High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15 , in sunflower (Helianthus annuus L.)

Abstract

A novel rust resistance gene, R , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance. The inbred line HA-R8 carries a gene conferring resistance to all known races of the rust pathogen in North America and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments of 140 F individuals derived from a cross of HA 89 with HA-R8, rust resistance in the population was found to be conferred by a single dominant gene (R ) originating from HA-R8. Genotypic analysis with the currently available SSR markers failed to find any association between rust resistance and any markers. Therefore, we used genotyping-by-sequencing (GBS) analysis to achieve better genomic coverage. The GBS data showed that R was located at the top end of linkage group (LG) 8. Saturation with 71 previously mapped SNP markers selected within this region further showed that it was located in a resistance gene cluster on LG8, and mapped to a 1.0-cM region between three co-segregating SNP makers SFW01920, SFW00128, and SFW05824 as well as the NSA_008457 SNP marker. These closely linked markers will facilitate marker-assisted selection and breeding in sunflower.

Development of drought‐tolerant breeding lines derived from Helianthus annuus × H. argophyllus interspecific crosses

“…Sunflower wild relatives have been valuable sources for genetic improvement of elite sunflower germplasm (Seiler, Qi, & Marek, ), and have been used to introgress cytoplasmic male sterility, resistance against biotic and abiotic stresses, herbicide resistance and fatty acid modifications (as reviewed in Warburton et al, ). H. argophyllus is a diploid species (2n = 34) and has been exploited for the introgression of fertility restorer genes (Havekes, Miller, & Jan, ), and resistance to rust (Ma, Song, Markell, & Qi, ; Qi et al, ), downy mildew (Ma et al, ), and charcoal rot (Shehbaz et al, ). It has also been found to be highly diverse for traits related to resistance against drought, heat and sucking pests (Hussain et al, , ).…”

“…H. argophyllus is a diploid species (2n = 34) and has been exploited for the introgression of fertility restorer genes (Havekes, Miller, & Jan, 1991), and resistance to rust (Ma, Song, Markell, & Qi, 2018;Qi et al, 2016), downy mildew (Ma et al, 2017), and charcoal rot (Shehbaz et al, 2018). It has also been found to be highly diverse for traits related to resistance against drought, heat and sucking pests .…”

Marker-Assisted Gene Pyramiding and the Reliability of Using SNP Markers Located in the Recombination Suppressed Regions of Sunflower (Helianthus annuus L.)

“…The first rust resistant cultivar was developed in Canada in 1954, and subsequently, two rust resistance genes (R genes), R 1 and R 2 , were discovered [3,4]. Since then, a total of 13 rust R genes, R 1 -R 5 , R 10 -R 15 , P u6 , and R adv , have been reported from sunflower and its wild relatives, which are summarized in Ma et al [5]. Major gene resistance against biotrophic pathogens, such as rust, is generally unstable and nondurable, due to the emergence of virulent races in pathogen populations.…”

“…Friskop et al [8] identified 29 NA P. helianthi races from 238 single-pustule isolates collected from fields in 2011 and 2012. Among the 13 rust R genes, only seven, R 11 , R 12 , R 13a , R 13b , R 14 , R 15 , and R 16 , remain effectively resistant to all P. helianthi races identified in the USA [5,[9][10][11][12]. In some areas, although a single gene confers resistance to the existing pathogen population, large-scale use of this gene results in the breakdown of resistance.…”

“…The rust R genes R 4 in HA-R3 and R 5 in HA-R2 confer resistance to 96.6% and 78.6% of 238 rust isolates tested, respectively, in the USA in 2011 and 2012 [8], while R 12 in RHA 464, R 13b in RHA 397, and R 15 in HA-R8 confer resistance to all P. helianthi races identified in the USA [10]. These genes have been mapped to different sunflower chromosomes corresponding to linkage groups with linked markers-R 5 on chromosome 2, R 15 on chromosome 8, R 12 on chromosome 11, and R 4 and R 13b on chromosome 13 [5,10,[26][27][28][29].…”