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

Tripop Thianthavon,Vinitchan Ruanjaichon,Wanchana Aesomnuk,Kanamon Riangwong,Yupin Sonsom,Phakchana Nubankoh,Wannapa Sattayachiti,Siwaret Arikit,Samart Wanchana,Theerayut Toojinda,Srihunsa Malichan,Mutiara K Pitaloka

doi:10.3390/genes12101587

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.

Highlights

Both bacterial leaf blight (BLB) and bacterial leaf streak (BLS) are caused by the Gram-negative bacterial pathogen Xanthomonas oryzae, but with different pathovars, as BLB is caused by X. oryzae pv.oryzae (Xoo) and BLS is caused by X. oryzae pv.oryzicola (Xoc)
Bacterial leaf streak (BLS) resistance screening was performed on 433 individuals of the segregating F2 population from a cross between IR62266 and Homcholasit (HCS)
We developed a Kompetitive Allele-Specific PCR (KASP) marker based on xa5 and validated the association between the marker and BLS resistance to Xanthomonas oryzae pv.oryzicola (Xoc) isolate 2NY2-2, another Thai Xoc isolate, in six different F2 populations developed based on three donors (IR62266, DV85 and MNTK75)

Summary

Introduction

Rice is susceptible to several diseases caused by bacteria, viruses and fungi [1]. Farmers lose an average of 37% of their rice yields to pests and diseases, with losses ranging from 24% to 41% depending on the production circumstances [2]. Two important rice diseases caused by bacteria, bacterial leaf blight (BLB) and bacterial leaf streak (BLS), are common in tropical and temperate regions [3]. BLB is one of the most devastating rice diseases, and BLS is growing more prevalent. Both BLB and BLS are caused by the Gram-negative bacterial pathogen Xanthomonas oryzae, but with different pathovars, as BLB is caused by X. oryzae pv.oryzae (Xoo) and BLS is caused by X. oryzae pv.oryzicola (Xoc). There are not many reports that have clearly stated the exact damage that can be caused by the disease

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