Genome-wide association study of the seed transmission rate of soybean mosaic virus and associated traits using two diverse population panels

Growing virus resistant varieties is a highly effective means to avoid yield loss due to infection by many types of virus. The challenge is to be able to detect resistance donors within plant species diversity and then quickly introduce alleles conferring resistance into elite genetic backgrounds. Until now, mainly monogenic forms of resistance with major effects have been introduced in crops. Polygenic resistance is harder to map and introduce in susceptible genetic backgrounds, but it is likely more durable. Genome wide association studies (GWAS) offer an opportunity to accelerate mapping of both monogenic and polygenic resistance, but have seldom been implemented and described in the plant–virus interaction context. Yet, all of the 48 plant–virus GWAS published so far have successfully mapped QTLs involved in plant virus resistance. In this review, we analyzed general and specific GWAS issues regarding plant virus resistance. We have identified and described several key steps throughout the GWAS pipeline, from diversity panel assembly to GWAS result analyses. Based on the 48 published articles, we analyzed the impact of each key step on the GWAS power and showcase several GWAS methods tailored to all types of viruses.

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“…Tomato ringspot virus (TRSV) Peanut mottle virus (PMV) Bean pod mosaic virus (BPMV) Soybean mosaic virus (SMV) (×3) [33,[67][68][69]…”

Section: Glycine Maxmentioning

confidence: 99%

Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances

Monnot

Desaint

Mary‐Huard

et al. 2021

Cells

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“…Several QTL contributing to various virus diseases in grain legumes have been identified ( Blair et al., 2007 ; Zheng et al., 2014 ; Ma et al., 2016 ; Mathivathana et al., 2019 ) ( Figure 1 ). The previous section mentioned the resistance gene(s) controlling SMV; subsequent biparental QTL mapping helped discover the QTL controlling resistance against various strains of SMV ( Wang et al., 2011 ; Zheng et al., 2014 ; Ma et al., 2016 ; Karthikeyan et al., 2017 ; Rui et al., 2017 ; Liu et al., 2019 ). Wang et al.…”

Section: Qtl Mapping For Various Virus-disease-resistant Grain Legumesmentioning

confidence: 99%

“…Several QTL contributing to various virus diseases in grain legumes have been identified (Blair et al, 2007;Zheng et al, 2014;Ma et al, 2016;Mathivathana et al, 2019) (Figure 1). The previous section mentioned the resistance gene(s) controlling SMV; subsequent biparental QTL mapping helped discover the QTL controlling resistance against various strains of SMV (Wang et al, 2011;Zheng et al, 2014;Ma et al, 2016;Karthikeyan et al, 2017;Rui et al, 2017;Liu et al, 2019). Wang et al (2011) reported that a single dominant gene on chromosome 2 flanked by BARCSOYSSR_02_0610 and BARCSOYSSR_02_0616 governed the genetics of SMV (SC18) resistance in a Kefeng No.1 × Nannong 1138-2 population.…”

Section: Qtl Mapping For Various Virusdisease-resistant Grain Legumesmentioning

confidence: 99%

“…For example, a comprehensive GWAS for TRSV in a set of 19,652 soybean genotypes using the SoySNP50K iSelect BeadChip detected a single locus associated with TRSV sensitivity on chromosome 2 and predicted two leucine-rich repeat receptor-like kinase genes Glyma02g13460 and Glyma02g13470 underlying the locus (Chang et al, 2016). Similarly, Liu et al (2019) conducted GWAS in two soybean populations containing 409 and 199 genotypes in a SoySNP50K assay to unearth significant marker-trait associations for SMV seed transmission rate, seed coat mottling, and seed yield loss due to SMV infection. The study identified a single locus contributing to SMV seed transmission rate on chromosome 9, loci for seed coat mottling on chromosome 3, and a single locus for seed yield loss due to SMV infection on chromosome 3 (Liu et al, 2019).…”

Section: Genome-wide Association Study Capturing Viral-disease-resist...mentioning

confidence: 99%

“…Similarly, Liu et al (2019) conducted GWAS in two soybean populations containing 409 and 199 genotypes in a SoySNP50K assay to unearth significant marker-trait associations for SMV seed transmission rate, seed coat mottling, and seed yield loss due to SMV infection. The study identified a single locus contributing to SMV seed transmission rate on chromosome 9, loci for seed coat mottling on chromosome 3, and a single locus for seed yield loss due to SMV infection on chromosome 3 (Liu et al, 2019). An earlier GWAS investigating SMV(SC7) resistance in 165 soybean genotypes identified three genes, homologous to WRKY72, eEF1Bb, and RLP9, conferring disease resistance in Arabidopsis on chromosomes 1, 3, and 9, respectively (Che et al, 2017).…”

Section: Genome-wide Association Study Capturing Viral-disease-resist...mentioning

confidence: 99%

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Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration

et al. 2023

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Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and ‘omics’ approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.

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Research Advances in Potyviruses: From the Laboratory Bench to the Field

Yang

Wang

2021

Annu. Rev. Phytopathol.

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Potyviruses (viruses in the genus Potyvirus, family Potyviridae) constitute the largest group of known plant-infecting RNA viruses and include many agriculturally important viruses that cause devastating epidemics and significant yield losses in many crops worldwide. Several potyviruses are recognized as the most economically important viral pathogens. Therefore, potyviruses are more studied than other groups of plant viruses. In the past decade, a large amount of knowledge has been generated to better understand potyviruses and their infection process. In this review, we list the top 10 economically important potyviruses and present a brief profile of each. We highlight recent exciting findings on the novel genome expression strategy and the biological functions of potyviral proteins and discuss recent advances in molecular plant–potyvirus interactions, particularly regarding the coevolutionary arms race. Finally, we summarize current disease control strategies, with a focus on biotechnology-based genetic resistance, and point out future research directions. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Genome-wide association study of the seed transmission rate of soybean mosaic virus and associated traits using two diverse population panels

Cited by 4 publications

References 68 publications

Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances

Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances

Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration

Research Advances in Potyviruses: From the Laboratory Bench to the Field

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