Identification and Physical Mapping of New PCR-Based Markers Specific for the Long Arm of Rye (Secale cereale L.) Chromosome 6

Li, Meng; Tang, Zongxiang; Qiu, Ling; Wang, Yangyang; Tang, Shuyao; Fu, Shulan

doi:10.1016/j.jgg.2015.11.005

Cited by 25 publications

(37 citation statements)

References 38 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: 85%

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: 85%

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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“…For primer pairs 120, 275, 566 and 713, gDNA of CS was used as the template, and for primer pair HvT01, gDNA of barley cultivar CNSimai 1 was used as the template. The PCR reactions were carried out according to the methods described by Li et al [22] with a slight modification in that the annealing temperature was 60 °C. The PCR products derived from each of the primer pairs were cloned and then sequenced according to the methods described by Tang et al [23].…”

Section: Methodsmentioning

confidence: 99%

New Oligonucleotide Probes for ND-FISH Analysis to Identify Barley Chromosomes and to Investigate Polymorphisms of Wheat Chromosomes

Tang

Qiu

Xiao

et al. 2016

Genes

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Oligonucleotide probes that can be used for non-denaturing fluorescence in situ hybridization (ND-FISH) analysis are convenient tools for identifying chromosomes of wheat (Triticum aestivum L.) and its relatives. New oligonucleotide probes, Oligo-HvT01, Oligo-pTa71-1, Oligo-s120.1, Oligo-s120.2, Oligo-s120.3, Oligo-275.1, Oligo-275.2, Oligo-k566 and Oligo-713, were designed based on the repetitive sequences HVT01, pTa71, pTa-s120, pTa-275, pTa-k566 and pTa-713. All these probes can be used for ND-FISH analysis and some of them can be used to detect polymorphisms of wheat chromosomes. Probes Oligo-HvT01, Oligo-pTa71-1, Oligo-s120.3, Oligo-275.1, Oligo-k566 and Oligo-713 can, respectively, replace the roles of their original sequences to identify chromosomes of some barley (Hordeum vulgare ssp. vulgare) and the common wheat variety Chinese Spring. Oligo-s120.1, Oligo-s120.2 and Oligo-275.2 produced different hybridization patterns from the ones generated by their original sequences. In addition, Oligo-s120.1, Oligo-s120.2 and Oligo-s120.3, which were derived from pTa-s120, revealed different signal patterns. Likewise, Oligo-275.1 and Oligo-275.2, which were derived from pTa-275, also displayed different hybridization patterns. These results imply that differently arranged or altered structural statuses of tandem repeats might exist on different chromosome regions. These new oligonucleotide probes provide extra convenience for identifying some wheat and barley chromosomes, and they can display polymorphisms of wheat chromosomes.

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“…Li et al [15] localized 20 specific length amplified fragment (SLAF) markers to S. cereale cv. Kustral 6R Ku S in a wheat background.…”

Section: Physical Localization Of 6r Afr S Specific Markersmentioning

confidence: 99%

“…Prolific, which is currently still effective in China [13]. Chromosome 6RL derived from S. cereale cultivars German White [13], JZHM [14], and Kustro [15,16] also possess gene(s) for powdery mildew resistance. Another new powdery mildew resistance gene Pm56, which originated from Chinese native rye cultivar (cv.)…”

Section: Introductionmentioning

confidence: 99%

Molecular dissection of Secale africanum chromosome 6Rafr in wheat enabled localization of genes for resistance to powdery mildew and stripe rust

et al. 2020

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Background: Introgression of chromatin from Secale species into common wheat has for decades been a successful strategy for controlling the wheat diseases. The wild Secale species, Secale africanum Stapf., is a valuable source for resistance to foliar disease of wheat. A wheat-S. africanum chromosome 6R afr substitution line displayed resistance to both powdery mildew and stripe rust at the adult-plant stage. Results: Wheat-S. africanum chromosome 6R afr deletion and translocation lines were produced and identified by sequential non-denaturing fluorescence in situ hybridization (ND-FISH) using multiple Oligo-based probes. Different ND-FISH patterns were observed between S. cereale 6R and S. africanum 6R afr. With reference to the physical map of the draft genome sequence of rye inbred line Lo7, a comprehensive PCR marker analysis indicated that insertions and deletions had occurred by random exchange between chromosomes 6R and 6R afr. A survey of the wheat-S. africanum 6R afr lines for disease resistance indicated that a powdery mildew resistance gene(s) was present on the long arm of 6R afr at FL0.85-1.00, and that a stripe rust resistance gene(s) was located in the terminal region of 6R afr S at FL0.95-1.00. The wheat-S. africanum 6R afr introgression lines also displayed superior agronomic traits, indicating that the chromosome 6R afr may have little linkage drag in the wheat background. Conclusions: The combination of molecular and cytogenetic methods allowed to precisely identify the chromosome rearrangements in wheat-S. africanum 6R afr substitution, deletion and translocation lines, and compare the structural difference between chromosomes 6R and 6R afr. The wheat-S. africanum 6R afr lines containing gene(s) for powdery mildew and stripe rust resistance could be used as novel germplasm for wheat breeding by chromosome engineering.

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Identification and Physical Mapping of New PCR-Based Markers Specific for the Long Arm of Rye (Secale cereale L.) Chromosome 6

Cited by 25 publications

References 38 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.)

New Oligonucleotide Probes for ND-FISH Analysis to Identify Barley Chromosomes and to Investigate Polymorphisms of Wheat Chromosomes

Molecular dissection of Secale africanum chromosome 6Rafr in wheat enabled localization of genes for resistance to powdery mildew and stripe rust

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