Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6–18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D, respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection.

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Rapid mapping of a chlorina mutant gene cn-A1 in hexaploid wheat by bulked segregant analysis and single nucleotide polymorphism genotyping arrays

Crop and Pasture Science ◽

10.1071/cp19165 ◽

2019 ◽

Vol 70 (10) ◽

pp. 827 ◽

Cited By ~ 2

Author(s):

H. B. Jiang ◽

N. Wang ◽

J. T. Jian ◽

C. S. Wang ◽

Y. Z. Xie

Keyword(s):

Single Nucleotide Polymorphism ◽

Single Nucleotide Polymorphism Array ◽

Bulked Segregant Analysis ◽

Recessive Gene ◽

Mutant Gene ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Chlorophyll Metabolism ◽

Specific Pcr ◽

Leaf Mutant

The yellow–green leaf mutant can be exploited in photosynthesis and plant development research. A Triticum aestivum mutant with the chlorina phenotype, here called B23, was produced by treatment with the chemical mutagen sodium azide. This B23 mutant showed significantly lower chlorophyll content than wild-type Saannong33, and its chloroplast structure was abnormal. All its yield-related traits, except for the number of spikes per plant, were also significantly decreased. Genetic analysis confirmed that the mutant phenotype was controlled by a recessive gene, here designated cn-A1. Using bulked segregant analysis and the wheat 660K single nucleotide polymorphism array, the cn-A1 gene was mapped to chromosome 7AL, and 11 polymorphic markers were developed. Further analysis showed that cn-A1 was located in a 1.1-cM genetic region flanked by Kompetitive allele specific PCR (KASP) markers 660K-7A12 and 660K-7A20, which corresponded to a physical interval of 3.48 Mb in T. aestivum cv. Chinese Spring chromosome 7AL containing 47 predicted genes with high confidence. These results are expected to accelerate the process of cloning the cn-A1 gene and facilitate understanding of the mechanisms underlying chlorophyll metabolism and chloroplast development in wheat.

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Phylogenetic assessment of selected Ghanaian groundnuts, in reference to U.S. mini-core based on Kompetitive allele-specific PCR (KASP) and axiom single nucleotide polymorphism (SNP) array protocols

Journal of Agricultural Biotechnology and Sustainable Development ◽

10.5897/jabsd2018.0333 ◽

2019 ◽

Vol 11 (3) ◽

pp. 27-39

Author(s):

D. Oppong-Sekyere ◽

R. Akromah ◽

Y. Chu ◽

P. Ozias-Akins ◽

D. Gimode

Keyword(s):

Single Nucleotide Polymorphism ◽

Snp Array ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Specific Pcr ◽

Allele Specific ◽

Allele Specific Pcr

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Single-Nucleotide-Polymorphism-Specific PCR for Quantification and Discrimination of Chlamydia pneumoniae Genotypes by Use of a “Locked” Nucleic Acid

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3785-3787.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3785-3787 ◽

Cited By ~ 11

Author(s):

Jan Rupp ◽

Werner Solbach ◽

Jens Gieffers

Keyword(s):

Single Nucleotide Polymorphism ◽

Chlamydia Pneumoniae ◽

Locked Nucleic Acid ◽

Nucleotide Polymorphisms ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Specific Pcr ◽

Intraspecies Diversity

ABSTRACT Single-nucleotide polymorphisms (SNPs) are targets to discriminate intraspecies diversity of bacteria and to correlate a genotype with a potential pathotype. Quantification of polygenotypic populations supports this task for in vitro and in vivo applications. We present a novel assay capable of quantifying mixtures of two genotypes differing by only one SNP.

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TNF-α -308G/A polymorphism and susceptibility to tuberculosis in Azeri population of Iran

Genetika ◽

10.2298/gensr1603819g ◽

2016 ◽

Vol 48 (3) ◽

pp. 819-826 ◽

Cited By ~ 1

Author(s):

Sajjad Ghorghanlu ◽

Mohammad Asgharzadeh ◽

Hossein Samadi-Kafil ◽

Fatemeh Khaki-Khatibi ◽

Jalil Rashedi ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Tuberculosis Patient ◽

P Value ◽

Nucleotide Polymorphisms ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Tuberculosis Patients ◽

Specific Pcr ◽

Allele Specific ◽

And Function

Single nucleotide polymorphisms (SNPs) in cytokine genes may alter the level and function of secreted cytokine; therefore, SNPs can influence the immune response. The aim of the present study was to determine the association of TNF-? -308G/A single nucleotide polymorphism in tuberculosis patients in the Azeri population of Iran. The TNF-308G/A single nucleotide polymorphism in the promoter region was genotyped by using the allele-specific PCR method in 200 healthy controls and 124 tuberculosis patients. The distribution of allele frequencies for TNF-? -308G/A polymorphism between control and tuberculosis patient groups was not significant (P-value = 0.058, OR = 1.5). Furthermore, no statistically significant association was found between TNF-? -308G/A genotype and resistance/susceptibility to TB (P-value = 0.102). Our results suggest that TNF-? -308G/A polymorphism has no measurable effect on the development of tuberculosis in Azeri population of Iran.

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