scholarly journals QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max)

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1163
Author(s):  
Jeong-Hyun Seo ◽  
Beom-Kyu Kang ◽  
Sanjeev K. Dhungana ◽  
Jae-Hyeon Oh ◽  
Man-Soo Choi ◽  
...  
Keyword(s):  
Growth Stages ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Reproductive Process ◽  
Pod Shattering ◽  
Selection For ◽  
Elite Cultivar ◽  
Variance Explained

Pod shattering is an important reproductive process in many wild species. However, pod shattering at the maturing stage can result in severe yield loss. The objectives of this study were to discover quantitative trait loci (QTLs) for pod shattering using two recombinant inbred line (RIL) populations derived from an elite cultivar having pod shattering tolerance, namely “Daewonkong”, and to predict novel candidate QTL/genes involved in pod shattering based on their allele patterns. We found several QTLs with more than 10% phenotypic variance explained (PVE) on seven different chromosomes and found a novel candidate QTL on chromosome 16 (qPS-DS16-1) from the allele patterns in the QTL region. Out of the 41 annotated genes in the QTL region, six were found to contain SNP (single-nucleotide polymorphism)/indel variations in the coding sequence of the parents compared to the soybean reference genome. Among the six potential candidate genes, Glyma.16g076600, one of the genes with known function, showed a highly differential expression levels between the tolerant and susceptible parents in the growth stages R3 to R6. Further, Glyma.16g076600 is a homolog of AT4G19230 in Arabidopsis, whose function is related to abscisic acid catabolism. The results provide useful information to understand the genetic mechanism of pod shattering and could be used for improving the efficiency of marker-assisted selection for developing varieties of soybeans tolerant to pod shattering.

scholarly journals A method for single nucleotide polymorphism selection for parentage assessment in goats

2016 ◽  
Vol 99 (5) ◽  
pp. 3646-3653 ◽  
Author(s):  
A. Talenti ◽  
E.L. Nicolazzi ◽  
S. Chessa ◽  
S. Frattini ◽  
R. Moretti ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Single Nucleotide Polymorphism Selection ◽  
Selection For

scholarly journals Glu504Lys Single Nucleotide Polymorphism of Aldehyde Dehydrogenase 2 Gene and the Risk of Human Diseases

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Yan Zhao ◽  
Chuancai Wang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Chronic Diseases ◽  
Aldehyde Dehydrogenase ◽  
Late Onset ◽  
Potential Candidate ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Asian Populations ◽  
Reactive Aldehydes ◽  
Aldehyde Dehydrogenase 2 Gene

Aldehyde dehydrogenase (ALDH) 2 is a mitochondrial enzyme that is known for its important role in oxidation and detoxification of ethanol metabolite acetaldehyde. ALDH2 also metabolizes other reactive aldehydes such as 4-hydroxy-2-nonenal and acrolein. The Glu504Lys single nucleotide polymorphism (SNP) ofALDH2gene, which is found in approximately 40% of the East Asian populations, causes defect in the enzyme activity of ALDH2, leading to alterations in acetaldehyde metabolism and alcohol-induced “flushing” syndrome. Evidence suggests thatALDH2Glu504Lys SNP is a potential candidate genetic risk factor for a variety of chronic diseases such as cardiovascular disease, cancer, and late-onset Alzheimer’s disease. In addition, the association betweenALDH2Glu504Lys SNP and the development of these chronic diseases appears to be affected by the interaction between the SNP and lifestyle factors such as alcohol consumption as well as by the presence of other genetic variations.

scholarly journals A targeted genotyping approach to enhance the identification of variants for lactation persistency in dairy cows

2019 ◽  
Vol 97 (10) ◽  
pp. 4066-4075
Author(s):  
Duy Ngoc Do ◽  
Nathalie Bissonnette ◽  
Pierre Lacasse ◽  
Filippo Miglior ◽  
Xin Zhao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Mixed Model ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genetic Selection ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Functional Variants ◽  
Selection For

Abstract Lactation persistency (LP), defined as the ability of a cow to maintain milk production at a high level after milk peak, is an important phenotype for the dairy industry. In this study, we used a targeted genotyping approach to scan for potentially functional single nucleotide polymorphisms (SNPs) within 57 potential candidate genes derived from our previous genome wide association study on LP and from the literature. A total of 175,490 SNPs were annotated within 10-kb flanking regions of the selected candidate genes. After applying several filtering steps, a total of 105 SNPs were retained for genotyping using target genotyping arrays. SNP association analyses were performed in 1,231 Holstein cows with 69 polymorphic SNPs using the univariate liner mixed model with polygenic effects using DMU package. Six SNPs including rs43770847, rs208794152, and rs208332214 in ADRM1; rs209443540 in C5orf34; rs378943586 in DDX11; and rs385640152 in GHR were suggestively significantly associated with LP based on additive effects and associations with 4 of them (rs43770847, rs208794152, rs208332214, and rs209443540) were based on dominance effects at P < 0.05. However, none of the associations remained significant at false discovery rate adjusted P (FDR) < 0.05. The additive variances explained by each suggestively significantly associated SNP ranged from 0.15% (rs43770847 in ADRM1) to 5.69% (rs209443540 in C5orf34), suggesting that these SNPs might be used in genetic selection for enhanced LP. The percentage of phenotypic variance explained by dominance effect ranged from 0.24% to 1.35% which suggests that genetic selection for enhanced LP might be more efficient by inclusion of dominance effects. Overall, this study identified several potentially functional variants that might be useful for selection programs for higher LP. Finally, a combination of identification of potentially functional variants followed by targeted genotyping and association analysis is a cost-effective approach for increasing the power of genetic association studies.

scholarly journals Association of a non-synonymous SNP of IL17RA gene with litter size traits in Large White and Landrace pigs

2021 ◽  
Vol 19 (3) ◽  
pp. 391-405
Author(s):  
Worrarak Norseeda ◽  
◽  
Guisheng Liu ◽  
Tawatchai Teltathum ◽  
Korawan Sringarm ◽  
...  
Keyword(s):  
Immune Responses ◽  
Litter Size ◽  
Interleukin 17 ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Large White ◽  
Single Nucleotide ◽  
Reproductive Process ◽  
Potential Candidate Gene

Interleukin-17 receptor A (IL17RA) is one of the cytokine receptors of the pro-inflammatory interleukin-17 (IL17) cytokine family. The IL17 and IL17RA genes are involved in inflammatory and immune responses as well as reproductive process of mammals. The purposes of this study were to examine polymorphisms in the porcine IL17RA gene and to assess its effects on litter size traits in Large White and Landrace pigs. Three non-synonymous single nucleotide polymorphisms (SNPs) in the porcine IL17RA gene were verified. The porcine IL17RA c.785C>T (p.Ala262Val) was found to be segregating in the Large White and Landrace pigs. No polymorphisms in the coding region of the porcine IL17RA gene at the two non-synonymous SNPs loci of c.997G>A (p.Val333Ile) and c.1962T>G (p.Asp654Glu) were found. The porcine IL17RA c.785C>T polymorphism was significantly associated with the total number born (TNB) and the number born alive (NBA) in Large White pigs (P<0.05). Moreover, the porcine IL17RA c.785C>T was significantly associated with the TNB, NBA, total birth weight (TBW), and total weaning weight of piglets at 21 days (TWW) in Landrace pigs (P<0.05). These results supported the importance of the porcine IL17RA gene in the litter size traits of pigs. Thus, the porcine IL17RA could be used as a potential candidate gene for improving litter size traits in pig breeding.

scholarly journals Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses

2015 ◽  
Vol 370 (1660) ◽  
pp. 20130386 ◽  
Author(s):  
Arne Ludwig ◽  
Monika Reissmann ◽  
Norbert Benecke ◽  
Rebecca Bellone ◽  
Edson Sandoval-Castellanos ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Night Blindness ◽  
Nucleotide Polymorphism ◽  
Fluctuating Selection ◽  
Single Nucleotide ◽  
Domestic Horses ◽  
Selection For ◽  
Frequency Changes ◽  
Approximate Bayesian

Leopard complex spotting is inherited by the incompletely dominant locus, LP , which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli–Kanligecit (Turkey) dating to 2700–2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.

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