Genome-wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice

Jiang, Nan; Fu, Jun; Zeng, Qin; Liang, Yi; Shi, Yanlong; Li, Zhuowei; Xiao, Yutao; He, Zhou; Wu, Yuntian; Long, Yu; Wang, Kai; Yang, Yuanzhu; Liu, Xionglun; Peng, Junhua

doi:10.1007/s00425-021-03612-5

Cited by 12 publications

(7 citation statements)

References 77 publications

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“…In particular, the reported QTL qBblsr5a was fine mapped and proved that its effect on BLS resistance was mainly, if not entirely, attributed to the known recessive gene, xa5 [ 30 , 31 ]. Jiang et al (2021) [ 28 ] presented seven BLS resistant QTNs, identified by a GWAS approach, and four of the QTNs ( qnBLS6.5 , qnBLS6.6 , qnBLS8.5 and qnBLS11.7 ) detected in our study appeared to be collinear with these QTNs. Our QTNs, qnBLS6.5 and qnBLS6.6 , were 926 kb and 387 kb, respectively, from the QTN detected in their study challenged by the pathogen strain, HNBI-19, while the QTN qnBLS11.7 identified by two models was 146 kb from the QTN in chromosome 11.…”

Section: Discussionsupporting

confidence: 54%

“…Our QTNs, qnBLS6.5 and qnBLS6.6 , were 926 kb and 387 kb, respectively, from the QTN detected in their study challenged by the pathogen strain, HNBI-19, while the QTN qnBLS11.7 identified by two models was 146 kb from the QTN in chromosome 11. Moreover, the QTN, qnBLS8.5 , which had the highest LOD score and was detected by three different models in our study, was only 21 kb away from the QTN obtained by the GWAS study using the same strain [ 28 ].…”

Section: Discussionmentioning

confidence: 99%

“…A high-density single-nucleotide polymorphism (SNP) map and comprehensive HapMap were constructed in rice [ 26 , 27 ], and were valuable for a GWAS of complex traits. Lately, a total of seven genomic loci associated with BLS resistance were detected, based on the mixed linear model (MLM), in one season trial [ 28 ]. In our study, by phenotyping a panel of rice accessions in two seasons, we performed a multi-locus GWAS analysis of BLS resistance, aiming to identify a substantial number of loci and SNP markers related to BLS resistance, which would accelerate the genetic improvement of BLS resistance in rice.…”

Section: Introductionmentioning

confidence: 99%

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

Xie

Zheng

et al. 2021

Plants

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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.

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Section: Discussionsupporting

confidence: 54%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Xie

Zheng

et al. 2021

Plants

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“…In the case of rice, fungal diseases like blast, sheath blight and sheath-rot, bacterial diseases like bacterial blight (BB) and the viral disease like rice tungro disease, are major diseases. GWAS approach has been deployed to identify and validate genomic regions for tolerance to BB ( Jiang et al., 2021 ; Shu et al., 2021 ), bacterial leaf streak tolerance ( Sattayachiti et al., 2020 ; Jiang et al., 2021 ), blast ( Volante et al., 2020 ; Frontini et al., 2021 ). Among 56 important QTLs/genomic regions associated with different blast isolates, a single genomic region was designated as the Pik allele that confirms resistance to all three isolates ( Li et al., 2019b ).…”

Section: Ricementioning

confidence: 99%

Two decades of association mapping: Insights on disease resistance in major crops

et al. 2022

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Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.

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“…Farmers have only a limited comprehension of the disease. This crisis diminishes the efficiency of rice production, hence reducing the agricultural income [13] [14] [15]. Not only are rice leaf diseases prevalent in India, but they are also prevalent in other countries.…”

Section: Introductionmentioning

confidence: 99%

Optimal Training Ensemble of Classifiers for Classification of Rice Leaf Disease

Sridevi¹,

Kumar²

2023

IJACSA

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Rice is one of the most extensively cultivated crops in India. Leaf diseases can have a significant impact on the productivity and quality of a rice crop. Since it has a direct impact on the economy and food security, the detection of rice leaf diseases is the most important factor. The most prevalent diseases affecting rice leaves are leaf blast, brown spots, and hispa. To address this issue, this research builds a new classification model for rice leaf diseases. The model begins with a preprocessing step that employs the Median Filter (MF) process. Improved BIRCH is then utilized for picture segmentation. Features such as LBP, GLCM, color, shape, and modified Median Binary Pattern (MBP) are retrieved from segmented images. Then, an ensemble of three classification models, including Bi-GRU, Convolutional Neural Network (CNN), and Deep Maxout (DMN) is utilized. By adjusting the model weights, the suggested Opposition Learning Integrated Hybrid Feedback Artificial and Butterfly algorithm (OLIHFA-BA) will train the model to improve the performance of the proposed work.

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Genome-wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice

Cited by 12 publications

References 77 publications

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

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

Two decades of association mapping: Insights on disease resistance in major crops

Optimal Training Ensemble of Classifiers for Classification of Rice Leaf Disease

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