of QTLs underlying water-logging tolerance in soybean. Mol. Breed. 16: 103-112.
Čurn, V., Ovesna, J., Sakova, L., and Sobotka, R. (2002). Identification of oilseed rape cultivars using AFLP markers. J Cent Eur Agric. 3(4): 285-292.
Dhungana, S.K., Kim, H.-S., Kang, B.-K., Seo, J.-H., Kim, H.-T., Shin, S.-O., Oh, J.-H., and Baek, I.-Y. (2021). Identification of QTL for tolerance to flooding stress at seedling stage of soybean (Glycine max L. Merr.). Agron. 11(5): 908.
Dimitrijevic, A., and Horn, R. (2018). Sunflower hybrid breeding: from markers to genomic selection. Front. Plant Sci. 8: 2238.
Dossa, K., Li, D., Zhou, R., Yu, J., Wang, L., Zhang, Y., You, J., Liu, A., Mmadi, M.A., and Fonceka, D. (2019). The genetic basis of drought tolerance in the high oil crop Sesamum indicum. Plant Biotechnol. J. 17(9): 1788-1803.
Fernandez, P., Di Rienzo, J., Fernandez, L., Hopp, H.E., Paniego, N., and Heinz, R.A. (2008). Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis. BMC Plant Biol. 8: 1-18.
Funatsuki, H., Kawaguchi, K., Matsuba, S., Sato, Y., and Ishimoto, M. (2005). Mapping of QTL associated with chilling tolerance during reproductive growth in soybean. Theor. Appl. Genet. 111: 851-861.
Gautami, B., Pandey, M., Vadez, V., Nigam, S., Ratnakumar, P., Krishnamurthy, L., Radhakrishnan, T., Gowda, M., Narasu, M., and Hoisington, D. (2012). Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Mol. Breed. 30: 757-772.
Githiri, S.M., Watanabe, S., Harada, K., and Takahashi, R. (2006). QTL analysis of flooding tolerance in soybean at an early vegetative growth stage. Plant Bree. 125(6): 613-618.
Hamwieh, A., Tuyen, D.D., Cong, H., Benitez, E.R., Takahashi, R., and Xu, D. (2011). Identification and validation of a major QTL for salt tolerance in soybean. Euphytica 179: 451-459.
Hasan, N., Choudhary, S., Naaz, N., Sharma, N., and Laskar, R.A. (2021a). Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Gen Eng Biotech 19(1): 128.
Hasan, N., Choudhary, S., Naaz, N., Sharma, N., and Laskar, R.A. (2021b). Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J. Genet. Eng. Biotechnol. 19(1): 128.
Hashemi-Petroudi, S.H., Arab, M., Dolatabadi, B., Kuo, Y.-T., Baez, M.A., Himmelbach, A., Nematzadeh, G., Maibody, S.A.M.M., Schmutzer, T., and Mälzer, M. (2022). Initial description of the Genome of Aeluropus littoralis, a halophile grass. Frontiers in Plant Science 13: 906462.
Havlíčková, L., Jozova, E., Rychla, A., Klima, M., Kučera, V., and Čurn, V. (2014). Genetic diversity assessment in winter Oilseed Rape (Brassica napus L.) collection using AFLP, ISSR and SSR markers. CZECH J Genet Plant 50(3).
Heidari, P., Hasanzadeh, S., Faraji, S., Ercisli, S., and Mora-Poblete, F. (2023). Genome-wide characterization of the sulfate transporter gene family in oilseed crops: Camelina sativa and Brassica napus. Plants 12(3): 628.
Hewezi, T., Léger, M., El Kayal, W., and Gentzbittel, L. (2006). Transcriptional profiling of sunflower plants growing under low temperatures reveals an extensive down-regulation of gene expression associated with chilling sensitivity. J. Exp. Bot. 57(12): 3109-3122.
Holsman, K.K. (2023). Climate Change 2022 :Impacts, Adaptation and Vulnerability.
Hosseinpour Azad, N. (2023). Genetic diversity of Satureja bachtiarica Bunge species collected from north-west Iran. J Plant Mol Breed. 11(2): 31-38.
Hu, T., Chitnis, N., Monos, D., and Dinh, A. (2021). Next-generation sequencing technologies: An overview. Human Immunology 82(11): 801-811.
Huang, L., Wu, B., Zhao, J., Li, H., Chen, W., Zheng, Y., Ren, X., Chen, Y., Zhou, X., and Lei, Y. (2016). Characterization and transferable utility of microsatellite markers in the wild and cultivated Arachis species. PLoS One 11(5): e0156633.
Ikeda, T., Ohnishi, S., Senda, M., Miyoshi, T., Ishimoto, M., Kitamura, K., and Funatsuki, H. (2009). A novel major quantitative trait locus controlling seed development at low temperature in soybean (Glycine max). Theor. Appl. Genet. 118: 1477-1488.
Jegadeesan, S., Yu, K., Poysa, V., Gawalko, E., Morrison, M.J., Shi, C., and Cober, E. (2010). Mapping and validation of simple sequence repeat markers linked to a major gene controlling seed cadmium accumulation in soybean [Glycine max (L.) Merr]. Theor. Appl. Genet. 121: 283-294.
Jones, R.A., Sharman, M., Trębicki, P., Maina, S., and Congdon, B.S. (2021). Virus diseases of cereal and oilseed crops in Australia: current position and future challenges. Viruses 13(10): 2051.
Kassem, M.A., Meksem, K., Kang, C., Njiti, V., Kilo, V., Wood, A., and Lightfoot, D. (2004). Loci underlying resistance to manganese toxicity mapped in a soybean recombinant inbred line population of ‘Essex2019; x ‘Forrest’. Plant  Soil 260: 197-204.
Ke, T., Yu, J., Dong, C., Mao, H., Hua, W., and Liu, S. (2015). ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. BMC plant biology 15: 1-11.
Kole, C., Thormann, C., Karlsson, B., Palta, J., Gaffney, P., Yandell, B., and Osborn, T. (2002). Comparative mapping of loci controlling winter survival and related traits in oilseed Brassica rapa and B. napus. Mol. Breed. 9: 201-210.
Kour, M., Kumari, L., and Sharma, S. (2023). Association of SSR Markers for primary branches in Brassica Juncea L. J Plant Mol Breed. 11(2): 77-92.
Kühn, N., Spiegel, M.P., Tovar, C., Willis, K.J., and Macias-Fauria, M. (2022). Seeing roots from space: aboveground fingerprints of root depth in vegetation sensitivity to climate in dry biomes. Environ. Res. Lett. 17(11): 114062.
Kumar, K.R., Cowley, M.J., and Davis, R.L. (Year). "Next-generation sequencing and emerging technologies", in: Seminars in thrombosis and hemostasis: Thieme Medical Publishers).
Lawrence, T.J., Vilbig, J.M., Kangogo, G., Fèvre, E.M., Deem, S.L., Gluecks, I., Sagan, V., and Shacham, E. (2023). Shifting climate zones and expanding tropical and arid climate regions across Kenya (1980–2020). Reg. Environ. Change 23(2): 59.
Lee, G., Boerma, H., Villagarcia, M., Zhou, X., Carter, T., Li, Z., and Gibbs, M. (2004). A major QTL conditioning salt tolerance in S-100 soybean and descendent cultivars. Theor. Appl. Genet. 109: 1610-1619.
Lesk, C., Anderson, W., Rigden, A., Coast, O., Jägermeyr, J., McDermid, S., Davis, K.F., and Konar, M. (2022). Compound heat and moisture extreme impacts on global crop yields under climate change. Nat. Rev. Earth Environ. 3(12): 872-889.
Li, C., Miao, H., Wei, L., Zhang, T., Han, X., and Zhang, H. (2014). Association mapping of seed oil and protein content in Sesamum indicum L. using SSR markers. PLoS One 9(8): e105757.
Li, D., Dossa, K., Zhang, Y., Wei, X., Wang, L., Zhang, Y., Liu, A., Zhou, R., and Zhang, X. (2018). GWAS uncovers differential genetic bases for drought and salt tolerances in sesame at the germination stage. Genes 9(2): 87.
Lindqvist-Kreuze, H., Cho, K., Portal, L., Rodríguez, F., Simon, R., Mueller, L.A., Spooner, D.M., and Bonierbale, M. (2013). Linking the potato genome to the conserved ortholog set (COS) markers. BMC Genetics 14: 1-12.
Lodenius, N. (2023). Identifying molecular markers for breeding a future oil crop, Lepidium campestre. Master Program, Swedish University of Agricultural Sciences.
Lynas, M., Adams, J., and Conrow, J. (2022). Misinformation in the media: global coverage of GMOs 2019-2021. GM Crops & Food: 1-10.
Mahjoob, B., Zarini, H., Hashemi, S., and Shamasbi, F. (2016). Comparison of ISSR, IRAP and REMAP markers for assessing genetic diversity in different species of Brassica sp. Russian J Gen 52: 1272-1281.
Malgaonkar, M., Shirolkar, A., Murthy, S.N., Mangal, A.K., and Pawar, S.D. (2020). DNA Based Molecular Markers: A Tool for Differentiation of Ayurvedic Raw Drugs and their Adulterants. Phcog Rev. 14(27).
Martin-Gutierrez, M.P., Schiff, E.R., Wright, G., Waseem, N., Mahroo, O.A., Michaelides, M., Moore, A.T., Webster, A.R., Arno, G., and Consortium, G.E.R. (2022). Dominant cone rod dystrophy, previously assigned to a missense variant in RIMS1, is fully explained by co-inheritance of a dominant allele of PROM1. Invest. Ophthalmol Vis. Sci. 63(9): 14-14.
Mian, M., Ashley, D., and Boerma, H. (1998). An additional QTL for water use efficiency in soybean. Crop Sci. 38(2): 390-393.
Mian, M., Bailey, M., Ashley, D., Wells, R., Carter Jr, T., Parrott, W., and Boerma, H. (1996). Molecular markers associated with water use efficiency and leaf ash in soybean. Crop Sci. 36(5): 1252-1257.
Miladinović, D., Vollmann, J., Molinero-Ruiz, L., and Torres, M. (2019). "advances in oil crops research—classical and new approaches to achieve sustainable productivity". Frontiers Media SA).
Mirzahashemi, M., Mohammadi-Nejad, G., and Golkar, P. (2015). A QTL linkage map of safflower for yield under drought stress at reproductive stage. Iran. j. genet. plant breed. 4(2): 20-27.
Monteros, M. (Year). "Identification and confirmation of QTL conditioning drought tolerance in Nepalese soybean", in: The 11th Biennial Conference on the Molecular and Cellular Biology of the Soybean, August 5-8, Lincoln, NE, 2006).
Negi, P., Rai, A.N., and Suprasanna, P. (2016). Moving through the stressed genome: emerging regulatory roles for transposons in plant stress response. Front. Plant Sci. 7: 1448.
Nguyen, V., Vuong, T., VanToai, T., Lee, J., Wu, X., Mian, M.R., Dorrance, A., Shannon, J., and Nguyen, H. (2012). Mapping of quantitative trait loci associated with resistance to Phytophthora sojae and flooding tolerance in soybean. Crop Sci. 52(6): 2481-2493.
O’Brown, Z.K., Boulias, K., Wang, J., Wang, S.Y., O’Brown, N.M., Hao, Z., Shibuya, H., Fady, P.-E., Shi, Y., and He, C. (2019). Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA. BMC Genom. 20: 1-15.
Pandey, M.K., Roorkiwal, M., Singh, V.K., Ramalingam, A., Kudapa, H., Thudi, M., Chitikineni, A., Rathore, A., and Varshney, R.K. (2016). Emerging genomic tools for legume breeding: current status and future prospects. Frontiers in Plant Science 7: 455.
Poodineh, M., Nezhad, N.M., Mohammadi-Nejad, G., Fakheri, B.A., and Ebrahimi, F. (2021). Identification of safflower (Carthamus tinctorius L.) QTL under drought stress and normal conditions. Ind. Crops Prod. 171: 113889.
Ragimekula, N., Varadarajula, N.N., Mallapuram, S.P., Gangimeni, G., Reddy, R.K., and Kondreddy, H.R. (2013). Marker assisted selection in disease resistance breeding. J. Plant Breed. Gen. 1(2): 90-109.
Ravi, K., Vadez, V., Isobe, S., Mir, R., Guo, Y., Nigam, S., Gowda, M., Radhakrishnan, T., Bertioli, D., and Knapp, S. (2011). Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.). Theor. Appl. Genet. 122: 1119-1132.
Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R.P., Banday, S., Mishra, A.K., and Das, G. (2023). Next-generation sequencing technology: current trends and advancements. Biology 12(7): 997.
Savadi, S., Lambani, N., Kashyap, P.L., and Bisht, D.S. (2017). Genetic engineering approaches to enhance oil content in oilseed crops. J. Plant Growth Regul. 83: 207-222.
Segelbacher, G., Bosse, M., Burger, P., Galbusera, P., Godoy, J.A., Helsen, P., Hvilsom, C., Iacolina, L., Kahric, A., and Manfrin, C. (2022). New developments in the field of genomic technologies and their relevance to conservation management. Conserv. Genet. 23(2): 217-242.
Sinha, D., Maurya, A.K., Abdi, G., Majeed, M., Agarwal, R., Mukherjee, R., Ganguly, S., Aziz, R., Bhatia, M., and Majgaonkar, A. (2023). Integrated genomic selection for accelerating breeding programs of climate-smart cereals. Genes 14(7): 1484.
Sobotka, R., Dolanska, L., Curn, V., and Ovesná, J. (2004). Fluorescence-based AFLPs occur as the most suitable marker system for oilseed rape cultivar identification. J Appl Genet. 45(2): 161-174.
Soltabayeva, A., Ongaltay, A., Omondi, J.O., and Srivastava, S. (2021). Morphological, physiological and molecular markers for salt-stressed plants. Plants 10(2): 243.
Song, X., Yang, Q., Bai, Y., Gong, K., Wu, T., Yu, T., Pei, Q., Duan, W., Huang, Z., and Wang, Z. (2021). Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants. Hortic. Res. 8.
Specht, J., Chase, K., Macrander, M., Graef, G., Chung, J., Markwell, J., Germann, M., Orf, J., and Lark, K. (2001). Soybean response to water: a QTL analysis of drought tolerance. Crop Sci. 41(2): 493-509.
Sunde, J., Yıldırım, Y., Tibblin, P., and Forsman, A. (2020). Comparing the performance of microsatellites and RADseq in population genetic studies: Analysis of data for pike (Esox lucius) and a synthesis of previous studies. Front. Genet. 11: 218.
Teixido, C., Castillo, P., Martinez-Vila, C., Arance, A., and Alos, L. (2021). Molecular markers and targets in melanoma. Cells 10(9): 2320.
VanToai, T.T., St. Martin, S.K., Chase, K., Boru, G., Schnipke, V., Schmitthenner, A.F., and Lark, K.G. (2001). Identification of a QTL associated with tolerance of soybean to soil waterlogging. Crop Sci. 41(4): 1247-1252.
Walker, F.C., Hassan, E., Peterson, S.T., Rodgers, R., Schriefer, L.A., Thompson, C.E., Li, Y., Kalugotla, G., Blum-Johnston, C., and Lawrence, D. (2021). Norovirus evolution in immunodeficient mice reveals potentiated pathogenicity via a single nucleotide change in the viral capsid. PLoS Pathog. 17(3): e1009402.
Wang, L., Xun, H., Aktar, S., Zhang, R., Wu, L., Ni, D., Wei, K., and Wang, L. (2022). Development of SNP markers for original analysis and germplasm identification in Camellia sinensis. Plants 12(1): 162.
Wenzl, P., Li, H., Carling, J., Zhou, M., Raman, H., Paul, E., Hearnden, P., Maier, C., Xia, L., and Caig, V. (2006). A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Gen 7: 1-22.
Yang, J., Benyamin, B., McEvoy, B.P., Gordon, S., Henders, A.K., Nyholt, D.R., Madden, P.A., Heath, A.C., Martin, N.G., and Montgomery, G.W. (2010). Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42(7): 565-569.
Yang, W., Liang, J., Hao, Q., Luan, X., Tan, Q., Lin, S., Zhu, H., Liu, G., Liu, Z., and Bu, S. (2021). Fine mapping of two grain chalkiness QTLs sensitive to high temperature in rice. Rice 14: 1-10.
Yu, Y., Zhi-Wei, W., Chang-Hui, F., ZHANG, Y.-X., Zhong-Xu, L., and ZHANG, X.-L. (2008). Genetic evaluation of EST-SSRs derived from Gossypium herbaceum. Acta Agron. Sin. 34(12): 2085-2091.
Zeng, X., Li, W., Wu, Y., Liu, F., Luo, J., Cao, Y., Zhu, L., Li, Y., Li, J., and You, Q. (2014). Fine mapping of a dominant thermo-sensitive genic male sterility gene (BntsMs) in rapeseed (Brassica napus) with AFLP-and Brassica rapa-derived PCR markers. Theor. Appl. Genet. 127: 1733-1740.
Zhang HaiYang, Z.H., Wei LiBin, W.L., Miao HongMei, M.H., Zhang TiDe, Z.T., and Wang CuiYing, W.C. (2012). Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genom. 13.
Zhou, H.J., Li, L., Li, Y., Li, W., and Li, J.J. (2022a). PCA outperforms popular hidden variable inference methods for molecular QTL mapping. Genome Biol. 23(1): 210.
Zhou, K., Chen, Z., Du, X., Huang, Y., Qin, J., Wen, L., Pan, X., and Lin, Y. (2022b). SMRT sequencing reveals candidate genes and pathways with medicinal value in Cipangopaludina chinensis. Frontiers in Genetics 13: 881952.
Volume 12, Issue 1
June 2024
Pages 106-119

  • Receive Date 31 October 2024
  • Revise Date 18 December 2024
  • Accept Date 22 December 2024
  • First Publish Date 22 December 2024