Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology

Liu, Liqin; Luo, Qiaoling; Teng, Wan; Li, Bin; Li, Hongwei; Li, Yiwen; Li, Zhensheng; Zheng, Qi

doi:10.1007/s00425-018-2845-6

Cited by 37 publications

(38 citation statements)

References 41 publications

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“…SLAF-seq is an efficient next-generation sequencing method that can rapidly obtain a large amount of high-quality enzymatic fragments [46]. Therefore, SLAF-seq can be effectively applied to development of alien chromosome specific markers [47,48]. In the present study, 418 markers derived from 1546 SLAFs were assigned to rye chromosomes, and finally 404 markers were assigned to universal chromosome arms, with a success rate of up to 26%.…”

Section: Discussionmentioning

confidence: 84%

Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

et al. 2020

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Background: Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will facilitate the transfer and utilization of elite genes derived from rye in wheat breeding. Results: In the present study, five rye cultivars including Imperial, German White, Jingzhouheimai, Baili and Guyuan were sequenced by specific-locus amplified fragment sequencing (SLAF-seq) to develop large-scale rye-specific markers. Based on SLAF-seq and bioinformatics analyses, a total of 404 universal PCR-based and a whole set of Kompetitive allele-specific PCR (KASP) markers specific for the 14 individual rye chromosome arms were developed and validated. Additionally, two KASP markers specific for 1RS and 2RL were successfully applied in the detection of 1RS translocations in a natural population and 2RL chromosome arms in wheat-rye derived progenies that conferred adult resistance to powdery mildew. Conclusion: The 404 PCR-based markers and 14 KASP markers specific for the 14 individual rye chromosome arms developed in this study can enrich the marker densities for gene mapping and accelerate the utilization of rye-derived genes in wheat improvement. Especially, the KASP markers achieved high-throughput and accurate detection of rye chromatin in wheat background, thus can be efficiently used in marker-assisted selection (MAS). Besides, the strategy of rye-specific PCR-based markers converting into KASP markers was high-efficient and low-cost, which will facilitate the tracing of alien genes, and can also be referred for other wheat relatives.

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Section: Discussionmentioning

confidence: 84%

Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

et al. 2020

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“…Primers for these sequences were developed using Primer3Plus (http://www.primer3plus.com/). After PCR, specific bands were detected on a 1% agarose gel (Liu et al, 2018b). A Venn diagram and an Upset plot were constructed using TBtools (http://mdr.tbtools.org/).…”

Section: Molecular Marker Developmentmentioning

confidence: 99%

“…Nonetheless, existing markers do not meet the demand for Th. ponticum chromatin detection (Liu et al, 2018b), and it is therefore particularly important to develop chromosome-specific markers for the detection of Th. ponticum genetic materials.…”

Section: Introductionmentioning

confidence: 99%

Cytogenetic Analysis and Molecular Marker Development for a New Wheat–Thinopyrum ponticum 1Js (1D) Disomic Substitution Line With Resistance to Stripe Rust and Powdery Mildew

et al. 2020

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Thinopyrum ponticum (2n = 10x = 70), a member of the tertiary gene pool of wheat (Triticum aestivum L.), harbors many biotic and abiotic stress resistance genes. CH10A5, a novel disomic substitution line from a cross of T. aestivum cv. 7182 and Th. ponticum, was characterized by cytogenetic identification, in situ hybridization, molecular marker analysis, and morphological investigation of agronomic traits and disease resistance. Cytological observations showed that CH10A5 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genome in situ hybridization (GISH) analysis indicated that two of its chromosomes came from the J s genome of Th. ponticum, and wheat 15K array mapping and fluorescence in situ hybridization (FISH) revealed that chromosome 1D was absent from CH10A5. Polymorphic analysis of molecular markers indicated that the pair of alien chromosomes belonged to homoeologous group one, designated as 1J s. Thus, CH10A5 was a wheat-Th. ponticum 1J s (1D) disomic substitution line. Field disease resistance trials demonstrated that the introduced Th. ponticum chromosome 1J s was probably responsible for resistance to both stripe rust and powdery mildew at the adult stage. Based on specific-locus amplified fragment sequencing (SLAF-seq), 507 STS molecular markers were developed to distinguish chromosome 1J s genetic material from that of wheat. Of these, 49 STS markers could be used to specifically identify the genetic material of Th. ponticum. CH10A5 will increase the resistance gene diversity of wheat breeding materials, and the markers developed here will permit further tracing of heterosomal chromosome fragments in the future.

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“…ponticum addition, substitution and translocation lines [ 9 , 10 ]. Fluorescence in situ hybridization (FISH), which uses repetitive DNA clones or oligonucleotides as a probe, is an extremely useful method for identifying chromosomes within a species or detecting intergenomic chromosome rearrangements in a polyploid species [ 5 , 15 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

Molecular cytogenetic identification of three rust-resistant wheat-Thinopyrum ponticum partial amphiploids

et al. 2018

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BackgroundThinopyrum ponticum (2n = 10× = 70, JSJSJSJSJJJJJJ) is an important wild perennial Triticeae species that has a unique gene pool with many desirable traits for common wheat. The partial amphiploids derived from wheat-Th. ponticum set up a bridge for transferring valuable genes from Th. ponticum into common wheat.ResultsIn this study, genomic in situ hybridization (GISH), multicolor GISH (mcGISH) and fluorescence in situ hybridization (FISH) were used to analyze the genomic constitution of SN0389, SN0398 and SN0406, three octoploid accessions with good resistance to rust. The results demonstrated that the three octoploids possessed 42 wheat chromosomes, while SN0389 contained 12 Th. ponticum chromosomes and SN0398 and SN0406 contained 14 Th. ponticum chromosomes. The genomic constitution of SN0389 was 42 W + 12JS, and for SN0398 and SN0406 it was 42 W + 12JS + 2 J. Chromosomal variation was found in chromosomes 1A, 3A, 6A, 2B, 5B, 6B, 7B, 1D and 5D of SN0389, SN0398 and SN0406 based on the FISH and McGISH pattern. A resistance evaluation showed that SN0389, SN0398 and SN0406 possessed good resistance to stripe and leaf rust at the seedling stage and adult-plant stage.ConclusionsThe results indicated that these wheat-Th. ponticum partial amphiploids are new resistant germplasms for wheat improvement.Electronic supplementary materialThe online version of this article (10.1186/s13039-018-0378-0) contains supplementary material, which is available to authorized users.

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Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology

Cited by 37 publications

References 41 publications

Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

Cytogenetic Analysis and Molecular Marker Development for a New Wheat–Thinopyrum ponticum 1Js (1D) Disomic Substitution Line With Resistance to Stripe Rust and Powdery Mildew

Molecular cytogenetic identification of three rust-resistant wheat-Thinopyrum ponticum partial amphiploids

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