Fine-scale genetic structure enhances biparental inbreeding by promoting mating events between more related individuals in wild soybean (Glycine soja; Fabaceae) populations

2009 ◽  
Vol 96 (6) ◽  
pp. 1138-1147 ◽  
Author(s):  
R. Zhao ◽  
H. xia ◽  
B.-r. Lu
Keyword(s):  
Genetic Structure ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Fine Scale ◽  
Biparental Inbreeding ◽  
Related Individuals

Evaluation of genetic structure of Korean wild soybean (Glycine soja) based on saponin allele polymorphism

2014 ◽  
Vol 61 (6) ◽  
pp. 1121-1130 ◽  
Author(s):  
Panneerselvam Krishnamurthy ◽  
Jae Min Lee ◽  
Chigen Tsukamoto ◽  
Yuya Takahashi ◽  
Ram J. Singh ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Allele Polymorphism

Phenotypic and genotypic signature of saponin chemical composition in Chinese wild soybean (Glycine soja): revealing genetic diversity, geographical variation and dispersal history of the species

2018 ◽  
Vol 69 (11) ◽  
pp. 1126
Author(s):  
Yuya Takahashi ◽  
Xiang-Hua Li ◽  
Chigen Tsukamoto ◽  
Ke-Jing Wang
Keyword(s):  
Genetic Diversity ◽  
Chemical Composition ◽  
Genetic Structure ◽  
Southern China ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Ice Age ◽  
High Genetic Diversity ◽  
The North ◽  
Or Genes

Saponin chemical composition was phenotyped and genotyped, and saponin composition-based geographical genetic diversity and differentiation were evaluated in Chinese wild soybean (Glycine soja Sieb. & Zucc.). Thirty-two phenotypes and 34 genotypes were confirmed from 3805 wild soybean accessions. Eleven phenotypes (AaαK, AaαIK, AaαIJK, AaBcEαJ, AaBcαK, AbEαIJ, AbαK, AbαIK, AbαIJK, AbβHAb and Aβ0) were newly detected. Four genes had frequencies: Sg-1a 78.8% and Sg-1b 21.0% at the Sg-1 locus; Sg-4 30.7% and Sg-6e 13.7% at their respective loci. The north-eastern and southern populations showed high genetic diversity; the Northeast region contained more novel variants (AuAe, A0, A0Bc, αH, αI αJ, αK, and AbβHAb), and the southern populations contained high frequencies of the Sg-4 gene. Gene differentiation (Fst) analysis suggested that Sg-4 and four group-α saponin alleles or genes (Sg-6e, Sg-6h, Sg-6i, Sg-6j) were important factors influencing the genetic structure and differentiation in Chinese wild soybeans. Geographical differentiation was characterised mainly by latitudinal differences, with two primary groups (north and south) based on saponin genes. Chinese wild soybean accessions differed from Japanese and South Korean ones in genetic structure based on saponin composition, the latter two being likely to have spread from southern China in the glacial stages during the last Ice Age.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals A Novel Pinkish-White Flower Color Variant Is Caused by a New Allele of Flower Color Gene W1 in Wild Soybean (Glycine soja)

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1001
Author(s):  
Jagadeesh Sundaramoorthy ◽  
Gyu Tae Park ◽  
Hyun Jo ◽  
Jeong-Dong Lee ◽  
Hak Soo Seo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Functional Activity ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Flower Color ◽  
Loss Of Function ◽  
Protein Variation ◽  
Color Variant ◽  
Color Gene

The enzyme flavonoid 3′,5′-hydroxylase (F3′5′H) plays an important role in producing anthocyanin pigments in soybean. Loss of function of the W1 locus encoding F3′5′H always produces white flowers. However, few color variations have been reported in wild soybean. In the present study, we isolated a new color variant of wild soybean accession (IT261811) with pinkish-white flowers. We found that the flower’s pinkish-white color is caused by w1-s3, a single recessive allele of W1. The SNP detected in the mutant caused amino acid substitution (A304S) in a highly conserved SRS4 domain of F3′5′H proteins. On the basis of the results of the protein variation effect analyzer (PROVEAN) tool, we suggest that this mutation may lead to hypofunctional F3′5′H activity rather than non-functional activity, which thereby results in its pinkish-white color.

scholarly journals Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin K. Esoh ◽  
Tobias O. Apinjoh ◽  
Steven G. Nyanjom ◽  
Ambroise Wonkam ◽  
Emile R. Chimusa ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Ethnic Groups ◽  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Genomic Region ◽  
Sub Saharan Africa ◽  
Genome Wide Association Studies ◽  
Fine Scale ◽  
Sub Saharan

AbstractInferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.

scholarly journals Fine‐scale genetic structure reflects limited and coordinated dispersal in the colonial monk parakeet, Myiopsitta monachus

2021 ◽  
Author(s):  
Francesca S. E. Dawson Pell ◽  
Juan Carlos Senar ◽  
Daniel W. Franks ◽  
Ben J. Hatchwell
Keyword(s):  
Genetic Structure ◽  
Fine Scale ◽  
Monk Parakeet ◽  
Myiopsitta Monachus
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