SNPs identify prospective genes related to response to Colletotrichum sublineola (anthracnose) in the sorghum association panel lines.
Sorghum association panel (SAP) lines were scored over several years for response to Colletotrichum sublineola, the causal agent of the disease anthracnose. Known resistant and susceptible lines were included each year to verify successful inoculation. Over 79,000 single-nucleotide polymorphic (SNP) loci from a publicly available genotype by sequencing dataset available for the SAP lines were used with TASSEL association mapping software to identify chromosomal locations associated with differences in disease response. When the top-scoring SNPs were mapped to the published sorghum genome, in each case, the nearest annotated gene has precedence for a role in host defense.
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Adeyanju A, Little C, Yu J, Tesso T (2015) Genome-wide association study on resistance to stalk rot diseases in grain sorghum. G3 Genes Genom Genet 5:1165. https://doi.org/10.1534/g3.114.016394
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) Tassel: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
Buiate EAS, Xavier KV, Moore N, Torres MF, Farman ML, Schardl CL, Vaillancourt LJ (2017) A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species colletotrichum graminicola and Colletotrichum sublineola. BMC Genom 18:67. https://doi.org/10.1186/s12864-016-3457-9
Cardwell KF (1989) Pathotypes of Colletotrichum graminicola and seed transmission of sorghum anthracnose. Plant Dis 73:255–257
Casa AM, Pressoir G, Brown PJ, Mitchell SE, Rooney WL, Tuinstra MR, Franks CD, Kresovich S (2008) Community resources and strategies for association mapping in sorghum. Crop Sci 48:30–40
Chala A, Tronsmo AM, Brurberg MB (2011) Genetic differentiation and gene flow in Colletotrichum sublineolum in Ethiopia, the centre of origin and diversity of sorghum, as revealed by AFLP analysis. Plant Pathol J 60:474–482
Cheng P, Gedling CR, Patil G, Vuong TD, Shannon JG, Dorrance AE, Nguyen HT (2017) Genetic mapping and haplotype analysis of a locus for quantitative resistance to Fusarium graminearum in soybean accession pi 567516c. Theroret Appl Genet 130:999–1010
Chopra R, Burow G, Burke JJ, Gladman N, Xin Z (2017) Genome-wide association analysis of seedling traits in diverse sorghum germplasm under thermal stress. BMC Plant Biol 17:12
Costa RV, Zambolim L, Cota LV, Silva DD, Parreira DF, Lanza FE, Souza AGC (2015) Pathotypes of Colletotrichum sublineolum in response to sorghum populations with different levels of genetic diversity in Sete Lagoas-MG. J Phytopathol 163:543–553
Cuevas HE, Prom LK, Cooper EA, Knoll JE, Ni X (2018) Genome-wide association mapping of anthracnose (Colletotrichum sublineoloum) resistance in the US sorghum association panel. Plant Genome 11:1. https://doi.org/10.3835/plantgenome2017.11.0099
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379
Guthrie PAI, Magill CW, Frederiksen RA (1992) Random amplified polymorphic DNA markers: a system for identifying and differentiating isolates of Colletotrichum graminicola. Phytopathology 82:832–835
Hammerschmidt R (1999) Induced disease resistance: how do induced plants stop pathogens? Physiol Mol Plant Pathol 55:77–84
Hwang IS, Hwang BK (2011) The pepper mannose-binding lectin Gene CaMBL1 is required to regulate cell death and defense responses to microbial pathogens. Plant Physiol 155(1):447–463
Irazoqui JE, Troemel ER, Feinbaum RL, Luhachack LG, Cezairliyan BO, Ausubel FM (2010) Distinct pathogenesis and host responses during infection of C. elegans by P. aeruginosa and S. aureus. PLoS Pathogens 6(7):e1000982. https://doi.org/10.1371/journal.ppat.1000982
Juliana P, Singh RP, Singh PK, Poland JA, Bergstrom GC, Huerta-Espino J, Bhavani S, Crossa J, Sorrells ME (2018) Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheat reveals potential candidate genes. Theor Appl Genet. https://doi.org/10.1007/s00122-018-3086-6
Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1363
Laluk K, AbuQamar S, Mengiste T (2011) The arabidopsis mitochondria-localized pentatricopeptide repeat protein PGN functions in defense against necrotrophic fungi and abiotic stress tolerance. Plant Physiol 156:2053–2068
Li W-T, Chen W-L, Yang C, Wang J, Yang L, He M, Wang J-C, Qin P, Wang Y-P, Ma B-T, Li S-G, Chen X-W (2014) Identification and network construction of zinc finger protein (ZFP) genes involved in the rice-‘Magnaporthe oryzae’ interaction [online]. Plant Omics 7:540–548
Li T, Ma X, Li N, Zhou L, Liu Z, Han H, Gui Y, Bao Y, Chen J, Dai X (2017) Genome-wide association study discovered candidate genes of verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). Plant Biotechnol J 15:1520–1532
Liao Y, Bai Q, Xu P, Wu T, Guo D, Peng Y, Zhang H, Deng X, Chen X, Luo M, Ali A, Wang W, Wu X (2018) Mutation in rice abscisic acid2 results in cell death, enhanced disease-resistance, altered seed dormancy and development. Front Plant Sci 9:405. https://doi.org/10.3389/fpls.2018.00405
Mace ES, Rami J-F, Bouchet S, Klein PE, Klein RR, Kilian A, Wenzl P, Xia L, Halloran K, Jordan DR (2009) A consensus genetic map of sorghum that integrates multiple component maps and high-throughput diversity array technology (DaRT) markers. BMC Plant Biol 9:13. https://doi.org/10.1186/1471-2229-9-13
McCormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers Brock D, McKinley B, Mattison A, Morishige Daryl T, Grimwood J, Schmutz J, Mullet JE (2018) The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. Plant J 93:338–354
Mohr PG, Cahill DM (2007) Suppression by aba of salicylic acid and lignin accumulation and the expression of multiple genes, in arabidopsis infected with Pseudomonas syringae pv. Tomato. Funct Integr Genom 7:181–191
Moore JW, Ditmore M, TeBeest DO (2008) Pathotypes of Colletotrichum sublineolum in Arkansas. Plant Dis 92:1415–1420
Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S (2013a) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci USA 110:453–458
Morris GP, Rhodes DH, Brenton Z, Ramu P, Thayil VM, Deshpande S, Hash CT, Acharya C, Mitchell SE, Buckler ES, Yu J, Kresovich S (2013b) Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits. G3 Genes Genom Genet 3:1. https://doi.org/10.1534/g3.113.008417
Nicholson RL, Kollipara SS, Vincent JR, Lyons PC, Cadena-Gomez G (1987) Phytoalexin synthesis by the sorghum mesocotyl in response to infection by pathogenic and nonpathogenic fungi. Proc Natl Acad Sci USA 84:5520–5524
Nürnberger T, Brunner F, Kemmerling B, Piater L (2004) Innate immunity in plants and animals: striking similarities and obvious differences. Immunol Rev 198:249–266
Paterson AH (2008) Genomics of sorghum. Int J Plant Genom 2008:1. https://doi.org/10.1155/2008/362451
Politis DJ (1975) The identity and perfect state of Colletotrichum graminicola. Mycologia 67:56–62
Prom LK, Perumal R, Erpelding J, Isakeit T, Montes-Garcia N, Magill CW (2009) A pictorial technique for mass screening of sorghum germplasm for anthracnose (Colletotrichum sublineolum) resistance. Open Agric J. https://doi.org/10.2174/1874331500903010020
Prom LK, Perumal R, Erattaimuthu SR, Little CR, No EG, Erpelding JE, Rooney WL, Odvody GN, Magill CW (2012) Genetic diversity and pathotype determination of Colletotrichum sublineolum isolates causing anthracnose in sorghum. Eur J Plant Pathol 133:671–685
Rhodes DH, Hoffmann L, Rooney WL, Ramu P, Morris GP, Kresovich S (2014) Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) moench] germplasm. J Agric Food Chem 62:10916–10927
Rosewich UL, Pettway RE, McDonald BA, Duncan RR, Frederiksen RA (1998) Genetic structure and emporal dynamics of a Colletotrichum graminicola population in a sorghum disease nursery. Phytopathology 88:1087–1093
Sekhwal KM, Li P, Lam I, Wang X, Cloutier S, You MF (2015) Disease resistance gene analogs (RGAs) in plants. Int J Mol Sci 16:19248–19290
Shen Y, Liu N, Li C, Wang X, Xu X, Chen W, Xing G, Zheng W (2017) The early response during the interaction of fungal phytopathogen and host plant. Open Biol 7(5):170057. https://doi.org/10.1098/rsob.170057
Sherriff C, Whelan MJ, Arnold GM, Bailey JA (1995) RDNA sequence analysis confirms the distinction between Colletotrichum graminicola and C. sublineolum. Mycol Res 99:475–478
Sutton BC (1968) The appressoria of Colletotrichum graminicola and C. falcatum. Can J Bot 46:873–876
Tesso TRP, Little CR, Adeyanju A, Radwan GL, Prom LK, Magill CW (2012) Sorghum pathology and biotechnology—a fungal disease perspective: part II. Anthracnose, stalk rot, and downy mildew. Eur J Plant Sci Biotechnol 6:33–44
Ton J, Flors V, Mauch-Mani B (2009) The multifaceted role of ABA in disease resistance. Trends Plant Sci 14:310–317
Upadhyaya HD, Wang Y, Sharma R, Sharma S (2013) Identification of genetic markers linked to anthracnose resistance in sorghum using association analysis. Theor Appl Genet 126:649–657. https://doi.org/10.1007/s00122-013-2081-1
Valèrio H, Rèsende M, Weikert-Oliveira R, Casela C (2005) Virulence and molecular diversity in Colletotrichum graminicola from Brazil. Mycopathologia 159:449–459
Vera-Estrella R, Barkla BJ, Higgins VJ, Blumwald E (1994) Plant defense response to fungal pathogens (activation of host-plasma membrane H+-atpase by elicitor-induced enzyme dephosphorylation). Plant Physiol 104:1. https://doi.org/10.1104/pp.104.1.209
Vorwerk S, Somerville S, Somerville C (2004) The role of plant cell wall polysaccharide composition in disease resistance. Trends Plant Sci 9:203–209
Woloshen V, Huang S, Li X (2011) RNA-binding proteins in plant immunity. J Pathog 2011:278697. https://doi.org/10.4061/2011/278697
Zanette GF, Nóbrega GMA, Meirelles LDP (2009) Morphogenetic characterization of Colletotrichum sublineolum strains, causal agent of anthracnose of sorghum. Trop Plant Pathol 34:146–151
Zhang D, Li J, Compton RO, Robertson J, Goff VH, Epps E, Kong W, Kim C, Paterson AH (2015) Comparative genetics of seed size traits in divergent cereal lineages represented by sorghum Panicoidae) and rice (Oryzoidae). G3 Genes Genom Genet 5:1. https://doi.org/10.1534/g3.115.017590
Zhou Y-L, Xu M-R, Zhao M-F, Xie X-W, Zhu L-H, Fu B-Y, Li Z-K (2010) Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, xanthomonas oryzae pv. Oryzicola. BMC Genom 11:1. https://doi.org/10.1186/1471-2164-11-78
Zhu X, Yin J, Liang S, Liang R, Zhou X, Chen Z (2016) The multivesicular bodies (MVBs)-localized AAA ATPase LRD6-6 inhibits immunity and cell death likely through regulating MVBs-mediated vesicular trafficking in rice. PLoS Genet 12(9):e1006311. https://doi.org/10.1371/journal.pgen.1006311
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Prom, L.K., Ahn, E., Isakeit, T. et al. GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola. Theor Appl Genet 132, 1389–1396 (2019). https://doi.org/10.1007/s00122-019-03285-5