Association Mapping and Development of Marker-Assisted Selection Tools for the Resistance to White Pine Blister Rust in the Alberta Limber Pine Populations

Liu, Junjun; Sniezko, Richard A.; Sissons, Robert; Krakowski, Jodie; Alger, Genoa; Schoettle, Anna W.; Williams, Holly; Zamany, Arezoo; Zitomer, Rachel A.; Kegley, Angelia

doi:10.3389/fpls.2020.557672

Cited by 7 publications

(6 citation statements)

References 69 publications

(102 reference statements)

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“…The existence of Cr4 in wide ranging geographical regions indicates its complicated genetic background [ 16 , 17 , 30 ], which limits Cr4 -linked markers shared by different germplasms for development of molecular selection tools for wild stands. The present study detected sequence variations of Cr4 candidate alleles, useful for tracing Cr4 origin in limber pine populations.…”

Section: Discussionmentioning

confidence: 99%

“…Cr1 , Cr2 , and Cr4 were localized on the Pinus consensus LG-2, LG-1, and LG-8, respectively [ 21 , 26 , 29 ]. A combination of linkage mapping and association study validated Cr4 or a locus very close to Cr4 for limber pine MGR in seed families that originated in both USA and Canada [ 30 ]. These comparative studies of syntenic genomic regions of closely related species identified NLR genes as R candidates, which serve as good starting points for the positional cloning of five-needle pine R genes against C. ribicola [ 24 , 31 ].…”

Section: Introductionmentioning

confidence: 99%

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Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family

et al. 2021

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Background Proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains (NLR) make up one of most important resistance (R) families for plants to resist attacks from various pathogens and pests. The available transcriptomes of limber pine (Pinus flexilis) allow us to characterize NLR genes and related resistance gene analogs (RGAs) in host resistance against Cronartium ribicola, the causal fungal pathogen of white pine blister rust (WPBR) on five-needle pines throughout the world. We previously mapped a limber pine major gene locus (Cr4) that confers complete resistance to C. ribicola on the Pinus consensus linkage group 8 (LG-8). However, genetic distribution of NLR genes as well as their divergence between resistant and susceptible alleles are still unknown. Results To identify NLR genes at the Cr4 locus, the present study re-sequenced a total of 480 RGAs using targeted sequencing in a Cr4-segregated seed family. Following a call of single nucleotide polymorphisms (SNPs) and genetic mapping, a total of 541 SNPs from 155 genes were mapped across 12 LGs. Three putative NLR genes were newly mapped in the Cr4 region, including one that co-segregated with Cr4. The tight linkage of NLRs with Cr4-controlled phenotypes was further confirmed by bulked segregation analysis (BSA) using extreme-phenotype genome-wide association study (XP-GWAS) for significance test. Local tandem duplication in the Cr4 region was further supported by syntenic analysis using the sugar pine genome sequence. Significant gene divergences have been observed in the NLR family, revealing that diversifying selection pressures are relatively higher in local duplicated genes. Most genes showed similar expression patterns at low levels, but some were affected by genetic background related to disease resistance. Evidence from fine genetic dissection, evolutionary analysis, and expression profiling suggests that two NLR genes are the most promising candidates for Cr4 against WPBR. Conclusion This study provides fundamental insights into genetic architecture of the Cr4 locus as well as a set of NLR variants for marker-assisted selection in limber pine breeding. Novel NLR genes were identified at the Cr4 locus and the Cr4 candidates will aid deployment of this R gene in combination with other major/minor genes in the limber pine breeding program.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family

et al. 2021

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“…SNP sangat efektif digunakan sebagai marka molekuler untuk studi genetik (Qi et al, 2017) dan setiap SNP berasosiasi dengan ekspresi gen (J. J. Liu et al, 2020). Penelitian sebelumnya telah mengembangkan marka SNAP (Single Nucleotide Amplified Polymorphism) berdasarkan sekuens transkriptomik pada lobak (Raphanus sativus L.) Wang et al, 2017), namun informasi SNP dari transkriptomik pada tanaman kelapa sawit untuk marka molekuler ketahanan GD belum dimanfaatkan secara optimal (Rosli et al, 2018).…”

Section: Rokhana Faizahunclassified

“…Tidak disebutkan OPGP project (Herrero et al, 2020) Rokhana Faizah biomolekuler masih diaplikasikan untuk proses seleksi karakteristik spesifik dalam pemuliaan tanaman (Bohry et al, 2021;Jang & Lee, 2021; J. J. Liu et al, 2020). Beberapa karakter penting pada kelapa sawit telah diseleksi menggunakan penanda molekuler, antara lain ketebalan cangkang, pertambahan hasil dan tinggi tanaman, konstruksi peta keterkaitan, kandungan asam lemak, morfologi dan sifat terkait hasil, perkembangan kalus, dan tanaman tahan Ganoderma (Tabel 1) .…”

Section: Opgp Projectunclassified

Pengembangan Biomarka Untuk Seleksi Tanaman Tahan Penyakit Busuk Pangkal Batang Pada Kelapa Sawit

Faizah

2022

war

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Penyakit busuk pangkal batang (BPB) yang disebabkan patogen Ganoderma boninense menjadi penyakit utama pada kelapa sawit yang menurunkan produktivitas secara signifikan. Pengembangan varietas kelapa sawit tahan penyakit BPB melalui beberapa tahapan dan evaluasi di setiap prosesnya. Tulisan ini akan menjelaskan hal-hal yang berkaitan dengan respon ketahanan dan tahapan pengembangan biomarka berbasis nukleotida untuk mendapatkan varietas kelapa sawit tahan Ganoderma. Evaluasi fenotipe dan genotipe plasma nutfah sebagai sumber material genetik, metode pemuliaan dan seleksi tanaman tahan, respon ketahanan tanaman, dan gen-gen yang terlibat dalam ketahanan penyakit menjadi komponen yang berkaitan dengan efektif dan efisien biomarka pada program pemuliaan kelapa sawit tahan penyakit BPB. Pengembangan biomarka untuk seleksi karakter unggul pada kelapa sawit dan tanaman lain juga dijelaskan pada artikel ini.

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“…The underpinning of the constant improvement of rice cultivars is the abundant phenotypic and genetic diversity that resides within domesticated populations and wild relatives. The classical approach of intentional interbreeding of closely related individuals to create new cultivars with desirable traits require great effort and long duration to produce several generations, which serves as a barrier to meet the increasing requirements of food needs and maintaining global food security (He et al 2014;Liu et al 2020). Therefore, an application of molecular plant breeding known as marker-assisted breeding, capable of discovering phenotypic variation by deploying markers linked to QTLs responsible for desirable traits, became popular.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

Peringottillam

Vasumathy

Kumar

et al. 2021

Preprint

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Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for creating opportunities to guide more realistic and applicable strategies for the sustainable management of genetically diverse rice resources. This study is a pioneering effort where GBS-SNP markers were employed to assess the tremendous genetic diversity and structure of rice landrace collections from northern Kerala. Kerala holds an immense diversity of rice landraces that encountered selection pressures of environmental heterogeneity, biotic and abiotic stresses, however competent rather provide good yields, whereby drawing the attention of the rice breeding sector. The population structure and diversity analyses separated the accessions into three distinct subpopulations with a huge amount of genetic variation within subpopulations. Nei’s genetic distance analysis confirmed the existence of strong genetic differentiation among rice landrace populations. The values of FST and Nm established the farmers’ effort to preserve the genetic purity of rice landraces despite the extensive seed exchange programs across the states of India. Moreover, this low level of gene flow among subpopulations could provide the opportunity for well-adapted combinations of genes to be established by natural selection. The clustering pattern based on SNP markers furnished sufficient knowledge in identifying rice genotypes that eliminates the likelihood of duplication among indigenous cultivars. Similar clustering patterns of genotypes revealed shared genetic characters among them. Collectively these analyses can be used to completely understand the population of rice landraces in Kerala while contributing insights toward the evolution and selective pressures underlying these unique landraces.

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Association Mapping and Development of Marker-Assisted Selection Tools for the Resistance to White Pine Blister Rust in the Alberta Limber Pine Populations

Abstract: demonstrates the successful translation and deployment of molecular genetic knowledge into specific MAS tools that can be easily applied in a selection or breeding program to efficiently screen MGR against WPBR in Alberta limber pine populations.

Cited by 7 publications

References 69 publications

Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family

Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family

Pengembangan Biomarka Untuk Seleksi Tanaman Tahan Penyakit Busuk Pangkal Batang Pada Kelapa Sawit

Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

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