scholarly journals Understanding the genetic relationships between Indonesian bambara groundnut landraces and investigating their origins

Genome ◽  
2020 ◽  
Vol 63 (6) ◽  
pp. 319-327 ◽  
Author(s):  
E.S. Redjeki ◽  
W.K. Ho ◽  
N. Shah ◽  
O.O. Molosiwa ◽  
N.R. Ardiarini ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Bambara Groundnut ◽  
Principal Coordinate Analysis ◽  
Vigna Subterranea ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
And Cluster Analysis ◽  
Simple Sequence

A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.

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.

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.

scholarly journals Genetic Diversity Analysis and Single-nucleotide Polymorphism Marker Development in Cultivated Bulb Onion Based on Expressed Sequence Tag–Simple Sequence Repeat Markers

2008 ◽  
Vol 133 (6) ◽  
pp. 810-818 ◽  
Author(s):  
John McCallum ◽  
Susan Thomson ◽  
Meeghan Pither-Joyce ◽  
Fernand Kenel ◽  
Andrew Clarke ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Snp Markers ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Bulb Onion ◽  
Expressed Sequence ◽  
Simple Sequence

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.

Genetic relationships among fruiting-mei (Prunus mume Sieb. et Zucc.) cultivars evaluated with AFLP and SNP markers

Genome ◽  
2006 ◽  
Vol 49 (10) ◽  
pp. 1256-1264 ◽  
Author(s):  
Jinggui Fang ◽  
Tal Twito ◽  
Zhen Zhang ◽  
ChihCheng T. Chao
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Snp Markers ◽  
Prunus Mume ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Past ◽  
China And Japan

Genetic relationships among 50 fruiting-mei (Prunus mume Sieb. et Zucc.) cultivars from China and Japan were investigated, using 767 amplified fragment length polymorphism (AFLP) and 103 single nucleotide polymorphism (SNP) markers. The polymorphism among the cultivars was found to be 69.77%, based on EcoR I + Mse I AFLP primer pairs. The sequence alignment of 11 group sequences, derived from 50 samples, yielded 103 SNPs; the total length of genomic sequences was 3683 bp. Among these SNPs, 73 were heterozygous in the loci of different cultivars. The SNP distribution was 58% transition, 40% transversion, and 2% InDels. There was also 1 trinucleotide deletion. AFLP and SNP markers allowed us to evaluate the genetic diversity of these 50 fruiting-mei cultivars. The 2 derived cladograms did display some differences: all cultivars formed 2 subclusters (1A and 1B) in the cladogram based on AFLP polymorphisms, and formed 3 subclusters (2A, 2B, and 2C) in the cladogram based on SNP polymorphisms; and, in the cladogram based on AFLP polymorphisms, most cultivars from the Guangdong to Fujian provinces (G–F) in China, from the Yunnan, Hunan, and Sichuan provinces (Y–S–H) in China, and from Japan grouped in cluster 1A, and 18 (78.26%) of 23 cultivars from Jiangsu to Zhejiang provinces in China (J–Z) grouped in cluster 1B. The results demonstrate that mei cultivars from Japan are clustered with cultivars from China, and support the hypothesis that mei in Japan were introduced from China. Cultivars from the J–Z region of China have more genetic similarities. Cultivars from the G–F and Y–S–H regions have fewer genetic similarities and suggest more germplasm exchanges in the past.

scholarly journals Genotyping by Multiplexed Sequencing (GMS) protocol in Barley

Euphytica ◽  
2021 ◽  
Vol 217 (4) ◽  
Author(s):  
Jonathan Eagle ◽  
Travis Ruff ◽  
Marcus Hooker ◽  
Sajal Sthapit ◽  
Elliott Marston ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Genotyping By Sequencing ◽  
Read Depth ◽  
Snp Markers ◽  
Direct Sequence ◽  
Nucleotide Polymorphism ◽  
Accurate Analysis ◽  
Single Nucleotide ◽  
Analysis Process ◽  
Robust Protocol

AbstractGenotyping by sequencing (GBS) and single nucleotide polymorphism (SNP) chip technologies are the primary SNP genotyping technologies used today. However, these genotyping technologies have some drawbacks that limit their usefulness in analysis. We have developed a robust protocol called genotyping by multiplexed sequencing (GMS) using SNP markers, providing informative genotypic data with greater flexibility. The genotypes derived from direct sequence reads reduce ambiguity in genetic analysis. The advantages of this protocol include: (1) This PCR-based direct sequencing protocol generates information from markers of interest and provides a more streamlined and accurate analysis process, by multiplexing hundreds of informative markers into a single sequencing run. (2) The marker sets are easily customized to the species of interest and can readily be changed. In this study we have taken the GMS protocol developed in wheat and adapted it to barley. We have identified 577 SNP markers that work well using this protocol providing adequate genome coverage for genomic selection and tag 267 QTL’s for genes of interest. Good markers have an adequate read depth of at least 5 amplicons and are reliably present across the population.

scholarly journals Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 737
Author(s):  
Maja Žulj Mihaljević ◽  
Edi Maletić ◽  
Darko Preiner ◽  
Goran Zdunić ◽  
Marijan Bubola ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Simple Sequence Repeat ◽  
Genetic Erosion ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Simple Sequence

Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories.

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