Identification of Novel QTL Conferring Sheath Blight Resistance in Two Weedy Rice Mapping Populations

Rice - Tập 13 - Trang 1-10 - 2020
David M. Goad1, Yulin Jia2, Andrew Gibbons3,4, Yan Liu5, David Gealy2, Ana L. Caicedo6, Kenneth M. Olsen1
1Department of Biology, Washington University in St. Louis, St. Louis, USA
2United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, USA
3University of Arkansas Rice Research and Extension Center, Stuttgart, USA
4Present address: Arkansas Department of Health, Little Rock, USA
5Present address: Department of Plant Pathology, Washington State University, Pullman, USA
6Department of Biology, University of Massachusetts, Amherst, USA

Tóm tắt

Rice sheath blight (ShB) disease, caused by the pathogenic fungus Rhizoctonia solani, causes significant yield losses globally. US weedy rice populations, which are de-domesticated forms of indica and aus cultivated rice, appear to be more resistant to ShB than local japonica cultivated rice. We mapped quantitative trait loci (QTL) associated with ShB resistance using two F8 recombinant inbred line populations generated from crosses of an indica crop variety, Dee-Geo-Woo-Gen (DGWG), with individuals representing the two major US weed biotypes, straw hull (SH) and black hull awned (BHA). We identified nine ShB resistance QTL across both mapping populations. Five were attributable to alleles that affect plant height (PH) and heading date (HD), two growth traits that are known to be highly correlated with ShB resistance. By utilizing an approach that treated growth traits as covariates in the mapping model, we were able to infer that the remaining four QTL are involved in ShB resistance. Two of these, qShB1–2 and qShB4, are different from previously identified ShB QTL and represent new candidates for further study. Our findings suggest that ShB resistance can be improved through favorable plant growth traits and the combined effects of small to moderate-effect resistance QTL. Additionally, we show that including PH and HD as covariates in QTL mapping models is a powerful way to identify new ShB resistance QTL.

Tài liệu tham khảo

Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/QTL: QTL mapping in experimental crosses. Bioinformatics 19:889–890. https://doi.org/10.1093/bioinformatics/btg112 Channamallikarjuna V, Sonah H, Prasad M et al (2010) Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice. Mol Breed 25:155–166. https://doi.org/10.1007/s11032-009-9316-5 Eizenga GC, Jia MH, Pinson SR et al (2015) Exploring sheath blight quantitative trait loci in a Lemont/O. meridionalis advanced backcross population. Mol Breed 35:140. https://doi.org/10.1007/s11032-015-0332-3 Eizenga GC, Prasad B, Jackson AK, Jia MH (2013) Identification of rice sheath blight and blast quantitative trait loci in two different O. sativa/O. nivara advanced backcross populations. Mol Breed 31:889–907 Fu L, Yu X, An C (2013) Overexpression of constitutively active OsCPK10 increases Arabidopsis resistance against Pseudomonas syringae pv. Tomato and rice resistance against Magnaporthe grisea. Plant Physiol Biochem 73:202–210. https://doi.org/10.1016/j.plaphy.2013.10.004 Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324. https://doi.org/10.1038/hdy.1992.131 Han Z, Hu W, Tan C, Xing Y (2017) QTLs for heading date and plant height under multiple environments in rice. Genetica 145:67–77. https://doi.org/10.1007/s10709-016-9946-6 Hu H, Xiong L, Yang Y (2005) Rice SERK1 gene positively regulates somatic embryogenesis of cultured cell and host defense response against fungal infection. Planta 222:107–117. https://doi.org/10.1007/s00425-005-1534-4 Iwai T, Miyasaka A, Seo S, Ohashi Y (2006) Contribution of ethylene biosynthesis for resistance to blast fungus infection in young Rice plants. Plant Physiol 142:1202–1215. https://doi.org/10.1104/pp.106.085258 Jia L, Yan W, Zhu C et al (2012) Allelic analysis of sheath blight resistance with association mapping in Rice. PLoS One 7:e32703. https://doi.org/10.1371/journal.pone.0032703 Jia Y, Liu G (2011) Mapping quantitative trait loci for resistance to rice blast. Phytopathol. 101:176–187. https://doi.org/10.1094/PHYTO-06-10-0151 Lee FN, Rush MC (1983) Rice sheath blight: a major rice disease. Plant Dis 67:829–832 Li L-F, Li Y-L, Jia Y et al (2017) Signatures of adaptation in the weedy rice genome. Nat Genet 49:811–814. https://doi.org/10.1038/ng.3825 Li Z, Pinson SRM, Marchetti MA et al (1995) Characterization of quantitative trait loci (QTLs) in cultivated rice contributing to field resistance to sheath blight (Rhizoctonia solani). Theor Appl Genet 91:382–388. https://doi.org/10.1007/BF00220903 Liu G, Jia Y, Correa-Victoria FJ et al (2009) Mapping quantitative trait loci responsible for resistance to sheath blight in Rice. Phytopathology 99:1078–1084. https://doi.org/10.1094/PHYTO-99-9-1078 Liu G, Jia Y, McClung A et al (2013) Confirming QTLs and finding additional loci responsible for resistance to Rice sheath blight disease. Plant Dis 97:113–117. https://doi.org/10.1094/PDIS-05-12-0466-RE Liu Y, Qi X, Gealy DR et al (2015) QTL analysis for resistance to blast disease in U.S. weedy Rice. Mol Plant-Microbe Interact 28:834–844. https://doi.org/10.1094/MPMI-12-14-0386-R Londo JP, Schaal BA (2007) Origins and population genetics of weedy red rice in the USA. Mol Ecol 16:4523–4535. https://doi.org/10.1111/j.1365-294X.2007.03489.x Lovell J (2017) qtlTools. https://github.com/jtlovell/qtlTools Molla KA, Karmakar S, Molla J et al (2019) Understanding sheath blight resistance in rice: the road behind and the road ahead. Plant Biotechnol J Accepted Author Manuscript. https://doi.org/10.1111/pbi.13312 Nelson JC, Oard JH, Groth D et al (2012) Sheath-blight resistance QTLS in japonica rice germplasm. Euphytica 184:23–34. https://doi.org/10.1007/s10681-011-0475-1 Ono E, Wong HL, Kawasaki T et al (2001) Essential role of the small GTPase Rac in disease resistance of rice. Proc Natl Acad Sci 98:759–764. https://doi.org/10.1073/pnas.98.2.759 Qi X, Liu Y, Vigueira CC et al (2015) More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms. Mol Ecol 24:3329–3344. https://doi.org/10.1111/mec.13256 Reagon M, Thurber CS, Gross BL et al (2010) Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evol Biol 10:180. https://doi.org/10.1186/1471-2148-10-180 Reagon M, Thurber CS, Olsen KM, et al (2011) The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in US weedy rice. Mol Ecol 2011 Sep;20(18):3743–3756. doi: https://doi.org/10.1111/j.1365-294X.2011.05216.x Sasaki A, Ashikari M, Ueguchi-Tanaka M et al (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–702. https://doi.org/10.1038/416701a Savary S, Teng PS, Willocquet L, Nutter FW (2006) Quantification and modeling of crop losses: a review of purposes. Annu Rev Phytopathol 44:89–112. https://doi.org/10.1146/annurev.phyto.44.070505.143342 Taguchi-Shiobara F, Ozaki H, Sato H et al (2013) Mapping and validation of QTLs for rice sheath blight resistance. Breed Sci 63:301–308. https://doi.org/10.1270/jsbbs.63.301 Thurber CS, Jia MH, Jia Y, Caicedo AL (2013) Similar traits, different genes? Examining convergent evolution in related weedy rice populations. Mol Ecol 22:685–698. https://doi.org/10.1111/mec.12147 Thurber CS, Reagon M, Olsen KM et al. (2014) The evolution of flowering strategies in US weedy rice. Amer J Bot 101:1737–1747 Wasano K, Hirota Y (1986) Varietal resistance of rice to sheath blight disease caused by Rhizoctonia solani Kuhn, by the syringe inoculation method. Bull Fac Agr Saga Univ 60:49–59 Wedger MJ, Olsen KM (2018) Evolving insights on weedy rice. Ecol Genet Genomics 7–8:23–26. https://doi.org/10.1016/j.egg.2018.03.005 Wei X, Xu J, Guo H et al (2010) DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol pp 110(156943). https://doi.org/10.1104/pp.110.156943 Wrather JA, Sweets L (2009) Rice sheath blight control. University of Missouri Extension. https://extension2.missouri.edu/mp646 Xie X-Z, Xue Y-J, Zhou J-J et al (2011) Phytochromes regulate SA and JA signaling pathways in Rice and are required for developmentally controlled resistance to Magnaporthe grisea. Mol Plant 4:688–696. https://doi.org/10.1093/mp/ssr005 Xu Q, Yuan X, Yu H et al (2011) Mapping quantitative trait loci for sheath blight resistance in rice using double haploid population. Plant Breed 130:404–406. https://doi.org/10.1111/j.1439-0523.2010.01806.x Yamamoto E, Yonemaru J-I, Yamamoto T, Yano M (2012) OGRO: the overview of functionally characterized genes in Rice online database. Rice N Y N 5:26. https://doi.org/10.1186/1939-8433-5-26 Yano M, Katayose Y, Ashikari M et al (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in Rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2483. https://doi.org/10.1105/tpc.12.12.2473 Zeng Y, Ji Z, Yang C (2015) The way to a more precise sheath blight resistance QTL in rice. Euphytica 203:33–45. https://doi.org/10.1007/s10681-014-1246-6 Zou JH, Pan XB, Chen ZX et al (2000) Mapping quantitative trait loci controlling sheath blight resistance in two rice cultivars (Oryza sativa L.). Theor Appl Genet 101:569–573. https://doi.org/10.1007/s001220051517 Zuo S, Yin Y, Pan C et al (2013) Fine mapping of qSB-11LE, the QTL that confers partial resistance to rice sheath blight. Theor Appl Genet 126:1257–1272. https://doi.org/10.1007/s00122-013-2051-7 Zuo S, Zhang Y, Yin Y et al (2014) Fine-mapping of qSB-9TQ, a gene conferring major quantitative resistance to rice sheath blight. Mol Breed 34:2191–2203