Mapping of a major quantitative trait locus for bakanae disease resistance in rice by genome resequencing
- 406 Downloads
Bakanae disease (BD) has emerged as a serious threat in almost all rice cultivation regions worldwide. Nampyeong is a Korean japonica rice variety known to be resistant to BD. In this study, quantitative trait locus (QTL) mapping was performed with F2 and F3 plants derived from a cross between the Nampyeong variety and a susceptible Korean japonica line, DongjinAD. First, resequencing of Nampyeong and DongjinAD was performed, which identified 171,035 single nucleotide polymorphisms (SNPs) between the two parental varieties. Using these SNPs, 161 cleaved amplified polymorphic sequence (CAPS) markers and six derived CAPS markers were developed; then, a genetic map was constructed from the genotypes of 180 plants from the DongjinAD/Nampyeong F2 plants. The total length of the constructed genetic map was 1386 cM, with an average interval of 8.9 cM between markers. The BD mortality rates of each F3 family were measured by testing 40 F3 progenies using in vitro seedling screening method. QTL analysis based on the genetic map and mortality rate data revealed a major QTL, qFfR1, on rice chromosome 1. qFfR1 was located at 89.8 cM with a logarithm of the odds (LOD) score of 22.7. Further, there were three markers at this point: JNS01033, JNS01037, and JNS01041. A total of 15 genes were identified with annotations related to defense against plant diseases among the 179 genes in the qFfR1 interval at 95% probability, thereby providing potential candidate genes for qFfR1. qFfR1 and its closely linked markers will be useful in breeding rice varieties resistant to BD.
KeywordsBakanae disease Resequencing Single nucleotide polymorphism Genetic map Quantitative trait locus
This research was supported by grants from the National Institute of Agricultural Sciences (NIAS), project code PJ01008902, Republic of Korea.
- Basten CJ, Weir BS, Zeng Z-B (1996) QTL cartographer: a reference manual and tutorial for QTL mapping. Department of Statistics, North Carolina State University, RaleighGoogle Scholar
- Fiyaz RA, Krishnan SG, Rajashekara H, Yadav AK, Bashyal BM, Bhowmick PK, Singh NK, Prabhu KV, Singh AK (2014) Development of high throughput screening protocol and identification of novel sources of resistance against bakanae disease in rice (Oryza sativa L.). Indian Journal of Genetics Plant Breeding 74:414–422CrossRefGoogle Scholar
- Gupta AK, Solanki IS, Bashyal BM, Singh Y, Srivastava K (2015) Bakanae of rice—an emerging disease in Asia. The Journal of Animal Plant Sciences 25:1499–1514Google Scholar
- Matic S, Gullino ML, Spadaro D (2017) The puzzle of bakanae disease through interactions between Fusarium fujikuroi and rice. Front Biosci (Elite Ed) 9:333–344Google Scholar
- Wiemann P, Sieber CM, von Bargen KW, Studt L, Niehaus EM, Espino JJ, Huss K, Michielse CB, Albermann S, Wagner D, Bergner SV, Connolly LR, Fischer A, Reuter G, Kleigrewe K, Bald T, Wingfield BD, Ophir R, Freeman S, Hippler M, Smith KM, Brown DW, Proctor RH, Munsterkotter M, Freitag M, Humpf HU, Guldener U, Tudzynski B (2013) Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog 9:e1003475CrossRefPubMedPubMedCentralGoogle Scholar
- Yang C-D, Guo L-B, Qian Q, Li X-M, Ji Z-J, Ma L-Y (2006) Analysis of QTLs for resistance to rice bakanae disease. Chin J Rice Sci 20:657–659Google Scholar