Login Register Cart 0
Generic placeholder image

Current Genomics

Editor-in-Chief

ISSN (Print): 1389-2029
ISSN (Online): 1875-5488

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance

Author(s): Milind Balkrishna Ratnaparkhe*, Niharika Marmat, Giriraj Kumawat, Maranna Shivakumar, Viraj Gangadhar Kamble, Vennampally Nataraj, Shunmugiah Veluchamy Ramesh, Milind Panjabrao Deshmukh, Ajay Kumar Singh, Humira Sonah, Rupesh Kailasrao Deshmukh, Manoj Prasad, Suresh Chand and Sanjay Gupta

Volume 21, Issue 7, 2020

Page: [504 - 511] Pages: 8

DOI: 10.2174/1389202921999200601142258

Price: $65

Abstract

Background: In this study, whole genome re-sequencing of rust resistant soybean genotype EC241780 was performed to understand the genomic landscape involved in the resistance mechanism.

Methods: A total of 374 million raw reads were obtained with paired-end sequencing performed with Illumina HiSeq 2500 instrument, out of which 287.3 million high quality reads were mapped to Williams 82 reference genome. Comparative sequence analysis of EC241780 with rust susceptible cultivars Williams 82 and JS 335 was performed to identify sequence variation and to prioritise the candidate genes.

Results: Comparative analysis indicates that genotype EC241780 has high sequence similarity with rust resistant genotype PI 200492 and the resistance in EC241780 is conferred by the Rpp1 locus. Based on the sequence variations and functional annotations, three genes Glyma18G51715, Glyma18G51741 and Glyma18G51765 encoding for NBS-LRR family protein were identified as the most prominent candidate for Rpp1 locus.

Conclusion: The study provides insights of genome-wide sequence variation more particularly at Rpp1 loci which will help to develop rust resistant soybean cultivars through efficient exploration of the genomic resource.

Keywords: Soybean, whole genome re-sequencing, disease resistance, rust, Phakopsora pachyrhizi, single nucleotide polymorphisms (SNPs).

« Previous Next »
Graphical Abstract

[1]
Kochman, J.K. Soybean rust in Australia. Rust of soybean-the problem and research needs; Ford, R.E.; Sinclair, J.B., Eds.; International Agricultural Publications: Manila, 1977, pp. 44-48..
[2]
Schneider, R.W.; Hollier, C.A.; Whitam, H.K.; Palm, M.E.; McKemy, J.M.; Hernández, J.R.; Levy, L.; DeVries-Paterson, R. First report of soybean rust caused by Phakopsora pachyrhizi in the continental United States. Plant Dis., 2005, 89(7), 774.
[http://dx.doi.org/10.1094/PD-89-0774A] [PMID: 30791253]
[3]
Yorinori, J.T.; Paiva, W.M.; Frederick, R.D.; Costamilan, L.M.; Bertagnolli, P.F.; Hartman, G.E.; Godoy, C.V.; Nunes, J., Jr Epidemics of soybean rust (Phakopsora pachyrhizi) in Brazil and Paraguay from 2001 to 2003. Plant Dis., 2005, 89(6), 675-677.
[http://dx.doi.org/10.1094/PD-89-0675] [PMID: 30795398]
[4]
Ivancovich, A. Soybean Rust in Argentina.Facing the Challenge of Soybean Rust in South America;; Kudo, H.; Suenaga, K.; Soares, RM.; Toledo, A., Eds.; Japan International Research Centre for Agricultural Science (JIRCAS): Tsukuba, Ibaraki, Japan, 2008, pp. 14-17.
[5]
Burdon, J.J.; Marshall, D.R. Evaluation of Australian native species of Glycine for resistance to soybean rust. Plant Dis., 1981, 65, 44-45.
[http://dx.doi.org/10.1094/PD-65-44]
[6]
Burdon, J.J. Major gene resistance to Phakopsora pachyrhizi in Glycine canescens, a wild relative of soybean. Theor. Appl. Genet., 1988, 75, 923-928.
[http://dx.doi.org/10.1007/BF00258055]
[7]
McDowell, J.M.; Simon, S.A. Recent insights into R gene evolution. Mol. Plant Pathol., 2006, 7(5), 437-448.
[http://dx.doi.org/10.1111/j.1364-3703.2006.00342.x] [PMID: 20507459]
[8]
Hyten, D.L.; Smith, J.R.; Frederick, R.D.; Tuker, M.L.; Song, Q.; Cregan, P.B. Bulk segregate analysis using the Golden Gate assay to locate the Rpp3 locus that confers resistance to Phakopsora pachyrhizi (soybean rust) in soybean. Crop Sci., 2009, 49, 265-271.
[http://dx.doi.org/10.2135/cropsci2008.08.0511]
[9]
Ray, J.D.; Morel, W.; Smith, J.R.; Frederick, R.D.; Miles, M.R. Genetics and mapping of adult plant rust resistance in soybean PI 587886 and PI 587880A. Theor. Appl. Genet., 2009, 119(2), 271-280.
[http://dx.doi.org/10.1007/s00122-009-1036-z] [PMID: 19396573]
[10]
Kendrick, M.D.; Harris, D.K.; Ha, B.K.; Hyten, D.L.; Cregan, P.B.; Frederick, R.D.; Boerma, H.R.; Pedley, K.F. Identification of a second Asian soybean rust resistance gene in Hyuuga soybean. Phytopathology, 2011, 101(5), 535-543.
[http://dx.doi.org/10.1094/PHYTO-09-10-0257] [PMID: 21244223]
[11]
Li, S.; Smith, J.R.; Ray, J.D.; Frederick, R.D. Identification of a new soybean rust resistance gene in PI 567102B. Theor. Appl. Genet., 2012, 125(1), 133-142.
[http://dx.doi.org/10.1007/s00122-012-1821-y] [PMID: 22374138]
[12]
Childs, S.P.; King, Z.R.; Walker, D.R.; Harris, D.K.; Pedley, K.F.; Buck, J.W.; Boerma, H.R.; Li, Z. Discovery of a seventh Rpp soybean rust resistance locus in soybean accession PI 605823. Theor. Appl. Genet., 2018, 131(1), 27-41.
[http://dx.doi.org/10.1007/s00122-017-2983-4] [PMID: 28980046]
[13]
Garcia, A.; Calvo, E.S.; de Souza Kiihl, R.A.; Harada, A.; Hiromoto, D.M.; Vieira, L.G.E. Molecular mapping of soybean rust (Phakopsora pachyrhizi) resistance genes: discovery of a novel locus and alleles. Theor. Appl. Genet., 2008, 117(4), 545-553.
[http://dx.doi.org/10.1007/s00122-008-0798-z] [PMID: 18506417]
[14]
Monteros, M.J.; Missaoui, A.M.; Phillips, D.V.; Walker, D.R.; Boerma, H.R. Mapping and confirmation of the ‘Hyuuga’ red-brown lesion resistance gene for Asian soybean rust. Crop Sci., 2007, 47, 829-836.
[http://dx.doi.org/10.2135/cropsci06.07.0462]
[15]
Chakraborty, N.; Curley, J.; Frederick, R.D.; Hyten, D.L.; Nelson, R.L.; Hartman, G.L.; Diers, B.W. Mapping and confirmation of a new allele at Rpp1 from soybean PI 594538A conferring RB lesion type resistance to soybean rust. Crop Sci., 2009, 49(3), 783-790.
[http://dx.doi.org/10.2135/cropsci2008.06.0335]
[16]
Hossain, M.M.; Akamatsu, H.; Morishita, M.; Mori, T.; Yamaoka, Y.; Suenaga, K.; Soares, R.M.; Bogado, A.N.; Ivancovich, A.J.G.; Yamanaka, N. Molecular mapping of Asian soybean rust resistance in soybean landraces PI 594767A, PI 587905 and PI 416764. Plant Pathol., 2015, 64, 147-156.
[http://dx.doi.org/10.1111/ppa.12226]
[17]
Dong, W.; Wu, D.; Li, G.; Wu, D.; Wang, Z. Next-generation sequencing from bulked segregant analysis identifies a dwarfism gene in watermelon. Sci. Rep., 2018, 8(1), 2908.
[http://dx.doi.org/10.1038/s41598-018-21293-1] [PMID: 29440685]
[18]
Sun, Q.; Qiao, J.; Zhang, S.; He, S.; Shi, Y.; Yuan, Y.; Zhang, X.; Cai, Y. Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development. PeerJ, 2018, 6(10) e4945.
[http://dx.doi.org/10.7717/peerj.4945] [PMID: 29915693]
[19]
Yadav, C.B.; Bhareti, P.; Muthamilarasan, M.; Mukherjee, M.; Khan, Y.; Rathi, P.; Prasad, M. Genome-Wide SNP identification and characterization in two soybean cultivars with contrasting mungbean yellow mosaic India virus disease resistance traits. PLoS One, 2015, 10(4) 0123897.
[http://dx.doi.org/10.1371/journal.pone.0123897]
[20]
Ensembl Plants.. http://plants.ensembl.org
[21]
Sourcefourge.net.. http://bio-bwa.sourcefourge.net
[22]
Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009, 25(14), 1754-1760.
[http://dx.doi.org/10.1093/bioinformatics/btp324] [PMID: 19451168]
[23]
Babraham Bioinformatics.. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
[24]
Babraham Bioinformatics.. https://sourceforge.net/projects/samtools/files/samtools/
[25]
Song, Q.; Hyten, D.L.; Jia, G.; Quigley, C.V.; Fickus, E.W.; Nelson, R.L.; Cregan, P.B. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS One, 2013, 8(1) e54985.
[http://dx.doi.org/10.1371/journal.pone.0054985] [PMID: 23372807]
[26]
Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol., 2016, 33(7), 1870-1874.
[http://dx.doi.org/10.1093/molbev/msw054] [PMID: 27004904]
[27]
Hyten, D.L.; Hartman, G.L.; Nelson, R.L.; Frederick, R.D.; Concibido, V.C.; Narvel, J.M.; Cregan, P.B. Map location of the Rpp1 locus that confers resistance to soybean rust in soybean. Crop Sci., 2007, 47, 837-840.
[http://dx.doi.org/10.2135/cropsci2006.07.0484]
[28]
Kim, K.S.; Unfried, J.R.; Hyten, D.L.; Frederick, R.D.; Hartman, G.L.; Nelson, R.L.; Song, Q.; Diers, B.W. Molecular mapping of soybean rust resistance in soybean accession PI 561356 and SNP haplotype analysis of the Rpp1 region in diverse germplasm. Theor. Appl. Genet., 2012, 125(6), 1339-1352.
[http://dx.doi.org/10.1007/s00122-012-1932-5] [PMID: 22837016]
[29]
Thudi, M.; Khan, A.W.; Kumar, V.; Gaur, P.M.; Katta, K.; Garg, V.; Roorkiwal, M.; Samineni, S.; Varshney, R.K. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biol., 2016, 16(Suppl. 1), 10.
[http://dx.doi.org/10.1186/s12870-015-0690-3] [PMID: 26822060]
[30]
Zhou, Z.; Jiang, Y.; Wang, Z.; Gou, Z.; Lyu, J.; Li, W.; Yu, Y.; Shu, L.; Zhao, Y.; Ma, Y.; Fang, C.; Shen, Y.; Liu, T.; Li, C.; Li, Q.; Wu, M.; Wang, M.; Wu, Y.; Dong, Y.; Wan, W.; Wang, X.; Ding, Z.; Gao, Y.; Xiang, H.; Zhu, B.; Lee, S.H.; Wang, W.; Tian, Z. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol., 2015, 33(4), 408-414.
[http://dx.doi.org/10.1038/nbt.3096] [PMID: 25643055]
[31]
Lam, H.M.; Xu, X.; Liu, X.; Chen, W.; Yang, G.; Wong, F.L.; Li, M.W.; He, W.; Qin, N.; Wang, B.; Li, J.; Jian, M.; Wang, J.; Shao, G.; Wang, J.; Sun, S.S.; Zhang, G. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet., 2010, 42(12), 1053-1059.
[http://dx.doi.org/10.1038/ng.715] [PMID: 21076406]
[32]
Valliyodan, B.; Dan, Qiu. Patil, G.; Zeng, P.; Huang, J.; Dai, L.; Chen, C.; Li, Y.; Joshi, T.; Song, L.; Vuong, T.D.; Musket, T.A.; Xu, D.; Shannon, J.G.; Shifeng, C.; Liu, X.; Nguyen, H.T. Landscape of genomic diversity and trait discovery in soybean. Sci. Rep., 2016, 6, 23598.
[http://dx.doi.org/10.1038/srep23598] [PMID: 27029319]
[33]
Hartwig, E.E.; Bromfield, K.R. Relationship among three genes conferring specific resistance to rust in soybeans. Crop Sci., 1983, 23, 237-239.
[http://dx.doi.org/10.2135/cropsci1983.0011183X002300020012x]
[34]
Bhor, T.J.; Chimote, V.P.; Deshmukh, M.P. Molecular tagging of asiatic soybean rust resistance in exotic genotype EC241780 reveals complementation of two genes. Plant Breed., 2015, 134(1), 70-77.
[http://dx.doi.org/10.1111/pbr.12240]
[35]
Kang, Y.J.; Kim, K.H.; Shim, S.; Yoon, M.Y.; Sun, S.; Kim, M.Y.; Van, K.; Lee, S.H. Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol., 2012, 12(1), 139.
[http://dx.doi.org/10.1186/1471-2229-12-139] [PMID: 22877146]
[36]
Innes, R.W.; Ameline-Torregrosa, C.; Ashfield, T.; Cannon, E.; Cannon, S.B.; Chacko, B.; Chen, N.W.; Couloux, A.; Dalwani, A.; Denny, R.; Deshpande, S.; Egan, A.N.; Glover, N.; Hans, C.S.; Howell, S.; Ilut, D.; Jackson, S.; Lai, H.; Mammadov, J.; Del Campo, S.M.; Metcalf, M.; Nguyen, A.; O’Bleness, M.; Pfeil, B.E.; Podicheti, R.; Ratnaparkhe, M.B.; Samain, S.; Sanders, I.; Ségurens, B.; Sévignac, M.; Sherman-Broyles, S.; Thareau, V.; Tucker, D.M.; Walling, J.; Wawrzynski, A.; Yi, J.; Doyle, J.J.; Geffroy, V.; Roe, B.A.; Maroof, M.A.; Young, N.D. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol., 2008, 148(4), 1740-1759.
[http://dx.doi.org/10.1104/pp.108.127902] [PMID: 18842825]
[37]
Ratnaparkhe, M.B.; Wang, X.; Li, J.; Compton, R.O.; Rainville, L.K.; Lemke, C.; Kim, C.; Tang, H.; Paterson, A.H. Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny. New Phytol., 2011, 192(1), 164-178.
[http://dx.doi.org/10.1111/j.1469-8137.2011.03800.x] [PMID: 21707619]
[38]
Van de Weyer, A.L.; Monteiro, F.; Furzer, O.J.; Nishimura, M.T.; Cevik, V.; Witek, K.; Jones, J.D.G.; Dangl, J.L.; Weigel, D.; Bemm, F. A species-wide inventory of NLR genes and alleles in Arabidopsis thaliana. Cell, 2019, 178(5), 1260-1272.
[http://dx.doi.org/10.1016/j.cell.2019.07.038] [PMID: 31442410]
[39]
Mondragón-Palomino, M.; Meyers, B.C.; Michelmore, R.W.; Gaut, B.S. Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res., 2002, 12(9), 1305-1315.
[http://dx.doi.org/10.1101/gr.159402] [PMID: 12213767]
[40]
Pedley, K.F.; Pandey, A.K.; Ruck, A.; Lincoln, L.M.; Whitham, S.A.; Graham, M.A. Rpp1 encodes a ULP1-NBS-LRR protein that controls immunity to Phakopsora pachyrhizi in soybean. Mol. Plant Microbe Interact., 2019, 32(1), 120-133.
[http://dx.doi.org/10.1094/MPMI-07-18-0198-FI] [PMID: 30303765]
[41]
Vuong, T.D.; Walker, D.R.; Nguyen, B.T.; Nguyen, T.T.; Dinh, H.X.; Hyten, D.L.; Cregan, P.B.; Sleper, D.A.; Lee, J.D.; Shannon, J.G.; Nguyen, H.T. Molecular characterization of resistance to soybean rust (Phakopsora pachyrhizi Syd.) in soybean cultivar DT 2000 (PI 635999). PLoS One, 2016, 11(12) e0164493.

Rights & Permissions Print Cite
Article Metrics
30
© 2024 Bentham Science Publishers | Privacy Policy