Identification of QTLs and critical genes related to sugarcane mosaic disease resistance

Authors: LU, GUILONG - Fujian Agricultural & Forestry University; WANG, ZHOUTAO - Fujian Agricultural & Forestry University; Pan, Yong-Bao; WU, QIBIN - Fujian Agricultural & Forestry University; CHENG, WEI - Fujian Agricultural & Forestry University; XU, FU - Fujian Agricultural & Forestry University; DAI, SHUMBIN - Fujian Agricultural & Forestry University; LI, BOYU - Fujian Agricultural & Forestry University; QUE, YOUXIONG - Fujian Agricultural & Forestry University; XU, LIPING - Fujian Agricultural & Forestry University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/23/2023
Publication Date: 2/2/2023
Citation: Lu, G., Wang, Z., Pan, Y.-B, Wu, Q., Cheng, W., Xu, F., Dai, S., Li, B., Que, Y., Xu, L. 2023. Identification of QTLs and critical genes related to sugarcane mosaic disease resistance. Frontiers in Plant Science. 14:1107314. https://doi.org/10.3389/fpls.2023.1107314.
DOI: https://doi.org/10.3389/fpls.2023.1107314

Interpretive Summary: If not managed, sugarcane mosaic diseases (SMD) can seriously reduce the yield and quality of sugar production. Growing resistant cultivars is the most economical and effective way to control SMD. However, it takes 12 years to produce a disease resistance variety through traditional breeding for any trait improvement. Furthermore, SMD resistance is controlled by many genes with strong environmental effects. Therefore, Identification and utilization of SMD resistance-related genetic markers can enhance the efficiency of the breeding program. The objectives of this research were: 1). to produce hundreds of offspring hybrids by crossing a SMD resistant variety Yuetang 93-159 with a highly susceptible variety ROC22; 2). to subject the offspring hybrids to both natural and artificial infections and conduct SMD surveys under multiple environments; and 3). to associate consolidated survey data with a high-quality genetic linkage map and to localize the positions of SMD responsive quantitative trait loci (QTL) markers and genes. The study identified 29 immune, 55 highly resistant, 70 moderately resistant, 62 susceptible, and 40 highly susceptible offspring hybrids. SMD resistance data from different test environments were highly significantly correlated, indicating that SMD resistance was a highly inheritable trait. Seven SMD responsive QTLs, namely, qRsm-Y12, qRsm-Y41, qRsm-Y52, qRsm-Y57, qRsm-R14, qRsm-R23, and qRsm-R92, were allocated to the genetic linkage map with each QTL accounted for 3.57% ~ 17.10% of SMD resistance. In addition, the expression levels of nine genes were significantly different between resistant and susceptible offspring hybrids. These genes may play key roles in SMD resistance. The seven QTLs and nine genes can serve as a good scientific reference in helping sugarcane breeders develop varieties resistant to mosaic diseases.

Technical Abstract: Mosaic viral diseases affect sugarcane productivity worldwide. Mining disease resistance-associated molecular markers or genes is a key component of disease resistance breeding programs. In the present study, 256 F1 progenies were produced from a cross between Yuetang 93-159, a moderately resistant variety, and ROC22, a highly susceptible variety. Mosaic disease symptoms of these progenies and the two parents were surveyed three times, either under natural infection in 11 different environments or after three artificial infections with mixed sugarcane mosaic virus (SCMV) and sorghum mosaic virus (SrMV) inoculum. Analysis of consolidated survey data enabled the identification of 29 immune, 55 highly resistant, 70 moderately resistant, 62 susceptible, and 40 highly susceptible progenies. The disease response data and a high-quality SNP genetic map were used in quantitative trait locus (QTL) mapping. The results showed that the correlation coefficients (0.26~0.91) between mosaic disease resistance and test environments were significant (p < 0.001) and that mosaic disease resistance was a highly heritable quantitative trait (H2 = 0.85). Seven mosaic resistance QTLs were located to the SNP genetic map, each QTL accounted for 3.57% ~ 17.10% of the phenotypic variation explained (PVE). Furthermore, 110 pathogen response genes and 69 transcription factors were identified in the QTLs interval. The expression levels of nine genes (Soffic.07G0015370-1P, Soffic.09G0015410-2T, Soffic.09G0016460-1T, Soffic.09G0016460-1P, Soffic.09G0017080-3C, Soffic.09G0018730-3P, Soffic.09G0018730-3C, Soffic.09G0019920-3C, and Soffic.03G0019710-2C) were significantly different between resistant and susceptible progenies, indicating their key roles in sugarcane resistance to SCMV and SrMV infection. The seven QTLs and nine genes can provide a certain scientific reference to help sugarcane breeders develop varieties resistant to mosaic diseases.