Identification and Validation of a QTL for Bacterial Leaf Streak Resistance in Rice (Oryza sativa L.) against Thai Xoc Strains

Abstract

Rice is one of the most important food crops in the world and is of vital importance to many countries. Various diseases caused by fungi, bacteria and viruses constantly threaten rice plants and cause yield losses. Bacterial leaf streak disease (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most devastating rice diseases. However, most modern rice varieties are susceptible to BLS. In this study, we applied the QTL-seq approach using an F2 population derived from the cross between IR62266 and Homcholasit (HSC) to rapidly identify the quantitative trait loci (QTL) that confers resistance to BLS caused by a Thai Xoc isolate, SP7-5. The results showed that a single genomic region at the beginning of chromosome 5 was highly associated with resistance to BLS. The gene xa5 was considered a potential candidate gene in this region since most associated single nucleotide polymorphisms (SNPs) were within this gene. A Kompetitive Allele-Specific PCR (KASP) marker was developed based on two consecutive functional SNPs in xa5 and validated in six F2 populations inoculated with another Thai Xoc isolate, 2NY2-2. The phenotypic variance explained by this marker (PVE) ranged from 59.04% to 70.84% in the six populations. These findings indicate that xa5 is a viable candidate gene for BLS resistance and may help in breeding programs for BLS resistance.

Highly specific and super-sensitive Dot-ELISA and colloidal gold immunochromatographic strip for detecting Xanthomonas oryzae pv. oryzicola of rice bacterial leaf streak

“…BLS is a significant rice quarantine disease that poses an enormous threat to the rice industry worldwide (Thianthavon et al 2021). In recent years, the severity and spread of BLS have increased, resulting in stricter quarantine (Cao et al 2020).…”

Allele Mining and Development of Kompetitive Allele Specific PCR (KASP) Marker in Plant Breeding

“…Other studies focused on drought and low nitrogen tolerances, bacterial leaf streak resistance, cold tolerance, grain yield and yield components, salt tolerance, brown planthopper resistance, and panicle disease resistance [32,[44][45][46][47][48][49].…”

Identification of Candidate Genes for Salt Tolerance at Seedling Stage in Rice Using QTL-Seq and Chromosome Segment Substitution Line-Derived Population

“…This approach integrates NGS technologies with bulk-segregant analysis (BSA) in analyzing allelic variations between contrasting bulks [16]. QTL-seq has been widely applied in crop breeding programs, including rice, to identify QTLs for various agronomic traits, i.e., yield [17], quality [18], disease resistance [19,20], and abiotic stress tolerance [21,22]. Different types of segregating population, e.g., F 2 , F 2:3 , near-isogenic lines (NILs), and recombinant inbred lines (RILs) have been applied to identify QTLs for traits of interest using the QTL-seq approaches [23].…”