Meta-analysis of constitutive QTLs for disease resistance in maize and its synteny conservation in the rice genome

Abstract In wheat, meta-QTLs (MQTLs), and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103; fusarium head blight (FHB), 184; karnal bunt (KB), 66, and loose smut (LS), 14. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of initial QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed genes (DEGs). Among the DEGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping of MDR genes and marker-assisted breeding.

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Evidence of Multiple Disease Resistance (MDR) and Implication of Meta-Analysis in Marker Assisted Selection

PLoS ONE ◽

10.1371/journal.pone.0068150 ◽

2013 ◽

Vol 8 (7) ◽

pp. e68150 ◽

Cited By ~ 9

Author(s):

Farhan Ali ◽

Qingchun Pan ◽

Genshen Chen ◽

Kashif Rafiq Zahid ◽

Jianbing Yan

Keyword(s):

Disease Resistance ◽

Marker Assisted Selection ◽

Meta Analysis ◽

Multiple Disease Resistance

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Homotypic clustering of OsMYB4 binding site motifs in promoters of the rice genome and cellular-level implications on sheath blight disease resistance

Gene ◽

10.1016/j.gene.2015.02.031 ◽

2015 ◽

Vol 561 (2) ◽

pp. 209-218 ◽

Cited By ~ 7

Author(s):

Singh Pooja ◽

Kumari Sweta ◽

A. Mohanapriya ◽

C. Sudandiradoss ◽

Ramamoorthy Siva ◽

...

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Rice Genome ◽

Cellular Level ◽

Sheath Blight ◽

Sheath Blight Disease ◽

Blight Disease

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Ranking Resistance of Buxus Cultivars to Boxwood Blight – an Integrated Analysis1

Journal of Environmental Horticulture ◽

10.24266/0738-2898-38.2.50 ◽

2020 ◽

Vol 38 (2) ◽

pp. 50-55 ◽

Cited By ~ 1

Author(s):

Matthew Kramer ◽

Yonghong Guo ◽

Margaret Pooler

Keyword(s):

Disease Resistance ◽

Cultural Practices ◽

Meta Analysis ◽

Resistance Screening ◽

Cultivar Resistance ◽

Detached Leaf ◽

Ascomycete Fungi ◽

Blight Disease ◽

The U.S

Abstract Boxwood (Buxus L. spp., Buxaceae) are popular woody landscape shrubs grown for their diverse forms and broad-leaved evergreen foliage, with an estimated $126 million economic impact in the U.S. alone. Boxwood plants grown in temperate zones worldwide are now threatened by a destructive blight disease caused by the ascomycete fungi, Calonectria pseudonaviculata and C. henricotiae. While the disease can be mitigated somewhat through cultural practices and fungicides, the most sustainable long-term solution is the development of disease-resistant boxwood cultivars. Hundreds of boxwood accessions from the National Boxwood Collection at the U.S. National Arboretum were screened for resistance using a lab-based, detached-leaf assay. Initial comparisons of our results with those of multiple other disease resistance assays found inconsistent ranking of cultivar resistance among studies. We used a meta-analysis approach on compiled data from six studies and were able to produce a consistent ordering of cultivars sorted by their susceptibility to boxwood blight, despite the diversity in materials and methods of the studies. Index words: Boxwood, Calonectria pseudonaviculata, Cylindrocladium buxicola, meta-analysis, plant breeding, resistance screening. Species used in this study: Buxus bodinieri H. Lev.; B. harlandii Hance; B. microphylla Seibold & Zucc.; B. sempervirens L.; B. sinica var. insularis (Nakai) M. Cheng; B. wallichiana Baill.; Calonectria pseudonaviculata (Crous, J.Z. Groenew. & C.F. Hill) L. Lombard M.J. Wingf. & Crous 2010.

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A systematic review and meta-analysis of genetic parameters for complex quantitative traits in aquatic animal species

10.1101/2021.05.20.445048 ◽

2021 ◽

Author(s):

Nguyen Hong Nguyen

Keyword(s):

Disease Resistance ◽

Reproductive Performance ◽

Quantitative Traits ◽

Genetic Parameters ◽

Animal Species ◽

Meta Analysis ◽

Genetic Correlations ◽

Aquatic Animal ◽

Genetic Associations ◽

Flesh Quality

A systematic review and meta-analysis of genetic parameters underlying inheritance and complex biological relationships for quantitative traits are not available for aquatic animal species. I synthesised and conducted a comprehensive meta-analysis of the published information from 1985 to 2017 on heritability, common full-sib effects and genetic correlations for quantitative characters of biological importance (growth, carcass and flesh quality, disease resistance, deformity and reproduction) for aquaculture species. A majority of the studies (73.5%) focussed on growth related traits (body weight), followed by those on disease resistance (15.9%), whereas only a limited number of studies (10.6%) reported heritability estimates for carcass and flesh quality, deformity or reproduction characteristics. The weighted means of heritability for growth (weight, food utilisation efficiency, maturity) and carcass (fillet weight and yield) traits were moderate. Resistance against various bacteria, virus and parasites were moderately to highly heritable. Across aquatic animal species, the weighted heritability for a range of deformity measures and reproductive traits (fecundity, early survival) was low and not significantly different from zero. The common full-sibs (c2) accounted for a large proportion of total variance for body traits but it was of smaller magnitude in later phase of the growth development. The c2 effects however were not significant or in many cases they were not reported for carcass and flesh quality attributes as well as survival and deformity. The maternal genetic effects were not available for all traits studied especially for reproductive and early growth characters. Genetic correlations between body and carcass traits were high and positive, suggesting that selection for rapid growth can improve fillet weight, a carcass trait of paramount importance. Body weight, the most commonly used selection criterion in aquatic animals, showed non-significant genetic correlation with disease resistance, likely because both positive and negative genetic associations between the two types of traits. Interestingly the genetic associations between growth and reproductive performance (fecundity) and fry traits (fry weight, fry survival) were favourable. To date, there are still no published data on genetic relationships of carcass and flesh quality with disease resistance or reproductive performance in any aquaculture species. Additionally, the present study discussed new traits, including functional, immunological, behavioural and social interaction as well as uniformity that are emerging as potential selection criteria and which can be exploited in future genetic improvement programs for aquatic animals.

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Genetic analysis of Verticillium wilt resistance in a backcross inbred line population and a meta-analysis of quantitative trait loci for disease resistance in cotton

BMC Genomics ◽

10.1186/s12864-015-1682-2 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 35

Author(s):

Jinfa Zhang ◽

Jiwen Yu ◽

Wenfeng Pei ◽

Xingli Li ◽

Joseph Said ◽

...

Keyword(s):

Disease Resistance ◽

Quantitative Trait Loci ◽

Genetic Analysis ◽

Verticillium Wilt ◽

Inbred Line ◽

Quantitative Trait ◽

Meta Analysis ◽

Wilt Resistance ◽

Verticillium Wilt Resistance ◽

Backcross Inbred Line

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OsWRKY13 Mediates Rice Disease Resistance by Regulating Defense-Related Genes in Salicylate- and Jasmonate-Dependent Signaling

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-20-5-0492 ◽

2007 ◽

Vol 20 (5) ◽

pp. 492-499 ◽

Cited By ~ 294

Author(s):

Deyun Qiu ◽

Jun Xiao ◽

Xinhua Ding ◽

Min Xiong ◽

Meng Cai ◽

...

Keyword(s):

Salicylic Acid ◽

Disease Resistance ◽

Bacterial Blight ◽

Growth Stage ◽

Rice Genome ◽

Binding Activity ◽

Breeding Programs ◽

Dna Binding Activity ◽

Rice Disease ◽

Dependent Pathway

Although 109 WRKY genes have been identified in the rice genome, the functions of most are unknown. Here, we show that OsWRKY13 plays a pivotal role in rice disease resistance. Overexpression of OsWRKY13 can enhance rice resistance to bacterial blight and fungal blast, two of the most devastating diseases of rice worldwide, at both the seedling and adult stages, and shows no influence on the fertility. This overexpression was accompanied by the activation of salicylic acid (SA) synthesis-related genes and SA-responsive genes and the suppression of jasmonic acid (JA) synthesis-related genes and JA-responsive genes. OsWRKY13 bound to the promoters of its own and at least three other genes in SA- and JA-dependent signaling pathways. Its DNA-binding activity was influenced by pathogen infection. These results suggest that OsWRKY13, as an activator of the SA-dependent pathway and a suppressor of JA-dependent pathways, mediates rice resistance by directly or indirectly regulating the expression of a subset of genes acting both upstream and downstream of SA and JA. Furthermore, OsWRKY13 will provide a transgenic tool for engineering wider-spectrum and whole-growth-stage resistance rice in breeding programs.

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A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.)

Planta ◽

10.1007/s00425-015-2419-9 ◽

2015 ◽

Vol 243 (2) ◽

pp. 459-471 ◽

Cited By ~ 30

Author(s):

Yijun Wang ◽

Jing Xu ◽

Dexiang Deng ◽

Haidong Ding ◽

Yunlong Bian ◽

...

Keyword(s):

Zea Mays ◽

Disease Resistance ◽

Zea Mays L ◽

Virus Disease ◽

Meta Analysis ◽

Plant Morphology ◽

Stay Green ◽

Resistance Qtl

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Gapless indica rice genome reveals synergistic effects of active transposable elements and segmental duplications that promote rice genome evolution

10.1101/2020.12.24.424264 ◽

2020 ◽

Author(s):

Kui Li ◽

Wenkai Jiang ◽

Yuanyuan Hui ◽

Mengjuan Kong ◽

Li-Zhi Gao ◽

...

Keyword(s):

Disease Resistance ◽

Transposable Elements ◽

Genome Evolution ◽

Genome Assembly ◽

Higher Plants ◽

Synergistic Effects ◽

Rice Genome ◽

Dose Effect ◽

Segmental Duplications ◽

Duplicated Genes

AbstractThe ultimate goal of genome assembly is a high-accuracy gapless genome. Here we report a new assembly pipeline which we have used to produce a gapless genome for the indica rice cultivar Minghui 63. The 395.82 Mb final assembly is composed of 12 contigs with a contig N50 size of 31.82 Mb. All chromosomes are now gapless, with each chromosome represented by a single contig. This is the first gapless genome assembly achieved for higher plants or animals. BUSCO evaluation showed that gene regions of our assembly have higher completeness than the current rice reference genome (IRGSP-1.0). Compared with japonica rice, indica has more transposable elements (TEs) and segmental duplications (SDs), the latter of which produce many duplicated genes that can affect plant traits through dose effect or sub-/neo-functionalization. The insertion of TEs can also affect the expression of duplicated genes, which may drive evolution of these genes. We also found the expansion of NBS-LRR disease resistance genes and cZOGT growth-related genes in SDs, suggesting that SDs contribute to the adaptative evolution of rice disease resistance and developmental processes. Our findings suggest that active TEs and SDs together provide synergistic effects to promote rice genome evolution.

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