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

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.

Molecular screening of domestic apple cultivars for scab resistance genes in Greece

Apple scab caused by Venturia inaequalis has the most destructive effects among other phytopathogens in apple crops all over the world. The integration of resistance genes from local and domestic cultivars is a prerequisite for the efficient control of this disease and is a main target in efficient breeding approaches. Across Greece, many domestic apple cultivars are reported without deep knowledge about the presence and diversity of scab resistance genes. In this study, the presence of five resistance genes (Rvi2, Rvi4, Rvi6, Rvi8 and Rvi11) was evaluated across twenty local and domestic apple genotypes, employing twelve molecular markers closely linked to known apple scab resistance loci. Significant differences and polymorphisms among the tested cultivars were detected suggesting that some of them carry a sufficient number of resistance genes. This observed genetic diversity could be exploited in ongoing breeding approaches as a natural source of polygenic resistance against apple scab.

A New Polygenic Model for Nonfamilial Colorectal Cancer Inheritance Based on the Genetic Architecture of the Azoxymethane-Induced Mouse Model

The azoxymethane model of colorectal cancer (CRC) was used to gain insights into the genetic heterogeneity of nonfamilial CRC. We observed significant differences in susceptibility parameters across 40 mouse inbred strains, with 6 new and 18 of 24 previously identified mouse CRC modifier alleles detected using genome-wide association analysis. Tumor incidence varied in F1 as well as intercrosses and backcrosses between resistant and susceptible strains. Analysis of inheritance patterns indicates that resistance to CRC development is inherited as a dominant characteristic genome-wide, and that susceptibility appears to occur in individuals lacking a large-effect, or sufficient numbers of small-effect, polygenic resistance alleles. Our results suggest a new polygenic model for inheritance of nonfamilial CRC, and that genetic studies in humans aimed at identifying individuals with elevated susceptibility should be pursued through the lens of absence of dominant resistance alleles rather than for the presence of susceptibility alleles.

Development of F1 hybrids of cabbage with complex resistance in the south of Russia

Relevance Breeding for resistance is one of the priorities when working with late-ripening cabbage.The most significant damage to this crop in the south of Russia is caused by diseases such as fusarium, black rot, and from pests – tobacco trips. Methods The purpose of the research is development of heat-resistant hybrids of medium-late and late maturity of various areas of use with complex resistance. For 2 decades much attention was paid to breeding and immunological work on development of inbred lines with group resistance: to fusarium and polygenic resistance to black rot. The study of race-specific resistance for better protection against black rot began in 2013. At that, the progeny of the lines were eveluated, which were selected by hydathogenic polygenic resistance on the infectious background of cabbage during inoculation of plants with the Krasnodar population of the pathogen.Since specific resistance to a particular race inherited in white cabbage is recessive and it is very difficult to develop lines and hybrids resistant to several races, a strategy was chosen to increase resistance to this dangerous disease based on a combination of field resistance, stem resistance to the main race 1 and leaf resistance to one or two races. Results As a result of the work carried out in 2018, 44 lines of medium-late maturity with stem resistance to race 1 were selected, of which a significant part of the lines had leaf resistance to a particular race, including 4 lines resistant to races 1 and 4, 1 line – to races 0, 1,4, and 1 line – to races 0, 3, 4. The heat-resistant hybrid for processing Sudarynya was passed to State Variety Testing, it has one parent with stem resistance to race 1, leaf resistance to races 0, 1.4 and hydatode resistance, and the second parent has stem resistance to race 1 and hydatode resistance. Every year, hybrids are evaluated for thrips damage. According to the results of the evaluation of hybrids, lines with a high tolerance to tobacco thrips were identified. In 2017-2018 9 lines with complex resistance to fusarium, black rot and thrips (Ten211, Yas111, Eubi122, Hn861, Hn270-21, Hn270-24, Br272-22, Hn270-14p-1, 272-510) were selected, on the basis of which promising combinations of economically valuable traits were obtained.