A linked SNP marker to genotype Fr-B2 in wheat

2018 ◽  
Vol 69 (9) ◽  
pp. 859
Author(s):  
H. A. Eagles ◽  
J. Hyles ◽  
Jayne Wilson ◽  
Karen Cane ◽  
K. L. Forrest ◽  
...  
Keyword(s):  
Triticum Aestivum L ◽  
Frost Tolerance ◽  
Large Deletion ◽  
Wheat Breeding ◽  
Snp Markers ◽  
Breeding Lines ◽  
Specific Pcr ◽  
Chromosome 5B ◽  
Allele Specific ◽  
Specific Pcr Assay

Fr-B2 is a complex locus on chromosome 5B that affects frost tolerance, days to heading, grain yield and probably other traits of commercial importance in wheat (Triticum aestivum L.). It interacts epistatically with other major genes, especially VRN1. There are two known alleles of Fr-B2: an intact, wild-type allele, and an allele with a large deletion. Published methods for identifying these alleles are slow and expensive, making the development of a high-throughput, co-dominant SNP (single-nucleotide polymorphism) marker highly desirable, especially for commercial wheat breeding. A diverse panel of cultivars and breeding lines was characterised for SNPs and alleles of Fr-B2. Four SNP markers co-segregated as a haplotype block with Fr-B2 across unrelated cultivars and related backcrosses differing for alleles of Fr-B2. A robust KASP (Kompetitive allele-specific PCR) assay was developed for one of the SNPs, KASP_IWB26333, which should facilitate the inclusion of Fr-B2 on genotyping platforms for breeding and research.

Development of robust PCR-based DNA markers for each homoeo-allele of granule-bound starch synthase and their application in wheat breeding programs

2001 ◽  
Vol 52 (12) ◽  
pp. 1409 ◽  
Author(s):  
A. McLauchlan ◽  
F. C. Ogbonnaya ◽  
B. Hollingsworth ◽  
M. Carter ◽  
K. R. Gale ◽  
...  
Keyword(s):  
Wheat Breeding ◽  
Starch Synthase ◽  
Quality Trait ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Starch Quality ◽  
Specific Pcr ◽  
Marker Selection ◽  
Allele Specific ◽  
Granule Bound Starch Synthase

The absence of expression of the granule-bound starch synthase I (GBSSI) allele from chromosome 4A of wheat is associated with improved starch quality for making Udon noodles. Several PCR-based methods for the analysis of GBSS alleles have been developed for application in wheat. A widely applied approach has involved a simple PCR followed by electrophoretic separation of DNA products on agarose gels. The PCR amplifies one band from each of the loci on chromosomes 4A (Wx-B1), 7A (Wx-A1), and 7D (Wx-D1), and the band from the Wx-B1 locus is diagnostic for the occurrence of the null Wx-B1 allele that is associated with improved starch quality. The reliable detection of the null Wx-B1 allele has been important in identifying wheat breeding lines. Allele-specific PCR has also been used to successfully detect the occurrence of the null Wx-B1 allele. In the present paper the various protocols were evaluated by testing a segregating double haploid population from a cross between Cranbrook and Halberd and the tests gave good agreement in different laboratories. The application of the DNAbased tests applied in wheat breeding programs provides one of the first examples of a molecular marker selection for a grain quality trait being successfully applied in an Australian wheat breeding program.

scholarly journals Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengjie Chen ◽  
Dengguo Tang ◽  
Jixing Ni ◽  
Peng Li ◽  
Le Wang ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Inbred Lines ◽  
Average Density ◽  
Snp Markers ◽  
Data Sets ◽  
Rna Seq ◽  
Specific Pcr ◽  
Maize Inbred Lines ◽  
Allele Specific ◽  
Allele Specific Pcr

Abstract Background Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

scholarly journals Fine mapping of Brassica napus blackleg resistance gene Rlm1 through bulked segregant RNA sequencing

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Fuyou Fu ◽  
Xunjia Liu ◽  
Rui Wang ◽  
Chun Zhai ◽  
Gary Peng ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Resistance Gene ◽  
Rna Sequencing ◽  
Catalytic Domain ◽  
Leptosphaeria Maculans ◽  
Snp Markers ◽  
Specific Pcr ◽  
Dual Specificity ◽  
Kinase Catalytic Domain ◽  
Allele Specific

Abstract The fungal pathogen Leptosphaeria maculans causes blackleg disease on canola and rapeseed (Brassica napus) in many parts of the world. A B. napus cultivar, ‘Quinta’, has been widely used for the classification of L. maculans into pathogenicity groups. In this study, we confirmed the presence of Rlm1 in a DH line (DH24288) derived from B. napus cultivar ‘Quinta’. Rlm1 was located on chromosome A07, between 13.07 to 22.11 Mb, using a BC1 population made from crosses of F1 plants of DH16516 (a susceptible line) x DH24288 with bulked segregant RNA Sequencing (BSR-Seq). Rlm1 was further fine mapped in a 100 kb region from 19.92 to 20.03 Mb in the BC1 population consisting of 1247 plants and a F2 population consisting of 3000 plants using SNP markers identified from BSR-Seq through Kompetitive Allele-Specific PCR (KASP). A potential resistance gene, BnA07G27460D, was identified in this Rlm1 region. BnA07G27460D encodes a serine/threonine dual specificity protein kinase, catalytic domain and is homologous to STN7 in predicted genes of B. rapa and B. oleracea, and A. thaliana. Robust SNP markers associated with Rlm1 were developed, which can assist in introgression of Rlm1 and confirm the presence of Rlm1 gene in canola breeding programs.

scholarly journals WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 275 ◽  
Author(s):  
Pongsakorn Wangkumhang ◽  
Kridsadakorn Chaichoompu ◽  
Chumpol Ngamphiw ◽  
Uttapong Ruangrit ◽  
Juntima Chanprasert ◽  
...  
Keyword(s):  
Pcr Assay ◽  
Web Based ◽  
Specific Pcr ◽  
Allele Specific ◽  
Specific Pcr Assay ◽  
Allele Specific Pcr

scholarly journals Identification of prospective sources of agronomically-valuable traits of bread wheat (Triticum aestivum L.) among breeding lines in the condition of Forest-Steppe of Ukraine

2020 ◽  
Vol 10 (5) ◽  
pp. 253-258
Author(s):  
S.O. Kovalchuk ◽  
S.I. Voloschuk ◽  
N.A. Kozub
Keyword(s):  
Bread Wheat ◽  
Seed Proteins ◽  
Seed Storage ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Brown Rust ◽  
Forest Steppe ◽  
Breeding Lines ◽  
Biochemical Compositions ◽  
Moderate Resistance

The aim of work was the estimation of valuable traits of bread wheat breeding lines, obtained from interspecies crosses with wild Aegilops and Triticum species growing in a condition of the Forest-Steppe of Ukraine. We used the seed proteins electrophoresis in PAAG for confirmation of the presence of rye seed storage components in the wheat parental lines genomes. The biochemical compositions of seeds had determined by the infrared spectroscopy method. As a result of researching from the set of 600 breeding lines were selected best lines with increased grain yield from 1 m2, with high protein content in grain, disease resistance, and winter hardiness significantly exceeded the standard variety Polesskaya-90. All lines have high and moderate resistance against diseases: Powdery Mildew, Brown Rust, Septoria Blotch. Based on obtained data had selected breeding lines, which were promising sources of single and complex agronomically valuable traits for bread wheat breeding and genetic researches.

scholarly journals Genetic Architecture of End-use Quality Traits in Soft White Winter Wheat

2021 ◽  
Author(s):  
Meriem Aoun ◽  
Arron H. Carter ◽  
Craig F. Morris ◽  
Alecia M. Kiszonas
Keyword(s):  
Winter Wheat ◽  
Genetic Architecture ◽  
The United States ◽  
Wheat Breeding ◽  
Snp Markers ◽  
Complex Nature ◽  
Quality Trait ◽  
Quality Traits ◽  
Breeding Lines ◽  
End Use

Abstract Background:Genetic improvement of end-use quality is an important objective in wheat breeding programs to meet the requirements of grain markets, millers, and bakers. However, end-use quality phenotyping is expensive and laborious thus, testing is often delayed until advanced generations. To better understand the underlying genetic architecture of end-use quality traits, we investigated the phenotypic and genotypic structure of 14 end-use quality traits in 672 advanced soft white winter wheat breeding lines and cultivars adapted to the Pacific Northwest region of the United States.Results:This collection of germplasm had continuous distributions for the 14 end-use quality traits with industrially significant differences for all traits. The breeding lines and cultivars were genotyped using genotyping-by-sequencing and 40,518 SNP markers were used for association mapping (GWAS). The GWAS identified 178 marker-trait associations (MTAs) distributed across all wheat chromosomes. A total of 40 MTAs were positioned within genomic regions of previously discovered end-use quality genes/QTL. Among the identified MTAs, 12 markers had large effects and thus could be considered in the larger scheme of selecting and fixing favorable alleles in breeding for end-use quality in soft white wheat germplasm. We also identified 15 loci (two of them with large effects) that can be used for simultaneous breeding of more than a single end-use quality trait. The results highlight the complex nature of the genetic architecture of end‑use quality, and the challenges of simultaneously selecting favorable genotypes for a large number of traits. This study also illustrates that some end-use quality traits were mainly controlled by a larger number of small-effect loci and may be more amenable to alternate selection strategies such as genomic selection.Conclusions:In conclusion, a breeder may be faced with the dilemma of balancing genotypic selection in early generation(s) versus costly phenotyping later on.

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