Innovative Advances in Plant Genotyping

Thomas, William J. W.; Zhang, Yueqi; Amas, Junrey C.; Cantila, Aldrin Y.; Zandberg, Jaco; Harvie, Samantha L.; Batley, Jacqueline

doi:10.1007/978-1-0716-3024-2_32

Cited by 5 publications

(2 citation statements)

References 95 publications

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“…Recent studies indicated that SVs have a profound impact in altering the phenotypes of a plant species (Yuan et al., 2021). Although the cost of WGS is greater than GBS, the high resolution in genetic variation discovery holds promise for comprehensively deciphering the genotype and phenotype relations to assist breeding (Thomas et al., 2023).…”

Section: Genomics‐assisted Breedingmentioning

confidence: 99%

Supporting crop plant resilience during climate change

Yuan,

Ton,

Thomas

et al. 2023

Crop Science

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The changing climate poses significant threats to agriculture and the ability to ensure sufficient global food production. With the expanding population, there is an urgent demand to increase crop productivity to meet the rising food demand. Producing climate‐smart crop varieties together with developing new agronomic management strategies are strategies that may help address this issue. Recent advances in genomics‐assistant breeding, the use of high‐throughput DNA sequencing, high‐resolution phenotyping, and advanced genome engineering can support the development of advanced, climate resilient crops. Here, we assess the potential to enhance the resilience of crops under the changing climate. Through the use of big data, advanced breeding strategies, and advanced agriculture practices, crop varieties could be produced with enhanced resilience and increased productivity and nutrition, supporting future global food security.

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Section: Genomics‐assisted Breedingmentioning

confidence: 99%

Supporting crop plant resilience during climate change

Yuan,

Ton,

Thomas

et al. 2023

Crop Science

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“…Brassicaceae species, especially the crop species, are vulnerable to various pathogenic organisms, for instance, Leptosphaeria species (L. maculans, L. biglobosa), Sclerotinia sclerotiorum, Albugo candida, Plasmodiophora brassicae, Rhizoctonia solani and Xanthomonas spp., which cause blackleg (BL), Sclerotinia stem rot (SSR), white rust (WR), clubroot (CR), hypocotyl rot (HR) and black rot (BR), respectively (Barbetti et al, 2015(Barbetti et al, , 2016Bhattacharya et al, 2014;Chattopadhyay et al, 2015;Mani et al, 2020), severely impacting their production (Thomas et al, 2022;Zhang et al, 2021). Crops overcome pathogenic diseases by having natural resistance in the form of qualitative and quantitative resistance.…”

mentioning

confidence: 99%

In silico prediction and analysis of transmembrane‐coiled‐coil resistance gene analogues in 27Brassicaceaespecies

Cantila,

Thomas,

Bayer

et al. 2023

Plant Pathology

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The Brassicaceae family is composed of a broad range of species, including the economically important crops from Brassica, Raphanus, Camelina and Sinapis genera. The production of Brassicaceae species, particularly the crop members, is threatened by major diseases. However, the impact of diseases can be minimized or even negated by improving disease resistance. Transmembrane‐coiled‐coil (TM‐CC) genes are a type of resistance gene analogue (RGA) that have been proven to play specific roles in resistance to several diseases. Here, TM‐CCs have been predicted in 27 genomes from Brassicaceae genera including Arabidopsis, Arabis, Barbarea, Boechera, Brassica, Camelina, Capsella, Cardamine, Eutrema, Leavenworthia, Lepidium, Raphanus, Sinapis, Sisymbrium, Schrenkiella and Thlaspi. The number of TM‐CCs varies throughout the studied genomes, as well as between genera, diploids and polyploids, and Brassica genomes and subgenomes. In total, 6788 TM‐CCs were identified, with 708 of them predicted with signalling function, 172 colocalized with previously known disease resistance regions and 70 phylogenetically related to cloned resistance genes, indicating the possible functional involvement of TM‐CCs in resistance. This study provides a resource for the identification of functional Brassicaceae TM‐CCs along with their clustering and duplication patterns and provides a benchmark for further studies investigating TM‐CCs.

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Allele-tagged TaqMan® PCR genotyping assays for high-throughput detection of soybean cyst nematode resistance

Usovsky,

Bilyeu,

Bent

et al. 2024

Mol Biol Rep

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Background Whole genome resequencing (WGRS) platforms provide exceptional fingerprinting of the entire genome but are expensive and less flexible to use as a routine genotyping tool for targeting causal polymorphisms within a germplasm collection or breeding program. Therefore, there has been a continuous effort to develop small-scale genotyping platforms that facilitate robust and quick assessments of the allelic status of causal variants for important traits within soybean breeding programs. The objective was to develop a comprehensive panel of soybean cyst nematode (SCN) resistance TaqMan ® assays via selecting the causative genes and analyzing their associated alleles. Methods The Soybean Allele Catalog was utilized to investigate WGRS-derived variants which are predicted to cause a change in the amino acid sequence of a gene product. This panel of TaqMan ® assays reflects current knowledge about known SCN resistance-causing genes and their associated alleles: GmSNAP18-a and -b , GmSNAP11 , GmSHMT08 , GmSNAP15 , GmNSF RAN07 , and GmSNAP02-ins and - del . Developed assays were tested using elite breeding lines and segregating populations. TaqMan assays were compared to other currently available KASP and CAPS assays. Conclusion All assays showed excellent allele determination efficiencies. This SCN genotyping assay panel can be utilized as a simplified, accurate and reliable genotyping platform further equipping the updated soybean breeding toolbox. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-024-10114-6.

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Innovative Advances in Plant Genotyping

Cited by 5 publications

References 95 publications

Supporting crop plant resilience during climate change

Supporting crop plant resilience during climate change

In silico prediction and analysis of transmembrane‐coiled‐coil resistance gene analogues in 27Brassicaceaespecies

Allele-tagged TaqMan® PCR genotyping assays for high-throughput detection of soybean cyst nematode resistance

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