Genetic Insight into Disease Resistance Gene Clusters by Using Sequencing-Based Fine Mapping in Sunflower (Helianthus annuus L.)

Ma, Guojia; Song, Qijian; Li, Xuehui; Qi, Lili

doi:10.3390/ijms23179516

Cited by 5 publications

(2 citation statements)

References 79 publications

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“…Moreover, using fragment length polymorphism for allelic discrimination will have a better accuracy since it is less affected by the variation of signal intensity or background signal noise due to PCR products from non-target amplifications. To date, STARP markers have been successfully used for genetic analysis in barley [15], common bean [16], potato [17], sunflower [18], and wheat [19].…”

Section: Introductionmentioning

confidence: 99%

Development of STARP Marker Platform for Flexible SNP Genotyping in Sugarbeet

et al. 2023

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Single nucleotide polymorphisms (SNPs) have been widely used for gene identification. Allelic discrimination for an individual SNP with high reliability and flexibility is critical for the accurate detection of beneficial genes linked to specific SNP sites. Several SNP genotyping platforms have been developed but most exclusively rely on fluorescence signals for allelic differentiation. Genotyping via a fluorescence signal can have a lower accuracy if strong background signal noise is present, a common challenge associated with crop genetics. The semi-thermal asymmetric reverse PCR (STARP) marker system introduces extra SNPs in its forward primers to ensure specificity of the PCR reaction and adds a 4-nucleotide insertion into one universal primer to create fragment length polymorphism among STARP markers, which makes SNP allelic discrimination possible through either fluorescence signals or traditional gel electrophoresis. The STARP marker system is preferable for SNP genotyping in crops such as sugarbeet (Beta vulgaris ssp. Vulgaris L.) that exhibit strong background signal noise during PCR reactions due to an abundant repetitive sequence and high levels of heterozygosity in the genome. In this study, SNPs among sugarbeet lines were detected through genotype-by-sequencing (GBS) and confirmed by sequencing PCR products containing SNP sites. STARP primers were designed, and they generated STARP markers clearly discriminated by SNP alleles among sugarbeet plants either through a fluorescence signal or fragment length polymorphism. In addition, by prolonging 5-nucleotide in an allele-specific forward primer F2 that increased fragment length polymorphism of STARP markers from 4-bp to 9-bp, genotyping individual SNPs can be performed using user-friendly agarose gels. This research resulted in the development of a STARP marker platform for the flexible genotyping of individual SNPs of sugarbeet as well as an improved STARP technique for easy SNP allelic discrimination that also has utilities in other plant species.

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Section: Introductionmentioning

confidence: 99%

Development of STARP Marker Platform for Flexible SNP Genotyping in Sugarbeet

et al. 2023

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“…The confection sunflower lines HA-DM2 with the rust and DM R genes R 12 and Pl Arg and HA-DM3 with R 13a and Pl 17 genes were released in 2017 by USDA and North Dakota State University (Ma et al, 2019a). Molecular markers closely linked to R 12 in sunflower linkage group (LG)11, R 13a in LG13, Pl Arg in LG1, and Pl 17 in LG4 have been developed to facilitate marker-assisted gene pyramiding (Ma et al, 2019b(Ma et al, , 2022(Ma et al, , 2023Qi et al, 2017). The inbred line HA-R8 harbors the rust gene R 15 mapped to LG8 with tightly linked DNA markers (Ma et al, 2018;Qi & Ma, 2020).…”

Section: Introductionmentioning

confidence: 99%

Registration of HA‐R20 and HA‐R21 confection sunflower germplasms resistant to rust and downy mildew

Ma,

Li,

Seiler

et al. 2023

J of Plant Registrations

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Rust and downy mildew (DM) are detrimental diseases in global sunflower (Helianthus annuus L.) production. Disease often results in yield loss and reduced seed quality. Host resistance to DM and rust is mediated by single dominant genes in sunflower. To better utilize genetic resistance, gene pyramiding is a common practice in crop breeding to extend the durability and longevity of resistance. Two confection sunflower germplasm lines, HA‐R20 (Reg. no. GP‐387, PI 702361) and HA‐R21 (Reg. no. GP‐388, PI 702362), were developed using the pedigree breeding method and DNA marker‐assisted selection and released by the USDA‐ARS Sunflower and Plant Biology Research Unit in collaboration with the North Dakota Agricultural Experiment Station in September 2022. HA‐R20 is an F3‐derived F4 confection restorer selection from the cross of HA‐DM2 and HA‐R8, carrying rust resistance genes R12 and R15 and DM resistance gene PlArg. HA‐R21 is an F3‐derived F4 confection maintainer selection from the cross of HA‐DM3 and HA‐R8, carrying rust resistance genes R13a and R15 and DM resistance gene Pl17. Disease reaction and marker testing for DM and rust confirmed that both germplasms harbor DM and rust R genes in the homozygous condition and are resistant to all DM and rust races identified in North America to date. These multiple disease‐resistant lines will provide the sunflower industry with durable disease‐resistant sources for the continued improvement of the crop.

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Introgression and targeting of the Pl37 and Pl38 genes for downy mildew resistance from wild Helianthus annuus and H. praecox into cultivated sunflower (Helianthus annuus L.)

Talukder

et al. 2023

Theor Appl Genet

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Genetic Insight into Disease Resistance Gene Clusters by Using Sequencing-Based Fine Mapping in Sunflower (Helianthus annuus L.)

Cited by 5 publications

References 79 publications

Development of STARP Marker Platform for Flexible SNP Genotyping in Sugarbeet

Development of STARP Marker Platform for Flexible SNP Genotyping in Sugarbeet

Registration of HA‐R20 and HA‐R21 confection sunflower germplasms resistant to rust and downy mildew

Introgression and targeting of the Pl37 and Pl38 genes for downy mildew resistance from wild Helianthus annuus and H. praecox into cultivated sunflower (Helianthus annuus L.)

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