scholarly journals Development of 79 SNP markers to individually genotype and sex-type endangered mountain gorillas (Gorilla beringei beringei)

2021 ◽  
Author(s):  
Benjamin N. Sacks ◽  
Tianyi Hu ◽  
Elizabeth M. Kierepka ◽  
Stevi L. Vanderzwan ◽  
Jena R. Hickey
Keyword(s):  
Snp Markers ◽  
Data Sets ◽  
Mountain Gorilla ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Gorilla Beringei Beringei ◽  
Sex Type ◽  
Gorilla Beringei ◽  
Capture Recapture ◽  
Dna Profiles

AbstractThe mountain gorilla (Gorilla beringei beringei) is one of two endangered subspecies of eastern gorilla. The principle approach to monitoring the two extant mountain gorilla populations has been to use fecal surveys to obtain DNA profiles for individuals that are then used for capture-recapture-based estimates of abundance. To date, 11 to 14 microsatellites have been used for this purpose. To adapt to ongoing changes in genotyping technologies and to facilitate the analysis of fecal DNA samples by multiple laboratories, we developed a panel of single nucleotide polymorphism (SNP) markers that can be used for future gorilla monitoring. We used published short read data sets for 3 individuals to develop a suite of 79 SNPs, including two sex markers, for a Fluidigm platform. This marker set provided high resolution to differentiate individuals and will facilitate future monitoring, leaving room for additional SNPs to be included in a 96-assay format.

scholarly journals Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 705
Author(s):  
John Carlos I. Ignacio ◽  
Maricris Zaidem ◽  
Carlos Casal ◽  
Shalabh Dixit ◽  
Tobias Kretzschmar ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
Genotyping Platform ◽  
Anaerobic Germination ◽  
Direct Seeded ◽  
Mapping By Sequencing ◽  
Simple Sequence

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

2021 ◽  
Vol 19 (1) ◽  
pp. 20-28
Author(s):  
Abush Tesfaye Abebe ◽  
Adesike Oladoyin Kolawole ◽  
Nnanna Unachukwu ◽  
Godfree Chigeza ◽  
Hailu Tefera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Glycine Max ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Lines ◽  
Soybean Germplasm ◽  
Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

scholarly journals A Cotton-Fiber-Associated Cyclin-Dependent Kinase A Gene: Characterization and Chromosomal Location

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Weifan Gao ◽  
Sukumar Saha ◽  
Din-Pow Ma ◽  
Yufang Guo ◽  
Johnie N. Jenkins ◽  
...  
Keyword(s):  
Cotton Fiber ◽  
Sequence Data ◽  
Snp Markers ◽  
Pcr Analysis ◽  
Cyclin Dependent Kinase ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Gene Characterization ◽  
Protein Levels ◽  
Catalytic Domains

A cotton fiber cDNA and its genomic sequences encoding an A-type cyclin-dependent kinase (GhCDKA) were cloned and characterized. The encoded GhCDKA protein contains the conserved cyclin-binding, ATP binding, and catalytic domains. Northern blot and RT-PCR analysis revealed that the GhCDKA transcript was high in 5–10 DPA fibers, moderate in 15 and 20 DPA fibers and roots, and low in flowers and leaves. GhCDKA protein levels in fibers increased from 5–15 DPA, peaked at 15 DPA, and decreased from 15 t0 20 DPA. The differential expression of GhCDKA suggested that the gene might play an important role in fiber development. The GhCDKA sequence data was used to develop single nucleotide polymorphism (SNP) markers specific for the CDKA gene in cotton. A primer specific to one of the SNPs was used to locate the CDKA gene to chromosome 16 by deletion analysis using a series of hypoaneuploid interspecific hybrids.

scholarly journals Two SNP Markers Identified Using Genotyping-by-Sequencing Are Associated with Remontancy in a Segregating F1 Population of Syringa meyeri ‘Palibin’ × S. pubescens ‘Penda’ Bloomerang®

2020 ◽  
Vol 145 (2) ◽  
pp. 104-109
Author(s):  
Hsuan Chen ◽  
Jason D. Lattier ◽  
Kelly Vining ◽  
Ryan N. Contreras
Keyword(s):  
Ornamental Plants ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Sequence Information ◽  
Specific Marker ◽  
Nucleotide Polymorphism ◽  
Additive Interaction ◽  
Single Nucleotide ◽  
Position Information ◽  
Flowering Season

Lilacs (Syringa sp.) have been used as ornamental plants since the mid-16th century and remain important in modern gardens due to their attractive and fragrant flowers. However, a short flowering season is a critical drawback for their ornamental value. Breeders have identified remontancy (reblooming) in dwarf lilac (Syringa pubescens), and have tried to introgress this trait into related species by interspecific hybridization. Molecular tools for lilac breeding are limited because of the shortage of genome sequence knowledge and currently no molecular markers are available to use in breeding for remontancy. In this study, an F1 population from crossing Syringa meyeri ‘Palibin’ × S. pubescens ‘Penda’ Bloomerang® Purple was created and subjected to genotyping-by-sequencing (GBS) analysis and phenotyped for remontancy. Plants were categorized as remontant, semi-remontant, and nonremontant based on the relative quantity of inflorescences during the second flush of flowers. A total of 20,730 single-nucleotide polymorphism (SNP) markers from GBS were used in marker-trait association to find remontant-specific marker(s) without marker position information. Two SNP markers, TP70580 (A locus) and TP82604 (B locus), were correlated with remontancy. The two loci showed a partial epistasis and additive interaction effects on the level of remontancy. Accumulation of recessive alleles at the two loci was positively correlated with increased reblooming. For example, 87% of aabb plants were remontant, and only 9% were nonremontant. In contrast, 100% of AaBB plants were nonremontant. These two SNP markers associated with remontancy will be useful in developing markers for future breeding and demonstrate the feasibility of developing markers for breeding woody ornamental taxa that lack a reference genome or extensive DNA sequence information.

scholarly journals Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2025
Author(s):  
Shyryn Almerekova ◽  
Yuliya Genievskaya ◽  
Saule Abugalieva ◽  
Kazuhiro Sato ◽  
Yerlan Turuspekov
Keyword(s):  
Population Structure ◽  
Heading Date ◽  
Snp Markers ◽  
Principal Coordinate Analysis ◽  
Neighbor Joining ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Ancestral Node

The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.

Occurrence and Molecular Analysis of Balantidium coli in Mountain Gorilla (Gorilla beringei beringei) in the Volcanoes National Park, Rwanda

2013 ◽  
Vol 49 (4) ◽  
pp. 1063-1065 ◽  
Author(s):  
James M. Hassell ◽  
Damer P. Blake ◽  
Michael R. Cranfield ◽  
Jan Ramer ◽  
Jennifer N. Hogan ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
National Park ◽  
Gorilla Gorilla ◽  
Mountain Gorilla ◽  
Balantidium Coli ◽  
Gorilla Beringei Beringei ◽  
Gorilla Beringei ◽  
Gorilla Gorilla Beringei

Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification

Euphytica ◽  
2010 ◽  
Vol 175 (1) ◽  
pp. 91-107 ◽  
Author(s):  
Jin-kee Jung ◽  
Soung-Woo Park ◽  
Wing Yee Liu ◽  
Byoung-Cheorl Kang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Cultivar Identification ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Species-Specific Marker Discovery in Tilapia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mochamad Syaifudin ◽  
Michaël Bekaert ◽  
John B. Taggart ◽  
Kerry L. Bartie ◽  
Stefanie Wehner ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Restriction Site ◽  
De Novo ◽  
Snp Markers ◽  
Specific Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Species Analysis ◽  
Species Specific ◽  
Marker Discovery

Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

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