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.

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.

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.

scholarly journals Linkage and Association Mapping Identifies Loci and Develops Kompetitive Allele Specific PCR Markers for Improving Wheat Grain Protein Content

2021 ◽  
Author(s):  
Peng Jiang ◽  
Peng Zhang ◽  
Lei Wu ◽  
Yi He ◽  
Chang Li ◽  
...  
Keyword(s):  
Association Mapping ◽  
Protein Content ◽  
Large Scale ◽  
Grain Protein Content ◽  
Grain Protein ◽  
Wheat Grain ◽  
Breeding Lines ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

Abstract Wheat grain protein content (GPC) is an important quality indicator. The GPC of wheat grown in the middle and lower reaches of the Yangtze River is often low. Marker-assisted selection (MAS) is an effective tool for improving quantitative traits; however, except Gpc-B1, most markers have not been effectively applied in GPC improvement, although many related loci have been identified. Linkage analysis using a recombinant inbred line population from the cross of core parents of Ningmai 9 and Yangmai 158 and association mapping using the local cultivated varieties were performed and nine candidate intervals were identified. The appropriate kompetitive allele specific PCR (KASP) markers associated with GPC were successfully developed and applied in 1163 F4 breeding lines. Three markers, Kgpc-2B, Kgpc-2D, and Kgpc-4A, were validated to be significantly related to GPC by large-scale association mapping, and they were combined to achieve the highest efficiency to enhance GPC. We applied these markers in 164 F6 breeding lines and obtained 15 lines with high GPC, indicating their high selective efficiency. Further, strategies for gene exploration in the three significant intervals were proposed. These results were expected to provide a novel route for improving GPC in wheat quality breeding.

Development of a kompetitive allele-specific PCR marker for selection of the mutatedWx-D1dallele in wheat breeding

2017 ◽  
Vol 136 (4) ◽  
pp. 460-466 ◽  
Author(s):  
Xin Yi ◽  
Zhengning Jiang ◽  
Wenjing Hu ◽  
Yun Zhao ◽  
Tongde Bie ◽  
...  
Keyword(s):  
Wheat Breeding ◽  
Pcr Marker ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr ◽  
Selection Of

scholarly journals Cost-Effective and Time-Efficient Molecular Assisted Selection for Ppv Resistance in Apricot Based on ParPMC2 Allele-Specific PCR

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1292 ◽  
Author(s):  
Ángela Polo-Oltra ◽  
Carlos Romero ◽  
Inmaculada López ◽  
María Luisa Badenes ◽  
Elena Zuriaga
Keyword(s):  
Woody Species ◽  
Cost Effective ◽  
Prunus Armeniaca ◽  
Host Susceptibility ◽  
Limiting Factor ◽  
Plum Pox Virus ◽  
Breeding Programs ◽  
Specific Pcr ◽  
Allele Specific ◽  
Ppv Resistance

Plum pox virus (PPV) is the most important limiting factor for apricot (Prunus armeniaca L.) production worldwide, and development of resistant cultivars has been proven to be the best solution in the long-term. However, just like in other woody species, apricot breeding is highly time and space demanding, and this is particularly true for PPV resistance phenotyping. Therefore, marker-assisted selection (MAS) may be very helpful to speed up breeding programs. Tightly linked ParPMC1 and ParPMC2, meprin and TRAF-C homology (MATH)-domain-containing genes have been proposed as host susceptibility genes required for PPV infection. Contribution of additional genes to PPV resistance cannot be discarded, but all available studies undoubtedly show a strong correlation between ParPMC2-resistant alleles (ParPMC2res) and PPV resistance. The ParPMC2res allele was shown to carry a 5-bp deletion (ParPMC2-del) within the second exon that has been characterized as a molecular marker suitable for MAS (PMC2). Based on this finding, we propose here a method for PPV resistance selection in apricot by combining high-throughput DNA extraction of 384 samples in 2 working days and the allele-specific genotyping of PMC2 on agarose gel. Moreover, the PMC2 genotype has been determined by PCR or by using whole-genome sequences (WGS) in 175 apricot accessions. These results were complemented with phenotypic and/or genotypic data available in the literature to reach a total of 325 apricot accessions. As a whole, we conclude that this is a time-efficient, cost-effective and straightforward method for PPV resistance screening that can be highly useful for apricot breeding programs.

Diagnostic DNA markers for cereal cyst nematode resistance in bread wheat

2001 ◽  
Vol 52 (12) ◽  
pp. 1367 ◽  
Author(s):  
F. C. Ogbonnaya ◽  
N. C. Subrahmanyam ◽  
O. Moullet ◽  
J. de Majnik ◽  
H. A. Eagles ◽  
...  
Keyword(s):  
Nematode Resistance ◽  
Wheat Breeding ◽  
Primary Objective ◽  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Aegilops Ventricosa ◽  
Breeding Lines ◽  
Marker Selection ◽  
Efficiency Of Selection ◽  
Wheat Lines

The development of cultivars resistant to cereal cyst nematode (CCN) is a primary objective in wheat breeding in the southern wheatbelt of Australia. Nine CCN resistance genes have been identified in wheat and its relatives, some of which confer resistance to the Australian pathotype of CCN (Ha13). Cultivars released in Australia with CCN resistance carry either the Cre1 or CreF gene, with the Cre3 gene present in advanced breeding lines. The biological assay for CCN resistance screening in wheat is time-consuming, not reliable on a single-plant basis, and prone to inconsistencies, thus reducing the efficiency of selection amongst breeding lines. Using gene sequences initially isolated from the Cre3 locus, a DNA-based marker selection system was developed and applied to unambiguously identify wheat lines carrying resistance alleles at theCre1 and/or Cre3 loci in breeding populations derived from diverse genetic backgrounds. Homologues of sequences from the Cre3 locus, located elsewhere in the wheat genome, can also be used to select wheat lines with a newly identified CCN resistance gene (Cre6) introgressed from Aegilops ventricosa. Application of these markers has become an integral part of the southern Australian breeding programs.

scholarly journals Increased Predictive Accuracy of Multi-Environment Genomic Prediction Model for Yield and Related Traits in Spring Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Vipin Tomar ◽  
Daljit Singh ◽  
Guriqbal Singh Dhillon ◽  
Yong Suk Chung ◽  
Jesse Poland ◽  
...  
Keyword(s):  
Complex Traits ◽  
Predictive Accuracy ◽  
Model Performance ◽  
Environmental Variation ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Environmental Variance ◽  
Breeding Programs ◽  
Breeding Lines ◽  
The Impact

Genomic selection (GS) has the potential to improve the selection gain for complex traits in crop breeding programs from resource-poor countries. The GS model performance in multi-environment (ME) trials was assessed for 141 advanced breeding lines under four field environments via cross-predictions. We compared prediction accuracy (PA) of two GS models with or without accounting for the environmental variation on four quantitative traits of significant importance, i.e., grain yield (GRYLD), thousand-grain weight, days to heading, and days to maturity, under North and Central Indian conditions. For each trait, we generated PA using the following two different ME cross-validation (CV) schemes representing actual breeding scenarios: (1) predicting untested lines in tested environments through the ME model (ME_CV1) and (2) predicting tested lines in untested environments through the ME model (ME_CV2). The ME predictions were compared with the baseline single-environment (SE) GS model (SE_CV1) representing a breeding scenario, where relationships and interactions are not leveraged across environments. Our results suggested that the ME models provide a clear advantage over SE models in terms of robust trait predictions. Both ME models provided 2–3 times higher prediction accuracies for all four traits across the four tested environments, highlighting the importance of accounting environmental variance in GS models. While the improvement in PA from SE to ME models was significant, the CV1 and CV2 schemes did not show any clear differences within ME, indicating the ME model was able to predict the untested environments and lines equally well. Overall, our results provide an important insight into the impact of environmental variation on GS in smaller breeding programs where these programs can potentially increase the rate of genetic gain by leveraging the ME wheat breeding trials.

An adaptation analysis of Australian and CIMMYT/ICARDA wheat germplasm in Australian production environments

2000 ◽  
Vol 51 (7) ◽  
pp. 903 ◽  
Author(s):  
S. Sivapalan ◽  
L. O'Brien ◽  
G. Ortiz-Ferrara ◽  
G. J. Hollamby ◽  
I. Barclay ◽  
...  
Keyword(s):  
Western Australia ◽  
Wheat Breeding ◽  
Yield Data ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Mediterranean Environments ◽  
Supplementary Irrigation ◽  
Production Environments ◽  
Wide Adaptation ◽  
The University

An adaptation analysis was conducted in an attempt to identify adapted germplasm and potential indicator or probe varieties that could be used for more efficient germplasm introduction and evaluation. A set of 39 advanced wheat breeding lines and named varieties from Australian breeding programs and 10 from the CIMMYT/ICARDA programs were tested using 20 environments across the Australian wheatbelt during a period of 3 years. AMMI analysis and classification analysis were performed on grain yield data. Five groups of genotypes with similar patterns in performance within each group were identified, mostly reflecting their origin and pedigree. Most of the genotypes from the CIMMYT/ICARDA programs clustered together as did most of those from the University of Adelaide and Agriculture Western Australia breeding programs. Four groups of environments with similar trends in discriminating genotypes within each group were identified. There was a clear discrimination between subtropical and Mediterranean environments. Subtropical environments with supplementary irrigation showed similar patterns to Mediterranean environments. Basic differences in adaptation and phenotypic stability among genotypes from the CIMMYT/ICARDA programs in relation to genotypes from several breeding programs in Australia were identified. CIMMYT/ICARDA genotypes such as Attila, Nesser, Pfau/Seri//Bow, Genaro 81, and Maya/Nac performed well, especially in subtropical environments. The Australian varieties Hartog and Vulcan showed similar performance and could be used as indicator varieties for assessing introduced germplasm for subtropical regions. University of Adelaide developed genotypes Trident, Spear, Excalibur, and RAC 655, along with the Agriculture Western Australia genotypes Tammin and 82Y:1186, showed wide adaptation to all environments and could be used as indicator varieties for wide adaptation. Similarly, genotypes such as BT Schomburgk, Pelsart, and Sunvale could be used as indicator varieties for the other genotype groups. The results of this study can serve as a basis for identification and introduction of germplasm from the CIMMYT/ICARDA programs for various Australian production environments. It has also provided an understanding of the pattern of discrimination of genotypes across each region of the Australian wheatbelt.

scholarly journals Molecular Markers and a Quality Trait Evaluation for Assessing the Genetic Diversity of Avocado Landraces from China

Agriculture ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 102 ◽  
Author(s):  
Yuanzheng Liu ◽  
Yu Ge ◽  
Rulin Zhan ◽  
Xinge Lin ◽  
Xiaoping Zang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Principal Component ◽  
Molecular Characteristics ◽  
Quality Trait ◽  
Sufficient Information ◽  
Flavonoid Content ◽  
Specific Pcr ◽  
Allele Specific ◽  
Artificial Flow ◽  
Allele Specific Pcr

Avocado is an economically important crop that is widely cultivated in the tropical and subtropical regions of China. However, there is a lack of sufficient information regarding the racial origins and genetic diversification of native avocado germplasm. On the basis of a race-specific kompetitive allele-specific PCR genotyping analysis, the 56 avocado accessions examined in this study were classified as complex hybrids, namely Guatemalan × Mexican × West Indian hybrids. The genetic relationships among the avocado accessions were assessed based on a quality trait evaluation and molecular characterization. The total flavonoid content was relatively useful for differentiating between native avocado accessions. A cluster analysis as well as principal component and coordinate analyses of quality traits and molecular characteristics differentiated the avocado accessions, but not according to geographical origins. Thus, the artificial flow of avocado germplasm or seed exchanges among farmers within specific regions may have contributed to the similar genetic backgrounds of avocado germplasm from different collections.

scholarly journals Identification of Accession-Specific Variants and Development of KASP Markers for Assessing the Genetic Makeup of Crop Seeds

2021 ◽  
Author(s):  
Seongmin Hong ◽  
Su Ryun Choi ◽  
Jihyeong Kim ◽  
Young-Min Jeong ◽  
Suk-Yoon Kwon ◽  
...  
Keyword(s):  
Core Collection ◽  
F1 Hybrids ◽  
Genetic Purity ◽  
Breeding Lines ◽  
Seed Testing ◽  
Specific Pcr ◽  
Allele Specific ◽  
Genetic Makeup ◽  
Allele Specific Pcr ◽  
Kasp Markers

Abstract Background Most crop seeds are F1 hybrids. Seed providers and plant breeders must be confident that the seed supplied to growers is of known, and uniform, genetic makeup. This requires maintenance of pure genotypes of the parental lines and testing to ensure the genetic purity of the F1 seed. Traditionally, seed testing for purity was done with a grow-out test (GOT) in the field, but these tests are time consuming and costly. Seed testing with molecular markers was introduced as a replacement for GOT early in the last decade. Recently, Kompetitive allele specific PCR (KASP) markers are promising tools for genetic testing of seeds. However, the markers available at that time could be inaccurate and could be used with only a small number of accessions or varieties due to the limited genetic information and reference genomes available. Results Here, we identified 4,925,742 SNPs in 50 accessions of the Brasscia rapa core collection. Furthermore, the total 2,925 SNPs were selected as accession-specific SNPs, considering properties of flanking region harboring accession-specific SNPs and genic region conservation among accessions by NGS analysis. In total, 100 accession-specific markers were developed as accession-specific KASP markers. Based on the results of our validation experiments, the accession-specific markers successfully distinguish individuals from the mixed population including 50 target accessions from B. rapa core collection and outgroup. Conclusions This study provides efficient methods for developing KASP markers to distinguish individuals from the mixture comprised of breeding lines and germplasms from the resequencing data of Chinese cabbage (Brassica rapa spp. pekinensis).

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