0
Views
0
CrossRef citations to date
0
Altmetric
Soil & Crop Sciences

Validation of SNP markers associated with late leaf spot resistance in groundnut

, ORCID Icon, , , , & show all
Article: 2367067 | Received 23 Mar 2024, Accepted 06 Jun 2024, Published online: 17 Jun 2024

References

  • Agarwal, G., Clevenger, J., Pandey, M. K., Wang, H., Shasidhar, Y., Chu, Y., Fountain, J. C., Choudhary, D., Culbreath, A. K., Liu, X., Huang, G., Wang, X., Deshmukh, R., Holbrook, C. C., Bertioli, D. J., Ozias-Akins, P., Jackson, S. A., Varshney, R. K., & Guo, B. (2018). High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnology Journal, 16(11), 1–9. https://doi.org/10.1111/pbi.12930
  • Banla, E. M. (2018). Characterization of cultivated groundnut (Arachis hypogea L.) and genetic analysis of late leaf spot resistance in Togo [PhD thesis]. University of Ghana, Legon.
  • Bertioli, D. J., Cannon, S. B., Froenicke, L., Huang, G., Farmer, A. D., Cannon, E. K. S., Liu, X., Gao, D., Clevenger, J., Dash, S., Ren, L., Moretzsohn, M. C., Shirasawa, K., Huang, W., Vidigal, B., Abernathy, B., Chu, Y., Niederhuth, C. E., Umale, P., … Ozias-Akins, P. (2016). The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanuts. Nature Genetics, 48(4), 438–446. https://doi.org/10.1038/ng.3517
  • Bertioli, D. J., Clevenger, J., Godoy, I. J., Stalker, H. T., Wood, S., Santos, J. F., Ballén-Taborda, C., Abernathy, B., Azevedo, V., Campbell, J., Chavarro, C., Chu, Y., Farmer, A. D., Fonceka, D., Gao, D., Grimwood, J., Halpin, N., Korani, W., Michelotto, M. D., … Leal-Bertioli, S. C. M. (2021). Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange. Proceedings of the National Academy of Sciences of the United States of America, 118(38), e2104899118. https://doi.org/10.1073/pnas.2104899118
  • CGIAR-Excellence in Breeding Platform (EBP). (2021). Low & mid-density genotyping services. https://excellenceinbreeding.org/module3/kasp
  • Chandra, B., Viswavidyalaya, K., & Bengal, W. (2005). Management of leafspot (Cercospora arachidicola and Phaeoisariopsis personata). 75, 3–4.
  • Clevenger, J., Chu, Y., Chavarro, C., Agarwal, G., Bertioli, D. J., Leal-Bertioli, S. C. M., Pandey, M. K., Vaughn, J., Abernathy, B., Barkley, N. A., Hovav, R., Burow, M., Nayak, S. N., Chitikineni, A., Isleib, T. G., Holbrook, C. C., Jackson, S. A., Varshney, R. K., & Ozias-Akins, P. (2017). Genome-wide SNP Genotyping resolves signatures of selection and tetrasomic recombination in peanut. Molecular Plant, 10(2), 309–322. https://doi.org/10.1016/j.molp.2016.11.015
  • Clevenger, J., Chu, Y., Chavarro, C., Botton, S., Culbreath, A., Isleib, T. G., Holbrook, C. C., & Ozias-Akins, P. (2018). Mapping late leaf spot resistance in peanut (Arachis hypogaea) using QTL-seq reveals markers for marker-assisted selection. Frontiers in Plant Science, 9, 83. https://doi.org/10.3389/fpls.2018.00083
  • Divyadharsini, R., Prabhu, R., Manivannan, N., & Vindhivavarman, P. (2017). Validation of SSR markers for foliar disease resistance in groundnut (Arachis hypogaea L.). International Journal of Current Microbiology and Applied Sciences, 6(4), 1310–1317. https://doi.org/10.20546/ijcmas.2017.604.160
  • Dwivedi, S. L., Pande, S., Rao, J. N., & Nigam, S. N. (2002). Components of resistance to late leaf spot and rust among interspecific derivatives and their significance in a foliar disease resistance breeding in groundnut (Arachis hypogaea L.). Euphytica, 125(1), 81–88. https://doi.org/10.1023/A:1015707301659
  • Gajjar, K. N., Mishra, G. P., Radhakrishnan, T., Dodia, S. M., Rathnakumar, A. L., Kumar, N., Kumar, S., & Kumar, A. (2014). Validation of SSR markers linked to the rust and late leaf spot diseases resistance in diverse peanut genotypes. Australian Journal of Crop Science, 8(6), 927–936.
  • Guo, B., Pandey, M. K., He, G., Zhang, X., Liao, B., Culbreath, A., Varshney, R. K., Nwosu, V., Wilson, R. F., & Stalker, H. T. (2013). Recent advances in molecular genetic linkage maps of cultivated peanut. Peanut Science, 40(2), 95–106. https://doi.org/10.3146/PS13-03.1
  • Ibrahim, Y. J. (2010). Screening of groundnuts (Arachis hypogaea L.) for resistance to early and late leaf spot [MSc. thesis]. Kwame Nkrumah University of Science and Technology.
  • International Rice Research Institute (IRRI). (2020). Plant breeding tools (PBTools) Version: 1.3. http://bbi.irri.org
  • Jadhav, Mangesh Pralhad, Patil, Malagouda D., Hampannavar, Mahesh, Dattatreya, Pavana, Shirasawa, Kenta, Pasupuleti, Janila, Pandey, Manish K., Varshney, Rajeev K., Bhat, Ramesh S., Venkatesh, (2021). Enhancing oleic acid content in two commercially released peanut varieties through marker-assisted backcross breeding. Crop Science, 61(4): 2435–2443. https://doi.org/10.1002/csc2.20512
  • Kelly, J. D., Gepts, P., Miklas, P. N., & Coyne, D. P. (2003). Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crops Research, 82(2-3), 135–154. https://doi.org/10.1016/S0378-4290(03)00034-0
  • Khan, A. R., Ijaz, M., Haq, I. U., Farzand, A., & Tariqjaved, M. (2014). Management of Cercospora leaf spot of groundnut (Cercospora arachidicola & use of systemic fungicides. Cercetari Agronimice in Moldova, XLVII(2), 98–102.
  • Khedikar, Y. P., Gowda, M. V. C., Sarvamangala, C., Patgar, K. V., Upadhyaya, H. D., & Varshney, R. K. (2010). A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.). Theoretical and Applied Genetics, 121(5), 971–984. https://doi.org/10.1007/s00122-010-1366-x
  • Knapp, S. J., Ozias-Akins, P., Hoisington, D., Aruna, R., & Varshney, R. (2011). G4008.06: Single nucleotide polymorphism discovery, validation, and mapping in groundnut. Project updates. CGIAR Generation Challenge Program.
  • Kolekar, R. M., Sujay, V., Shirasawa, K., Sukruth, M., Khedikar, Y. P., Gowda, M. V. C., Pandey, M. K., Varshney, R. K., & Bhat, R. S. (2016). QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.). Euphytica, 209(1), 147–156. https://doi.org/10.1007/s10681-016-1651-0
  • Kukanur, S., Savithramma, D. L., Duddagi, S., Vijayabharathi, A., Mallikarjuna, B. P., & Pushpa, H. D. (2014). Validation of SSR markers linked to late leaf spot and rust in Groundnut (Arachis hypogaea L.). Ecology, Environment and Conservation, 20(1), 357–361.
  • Leal-Bertioli, S. C. M., José, A. C. V. F., Alves-Freitas, D. M. T., Moretzsohn, M. C., Guimarães, P. M., Nielen, S., Vidigal, B. S., Pereira, R. W., Pike, J., Fávero, A. P., Parniske, M., Varshney, R. K., & Bertioli, D. J. (2009). Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biology, 9(1), 112. https://doi.org/10.1186/1471-2229-9-112
  • Liang, Y., Baring, M., Wang, S., & Septiningsih, E. M. (2017). Mapping QTLs for leafspot resistance in peanut using SNP-based next-generation sequencing markers. Plant Breeding and Biotechnology, 5(2), 115–122. https://doi.org/10.9787/PBB.2017.5.2.115
  • Mace, E. S., Phong, D. T., Upadhyaya, H. D., Chandra, S., & Crouch, J. H. (2006). SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases. Euphytica, 152(3), 317–330. https://doi.org/10.1007/s10681-006-9218-0
  • Mammadov, J., Aggarwal, R., Buyyarapu, R., & Kumpatla, S. (2012). SNP markers and their impact on plant breeding. International Journal of Plant Genomics, 2012, 728398. https://doi.org/10.1155/2012/728398
  • Mishra, G. P., Radhakrishnan, T., Kumar, A., Thirumalaisamy, P. P., Kumar, N., Bosamia, T. C., Nawade, B., & Dobaria, J. R. (2015). Advancements in molecular marker development and their applications in the management of biotic stresses in peanuts. Crop Protection, 77, 74–86. https://doi.org/10.1016/j.cropro.2015.07.019
  • MoFA. (2019). Catalogue of crop varieties released and registered in Ghana. Ministry of Food and Agriculture.
  • Mohammed, K., Afutu, E., Odong, T., Okello, D., Nuwamanya, E., Grigon, O., Rubaihayo, P., & Okori, P. (2018). Assessment of groundnut (Arachis hypogaea L.) genotypes for yield and resistance to late leaf spot and rosette diseases. Journal of Experimental Agriculture International, 21(5), 1–13. https://doi.org/10.9734/JEAI/2018/39912
  • Morgil, H., Gercek, Y. C., & Tulum, I. (2020). Single nucleotide polymorphisms (SNPs) in plant genetics and breeding. In M. Çalışkan, O. Erol, & G. C. Öz (Eds.), The recent topics in genetic polymorphisms. IntechOpen. https://doi.org/10.5772/intechopen.91886
  • Muhammad, A., & Bdliya, B. (2011). Effects of variety and fungicidal rate on Cercospora leaf spot disease of groundnut in the Sudan Savanna. Nigerian Journal of Basic and Applied Sciences, 19(1), 135–141. https://doi.org/10.4314/njbas.v19i1.69359
  • Nevill, D. J. (1981). Components of resistance to Cercospora arachidicola and Cercosporidium personatum in groundnuts (Arachis hypogaea). Annals of Applied Biology, 99, 77–86.
  • Oteng-Frimpong, R., Karikari, B., Sie, E. K., Kassim, Y. B., Puozaa, D. K., Rasheed, M. A., Fonceka, D., Okello, D. K., Balota, M., Burow, M., & Ozias-Akins, P. (2022). Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm. Frontiers in Plant Science, 13, 1076744. PMID: 36684745; PMCID: PMC9849250. https://doi.org/10.3389/fpls.2022.1076744
  • Pandey, M. K., Khan, A. W., Singh, V. K., Vishwakarma, M. K., Shasidhar, Y., Kumar, V., Garg, V., Bhat, R. S., Chitikineni, A., Janila, P., Guo, B., & Varshney, R. K. (2017). QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnology Journal, 15(8), 927–941. https://doi.org/10.1111/pbi.12686
  • Peanut Genome Initiative, PGI. (2017). 2012–2017 Accomplishment report to the U.S. Peanut Industry. October, 2017.
  • Shaibu, S. A., Sneller, C., Motagi, B. N., Chepkoech, J., Chepngetich, M., Miko, Z. L., Isa, A. M., Ajeigbe, H. A., & Mohammed, S. G. (2020). Genome-wide detection of SNP markers associated with four physiological traits in groundnut (Arachis hypogaea L.) mini core collection. Agronomy, 10(2), 192. https://doi.org/10.3390/agronomy100201
  • Shapiro, S. S., & Wilk, M. B. (1965). An analysis of variance test for normality (complete samples). Biometrika, 52(3-4), 591–611. https://doi.org/10.2307/2333709
  • Shirasawa, K., Bhat, R. S., Khedikar, Y. P., Sujay, V., Kolekar, R. M., Yeri, S. B., Sukruth, M., Cholin, S., Asha, B., Pandey, M., Varshney, R. K., & Gowda, M. V. C. (2018). Sequencing analysis of genetic loci for resistance for late leaf spot and rust in peanut (Arachis hypogaea L. (2018). Frontiers in Plant Science, 9, 1727. https://doi.org/10.3389/fpls.2018.01727
  • Shirasawa, K., Kuwata, C., Watanabe, M., Fukami, M., Hirakawa, H., & Isobe, S. (2016). Target amplicon sequencing for genotyping genome-wide single nucleotide polymorphisms identified by whole-genome resequencing in peanut. The Plant Genome, 9(3), plantgenome2016.06.0052. https://doi.org/10.3835/plantgenome2016.06.0052
  • Shoba, D., Manivannan, N., Vindhiyavarman, P., & Nigam, S. N. (2012). SSR markers associated for late leaf spot disease resistance by bulked segregant analysis in groundnut (Arachis hypogaea L.). Euphytica, 188(2), 265–272. https://doi.org/10.1007/s10681-012-0718-9
  • Stalker, H. T. (2017). Utilizing wild species for peanut improvement. Crop Science, 57(3), 1102–1120. https://doi.org/10.2135/cropsci2016.09.0824
  • Stalker, H. T., Tallury, S. P., Ozias-Akins, P., Bertioli, D. J., & Bertioli, S. C. L. (2013). The Value of diploid peanut relatives for breeding and genomics. Peanut Science, 40(2), 70–88. https://doi.org/10.3146/PS13-6.1
  • Subrahmanyam, P., McDonald, D., Waliyar, F., Reddy, L. J., Nigam, S. N., Gibbons, R. W., Ramanatha, R. V., Singh, A. K., Pande, S., Reddy, P. M., & Subba, R. (1995). Groundnut diseases. Information bulletin no. 47 ICRISAT
  • Sujay, V., Gowda, M. V., Pandey, M. K., Bhat, R. S., Khedikar, Y. P., Nadaf, H. L., Gautami, B., Sarvamangala, C., Lingaraju, S., Radhakrishan, T., Knapp, S. J., & Varshney, R. K. (2012). Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Molecular Breeding: new Strategies in Plant Improvement, 30(2), 773–788. https://doi.org/10.1007/s11032-011-9661-z
  • Sukruth, M., Paratwagh, S. A., Sujay, V., Kumari, V., Gowda, M. V. C., Nadaf, H. L., Motagi, B. N., Lingaraju, S., Pandey, M. K., Varshney, R. K., & Bhat, R. S. (2015). Validation of markers linked to late leaf spot and rust resistance, and selection of superior genotypes among diverse recombinant inbred lines and backcross lines in peanut (Arachis hypogaea L.). Euphytica, 204(2), 343–351. https://doi.org/10.1007/s10681-014-1339-2
  • Zhang, H., Chu, Y., Dang, P., Tang, Y., Jiang, T., Clevenger, J. P., Ozias-Akins, P., Holbrook, C., Wang, M. L., Campbell, H., Hagan, A., & Chen, C. (2020). Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 133(7), 2051–2061. https://doi.org/10.1007/s00122-020-03576-2
  • Zhou, X., Xia, Y., Ren, X., Chen, Y., Huang, L., Huang, S., Liao, B., Lei, Y., Yan, L., & Jiang, H. (2014). Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics, 15(1), 351. https://doi.org/10.1186/1471-2164-15-351
  • Zhou, X., Xia, Y., Liao, J., Liu, K., Li, Q., Dong, Y., Ren, X., Chen, Y., Huang, L., Liao, B., Lei, Y., Yan, L., & Jiang, H. (2016). Quantitative trait locus analysis of late leaf spot resistance and plant-type-related traits in cultivated peanut (Arachis hypogaea L.) under multi-environments. PloS One, 11(11), e0166873. https://doi.org/10.1371/journal.pone.0166873
  • Zongo, A., Khera, P., Sawadogo, M., Shasidhar, Y., Sriswathi, M., Vishwakarma, M. K., Sankara, P., Ntare, B. R., Varshney, R. K., Pandey, M. K., & Desmae, H. (2017). SSR markers associated with early leaf spot disease resistance through selective genotyping and single marker analysis in groundnut (Arachis hypogaea L.). Biotechnology Reports, 15, 132–137. https://doi.org/10.1016/j.btre.2017.07.005