Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis

Zhang, Hui; Chu, Ye; Dang, Phat; Tang, Yueyi; Jiang, Tao; Clevenger, Josh; Ozias‐Akins, Peggy; Holbrook, C. Corley; Wang, Ming Li; Campbell, Howard; Hagan, Austin K.; Chen, Charles

doi:10.1007/s00122-020-03576-2

Cited by 42 publications

(27 citation statements)

References 47 publications

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“…Candidate R-genes with NBS-LRR motifs and threonine-protein phosphatases were within proximal genomics location to QTL qLLS.A03 locus covering a range of 95 to 132 Mb segment. Zhang et al [9] identified 2 QTLs on chromosome B09 that are significantly associated with ELS and LLS resistance evaluating the US mini-core peanut collection. Candidate R-genes include TIR-NBS-LRR class, LRR family proteins, and putative disease resistance RPP13-like proteins within proximal distance form QTLs.…”

Section: Discussionmentioning

confidence: 99%

“…Identification of major genes for disease resistance has been very elusive based on strong environmental and genetic interactions and the involvement of multiple QTLs [7][8][9]. The nature of plant and fungal interactions makes visual selections highly variable based on years and locations.…”

Section: Introductionmentioning

confidence: 99%

“…Chu et al [8] identified 3 resistance QTLs on chromosome 3 and 1 on chromosome 5 evaluating recombinant inbred lines (RILs) from a population (Florida-07 × GP-NC WS16) segregating for resistance. Zhang et al [9] identified 2 QTLs on chromosome B09 that were significantly associated with ELS and LLS resistance evaluating the US mini-core peanut collection. A high number of QTLs were identified, and the variability of field disease evaluations highlight the complexity of breeding for leaf spot resistance.…”

Section: Introductionmentioning

confidence: 99%

“…A joint peanut breeding program between Auburn University, AL and the National Peanut Research Laboratory, Dawson, Ga was established to develop peanut varieties with desired agronomic traits for the peanut industry. One of a major goal is to develop disease resistant peanut varieties, currently focusing on leaf spot resistance, through plant selection and applications of genomics and molecular breeding strategies [9,17]. A strategy is to develop several strategic crosses, followed by field performance studies, and evaluation of specific gene-expression to identify potential leaf spot resistance genes.…”

Section: Introductionmentioning

confidence: 99%

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Association of differentially expressed R-gene candidates with leaf spot resistance in peanut (Arachis hypogaea L.)

2021

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Early leaf spot (ELS) and late leaf spot (LLS) are major fungal diseases of peanut that can severely reduce yield and quality. Development of acceptable genetic resistance has been difficult due to a strong environmental component and many major and minor QTLs. Resistance genes (R-genes) are an important component of plant immune system and have been identified in peanut. Association of specific R-genes to leaf spot resistance will provide molecular targets for marker-assisted breeding strategies. In this study, advanced breeding lines from different pedigrees were evaluated for leaf spot resistance and 76 candidate R-genes expression study was applied to susceptible and resistant lines. Thirty-six R-genes were differentially expressed and significantly correlated with resistant lines, of which a majority are receptor like kinases (RLKs) and receptor like proteins (RLPs) that sense the presence of pathogen at the cell surface and initiate protection response. The largest group was receptor-like cytoplasmic kinases (RLCKs) VII that are involved in pattern-triggered kinase signaling resulting in the production reactive oxygen species (ROS). Four R-genes were homologous to TMV resistant protein N which has shown to confer resistance against tobacco mosaic virus (TMV). When mapped to peanut genomes, 36 R-genes were represented in most chromosomes except for A09 and B09. Low levels of gene-expression in resistant lines suggest expression is tightly controlled to balance the cost of R-gene expression to plant productively. Identification and association of R-genes involved in leaf spot resistance will facilitate genetic selection of leaf spot resistant lines with good agronomic traits.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Association of differentially expressed R-gene candidates with leaf spot resistance in peanut (Arachis hypogaea L.)

2021

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“…Compared to linkage maps, the use of GWAS methodologies has advantages such as using genetically diverse populations with different rates of recombination and linkage disequilibrium (LD; Myles et al, 2009). Despite the observed GWAS efficiency in several crops (Warraich et al, 2020;Zhang et al, 2020;Verzegnazzi et al, 2021), this methodology still presents limitations related to the low proportion of phenotypic variance explained by the identified genomic regions (Manolio et al, 2009). As an alternative, the combination of GWAS results with other molecular methodologies, such as transcriptomics and proteomics analyses, can contribute to better knowledge of the genetic mechanisms involved in the definition of a trait (Tam et al, 2019), overcoming the statistical limitations on the characterization of a broad set of causal genomic regions.…”

Section: Introductionmentioning

confidence: 99%

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

et al. 2021

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Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.

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Recent Advances and Applicability of GBS, GWAS, and GS in Polyploid Crops

Thakral

Yadav

Padalkar

et al. 2022

Genotyping by Sequencing for Crop Improvement

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Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis

Cited by 42 publications

References 47 publications

Association of differentially expressed R-gene candidates with leaf spot resistance in peanut (Arachis hypogaea L.)

Association of differentially expressed R-gene candidates with leaf spot resistance in peanut (Arachis hypogaea L.)

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

Recent Advances and Applicability of GBS, GWAS, and GS in Polyploid Crops

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