Allelic variation for alpha-Glucan Water Dikinase is associated with starch phosphate content in tetraploid potato

Abstract Key message Association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content which was verified in diploid and tetraploid potato mapping populations. Abstract Potatoes are grown for various purposes like French fries, table potatoes, crisps and for their starch. One of the most important aspects of potato starch is that it contains a high amount of phosphate ester groups which are considered to be important for providing improved functionalization after derivatization processes. Little is known about the variation in phosphate content as such in different potato varieties and thus we studied the genetic diversity for this trait. From other studies it was clear that the phosphate content is controlled by a quantitative trait locus (QTL) underlying the candidate gene α-Glucan Water Dikinase (StGWD) on chromosome 5. We performed direct amplicon sequencing of this gene by Sanger sequencing. Sequences of two StGWD amplicons from a global collection of 398 commercial cultivars and progenitor lines were used to identify 16 different haplotypes. By assigning tag SNPs to these haplotypes, each of the four alleles present in a cultivar could be deduced and linked to a phosphate content. A high value for intra-individual heterozygosity was observed (Ho = 0.765). The average number of different haplotypes per individual (Ai) was 3.1. Pedigree analysis confirmed that the haplotypes are identical-by-descent (IBD) and offered insight in the breeding history of elite potato germplasm. Haplotypes originating from introgression of wild potato accessions carrying resistance genes could be traced. Furthermore, association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content varying from 12 nmol PO4/mg starch to 38 nmol PO4/mg starch. These allele effects were verified in diploid and tetraploid mapping populations and offer possibilities to breed and select for this trait.

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Genetic diversity and selection of genotypes to enhance Zn and Fe content in common bean

Canadian Journal of Plant Science ◽

10.4141/cjps09096 ◽

2010 ◽

Vol 90 (1) ◽

pp. 49-60 ◽

Cited By ~ 13

Author(s):

Z I Talukder ◽

E Anderson ◽

P N Miklas ◽

M W Blair ◽

J Osorno ◽

...

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Allelic Variation ◽

Gene Pools ◽

Gene Sequences ◽

Mineral Contents ◽

Discriminatory Ability ◽

Fe Content ◽

Mapping Populations ◽

Selection Of

Common bean (Phaseolus vulgaris L.) is an important source of dietary protein and minerals worldwide. Genes conditioning variability for mineral contents are not clearly understood. Our ultimate goal is to identify genes conditioning genetic variation for Zn and Fe content. To establish mapping populations for this objective, we tested mineral content of 29 common bean genotypes. Chemical analyses revealed significant genetic variability for seed Zn and Fe contents among the genotypes. Genetic diversity was evaluated with 49 primer pairs, of which 23 were simple sequence repeats (SSR), 16 were developed from tentative consensus (TC) sequences, and 10 were generated from common bean NBS-LRR gene sequences. The discriminatory ability of molecular markers for identifying allelic variation among genotypes was estimated by polymorphism information content (PIC) and the genetic diversity was measured from genetic similarities between genotypes. Primers developed from NBS-LRR gene sequences were highly polymorphic in both PIC values and number of alleles (0.82 and 5.3), followed by SSRs (0.56 and 3.0), and markers developed from TC (0.39 and 2.0). genetic similarity values between genotypes ranged from 14.0 (JaloEEP558 and DOR364) to 91.4 (MIB152 and MIB465). Cluster analysis clearly discriminated the genotypes into Mesoamerican and Andean gene pools. Common bean genotypes were selected to include in crossing to enhance seed Zn and Fe content based on genetic diversity and seed mineral contents of the genotypes. Key words: Common bean, genetic diversity, mineral nutrients, breeding

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Identification of a compound heterozygote in LYST gene: a case report on Chediak-Higashi syndrome

BMC Medical Genetics ◽

10.1186/s12881-019-0922-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Yinsen Song ◽

Zhengping Dong ◽

Shuying Luo ◽

Junmei Yang ◽

Yuebing Lu ◽

...

Keyword(s):

Missense Mutation ◽

Genetic Diseases ◽

Amplicon Sequencing ◽

Bone Marrow Examination ◽

Pathogenic Mutation ◽

Pedigree Analysis ◽

Compound Heterozygote ◽

Loss Of Function ◽

Causative Gene ◽

Chediak Higashi Syndrome

Abstract Background Chediak-Higashi Syndrome (CHS) is a rare autosomal recessive disease caused by loss of function of the lysosomal trafficking regulator protein. The causative gene LYST/CHS1 was cloned and identified in 1996, which showed significant homology to other species such as bovine and mouse. To date, 74 pathogenic or likely pathogenic mutations had been reported. Case presentation Here we describe a compound heterozygote in LYST gene, which was identified in a 4-year-old female patient. The patient showed skin hypopigmentation, sensitivity to light, mild splenomegaly and reduction of platelets in clinical examination. Giant intracytoplasmic inclusions were observed in the bone marrow examination, suggesting the diagnosis of CHS. Amplicon sequencing was performed to detect pathogenic mutation in LYST gene. The result was confirmed by two-generation pedigree analysis base on sanger sequencing. Conclusion A compound heterozygote in LYST gene, consisting of a missense mutation c.5719A > G and an intron mutation c.4863-4G > A, was identified from the patient by using amplicon sequencing. The missense mutation is reported for the first time. Two-generation pedigree analysis showed these two mutations were inherited from the patient’s parents, respectively. Our result demonstrated that amplicon sequencing has great potential for accelerating and improving the diagnosis of rare genetic diseases.

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NIR Spectroscopy and Partial Least Squares Regression for the Determination of Phosphate Content and Viscosity Behaviour of Potato Starch

Journal of Near Infrared Spectroscopy ◽

10.1255/jnirs.300 ◽

2001 ◽

Vol 9 (2) ◽

pp. 133-139 ◽

Cited By ~ 8

Author(s):

L.G. Thygesen ◽

S.B. Engelsen ◽

M.H. Madsen ◽

O.B. Sørensen

Keyword(s):

Least Squares ◽

Partial Least Squares ◽

Partial Least Squares Regression ◽

Near Infrared ◽

Potato Starch ◽

Nir Spectroscopy ◽

Peak Time ◽

Phosphate Content ◽

Least Squares Regression ◽

Data Prediction

A set of 97 potato starch samples with a phosphate content corresponding to a phosphorus content between 0.029 and 0.11 g per 100 g dry matter was analysed using a Rapid Visco Analyzer (RVA) and near infrared (NIR) spectroscopy, (700–2498 nm). NIR-based prediction of phosphate content was possible with a root mean square error of cross-validation ( RMSECV) of 0.006% using PLSR (partial least squares regression). However, the NIR/PLSR model relied on weak spectral signals, and was highly sensitive to sample preparation. The best prediction of phosphate content from the RVA viscograms was a linear regression model based on the RVA variable Breakdown, which gave a RMSECV of 0.008%. NIR/PLSR prediction of the RVA variables Peak viscosity and Breakdown was successful, probably because they were highly related to phosphate content in the present data. Prediction of the other RVA variables from NIR/PLSR was mediocre (Through, Final Viscosity) or not possible (Setback, Peak time, Pasting temperature).

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Engineering Potato Starch with a Higher Phosphate Content

PLoS ONE ◽

10.1371/journal.pone.0169610 ◽

2017 ◽

Vol 12 (1) ◽

pp. e0169610 ◽

Cited By ~ 8

Author(s):

Xuan Xu ◽

Xing-Feng Huang ◽

Richard G. F. Visser ◽

Luisa M. Trindade

Keyword(s):

Potato Starch ◽

Phosphate Content

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Search for sources of early blight (Alternaria solani) field resistance not associated with vegetative late maturity in tetraploid potato germplasm

Euphytica ◽

10.1007/bf01677862 ◽

1995 ◽

Vol 83 (1) ◽

pp. 63-70 ◽

Cited By ~ 14

Author(s):

L. S. Boiteux ◽

F. J. B. Reifschneider ◽

M. E. N. Fonseca ◽

J. A. Buso

Keyword(s):

Early Blight ◽

Alternaria Solani ◽

Field Resistance ◽

Tetraploid Potato ◽

Potato Germplasm ◽

Late Maturity

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Genome-Wide Association Analysis of Late Blight Resistance Traits in Potato Germplasm Resources

10.21203/rs.3.rs-113697/v1 ◽

2020 ◽

Author(s):

Fang Wang ◽

Meiling Zou ◽

Long Zhao ◽

Huaqing Li ◽

Zhiqiang Xia ◽

...

Keyword(s):

Late Blight ◽

Candidate Genes ◽

Association Analysis ◽

Late Blight Resistance ◽

Genome Wide Association ◽

Blight Resistance ◽

Germplasm Resources ◽

Potato Germplasm ◽

Genome Wide ◽

Population Structure Analysis

Abstract Background: Potatoes are dicotyledonous plants of the genus Solanum, family Solanaceae, and contain large amounts of starch, proteins, and trace elements required by the human. Potato late blight is the main disease hindering potato production. In this study, Phytophthora infestans were used to quantify late blight resistance in 284 germplasm resources, and resistance genes were mined through genome-wide association analysis.Results: The results showed that among the 284 potato germplasm resources, 37 showed immunity, 15 were highly resistant to late blight, 30 were moderately resistant to late blight, 107 were moderately susceptible to late blight, and 95 were highly susceptible to late blight. Through screening and filtering, 22,489 high-quality single-nucleotide polymorphisms (SNPs) and indels were obtained. Through population structure analysis and principal-component analysis, 284 germplasm resources were divided into eight subgroups, which was consistent with the results of the phylogenetic tree analysis. The genetic diversity index of the 284 potato germplasm resources was 0.2161, and the differentiation index of each subgroup was 0.0251-0.1489. A mixed linear model was built to perform an association analysis on the diameter of the lesions identified from isolated leaves of potato affected by late blight. The genes within 100 kb of both sides of the obtained significant SNP loci were searched and functionally annotated, and 18 candidate genes were obtained. Twenty-two candidate genes were obtained from the association analysis of disease resistance grade.Conclusions: 284 potato germplasm resources were used to identify for Phytophthora infestans resistance. The potato germplasm resources were divided into 8 subgroups by population structure analysis, and the main differentiation among subgroups was moderate. Candidate genes were mined by genome-wide association analysis.The results of this study provides the foundation for the genetic improvement of potato varieties resistant to late blight.

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Association Study of the M132L Single Nucleotide Polymorphism With Susceptibility to Chronic Wasting Disease in Korean Elk: A Meta-Analysis

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.804325 ◽

2022 ◽

Vol 8 ◽

Author(s):

In-Soon Roh ◽

Yong-Chan Kim ◽

Sae-Young Won ◽

Kyung-Je Park ◽

Hoo-Chang Park ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Prion Protein ◽

Association Analysis ◽

Chronic Wasting Disease ◽

Meta Analysis ◽

Strong Association ◽

Amplicon Sequencing ◽

Nucleotide Polymorphism ◽

Wasting Disease ◽

Single Nucleotide

Chronic wasting disease (CWD) is a deleterious brain proteinopathy caused by a pathogenic form of prion protein (PrPSc), which is converted from a benign form of prion protein (PrPC) encoded by the prion protein gene (PRNP). In elk, the M132L single nucleotide polymorphism (SNP) of the PRNP gene likely plays a pivotal role in susceptibility to CWD. However, the association of the M132L SNP with susceptibility to CWD has not been evaluated in Korean elk to date. To estimate the association of the M132L SNP with susceptibility to CWD in Korean elk, we investigated the genotype and allele frequencies of the M132L SNP by amplicon sequencing and performed association analysis between CWD-positive and CWD-negative elk. In addition, we performed a meta-analysis to evaluate the association between the M132L SNP and susceptibility to CWD in quantitatively synthesized elk populations. Furthermore, we estimated the effect of the M132L SNP on elk PrP using in silico programs, including PolyPhen-2, PROVEAN, AMYCO and Swiss-PdbViewer. We did not identify a significant association between the M132L SNP of PRNP and susceptibility to CWD in Korean elk. The meta-analysis also did not identify a strong association between the M132L SNP of PRNP and susceptibility to CWD in quantitatively synthesized elk populations. Furthermore, we did not observe significant changes in structure, amyloid propensity or electrostatic potential based on the M132L SNP in elk PrP. To the best of our knowledge, this was the first report of an association analysis and meta-analysis in Korean elk and quantitatively synthesized elk populations, respectively.

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Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Paeonia rockii) Using Association Mapping

Frontiers in Genetics ◽

10.3389/fgene.2021.664814 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xin Guo ◽

Chunyan He ◽

Fangyun Cheng ◽

Yuan Zhong ◽

Xinyun Cheng ◽

...

Keyword(s):

Genetic Diversity ◽

Association Analysis ◽

Complex Traits ◽

Allelic Variation ◽

Phenotypic Diversity ◽

Woody Species ◽

Fruit Traits ◽

Tree Peony ◽

Single Marker ◽

Paeonia Rockii

Allelic variation in floral quantitative traits, including the elements of flowers and fruits, is caused by extremely complex regulatory processes. In the genetic improvement of flare tree peony (Paeonia rockii), a unique ornamental and edible oil woody species in the genus Paeonia, a better understanding of the genetic composition of these complex traits related to flowers and fruits is needed. Therefore, we investigated the genetic diversity and population structure of 160 P. rockii accessions and conducted single-marker association analysis for 19 quantitative flower and fruit traits using 81 EST-SSR markers. The results showed that the population had a high phenotypic diversity (coefficients of variation, 11.87–110.64%) and a high level of genetic diversity (mean number of alleles, NA = 6.09). These accessions were divided into three subgroups by STRUCTURE analysis and a neighbor-joining tree. Furthermore, we also found a low level of linkage disequilibrium between these EST-SSRs and, by single-marker association analysis, identified 134 significant associations, including four flower traits with 11 EST-SSRs and 10 fruit traits with 32 EST-SSRs. Finally, based on the sequence alignment of the associated markers, P280, PS2, PS12, PS27, PS118, PS131, and PS145 may be considered potential loci to increase the yield of flare tree peony. These results laid the foundation for further analysis of the genetic structure of some key traits in P. rockii and had an obvious potential application value in marker-assisted selection breeding.

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