Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice.

Xiaofang Xie,Yanyi Lin,Yinsong Liu,Huazhong Guan,Weiren Wu,Suhong Bu,Libin Lu,Jiazheng Yuan,Yan Zheng,Jie Hu

doi:10.3390/plants10102039

Abstract

Bacterial leaf streak (BLS) is a devastating rice disease caused by the bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), which can result in severe damage to rice production worldwide. Based on a total of 510 rice accessions, trialed in two seasons and using six different multi-locus GWAS methods (mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA and pKWmEB), 79 quantitative trait nucleotides (QTNs) reflecting 69 QTLs for BLS resistance were identified (LOD > 3). The QTNs were distributed on all chromosomes, with the most distributed on chromosome 11, followed by chromosomes 1 and 5. Each QTN had an additive effect of 0.20 (cm) and explained, on average, 2.44% of the phenotypic variance, varying from 0.00–0.92 (cm) and from 0.00–9.86%, respectively. Twenty-five QTNs were detected by at least two methods. Among them, qnBLS11.17 was detected by as many as five methods. Most of the QTNs showed a significant interaction with their environment, but no QTNs were detected in both seasons. By defining the QTL range for each QTN according to the LD half-decay distance, a total of 848 candidate genes were found for nine top QTNs. Among them, more than 10% were annotated to be related to biotic stress resistance, and five showed a significant response to Xoc infection. Our results could facilitate the in-depth study and marker-assisted improvement of rice resistance to BLS.

Highlights

Bacterial leaf streak (BLS) is a disease caused by the bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), in rice
Population Structure and LD Pattern in the Panel. Both PCA and fastSTRUCTURE analysis indicated that the panel of 510 rice accessions used in this study could be approximately divided into three major groups: indica group, japonica group, and circum-Aus group
In this study, based on a set of 510 rice varieties trialed in two seasons and using six different statistical methods, a total of 79 quantitative trait nucleotides (QTNs) corresponding to 69 QTLs for BLS resistance were detected, indicating that a genome-wide association study (GWAS) was much more efficient for QTL mapping than the conventional method

Summary

Introduction

Bacterial leaf streak (BLS) is a disease caused by the bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), in rice. Quantitative disease resistance is controlled by multiple genes, non-race-specific and durable [3]. The breeding of disease-resistant cultivars is a desirable approach to manage BLS in rice. To this end, it is necessary to map the quantitative trait loci (QTLs) which confer BLS resistance. Chen et al (2006) [5] mapped a major QTL for BLS resistance on chromosome 11. A non-host resistance gene Rxo from maize displayed a qualitative resistance to BLS [8] by activating multiple defense pathways related to a hypersensitive response (HR) against Xoc in rice [9]

Methods

Results

Conclusion