scholarly journals Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

Euphytica ◽  
2017 ◽  
Vol 213 (12) ◽  
Author(s):  
Pietro Gramazio ◽  
Jaime Prohens ◽  
Dionís Borràs ◽  
Mariola Plazas ◽  
Francisco Javier Herraiz ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Simple Sequence Repeat ◽  
Snp Markers ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Genetic Fingerprinting ◽  
Single Nucleotide ◽  
Simple Sequence ◽  
Diversity Evaluation

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.

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.

scholarly journals Mapping Genes Governing Flower and Seedcoat Color in Asparagus Bean (Vigna unguiculata ssp. sesquipedalis) Based on Single Nucleotide Polymorphism and Simple Sequence Repeat Markers

HortScience ◽  
2011 ◽  
Vol 46 (8) ◽  
pp. 1102-1104 ◽  
Author(s):  
Pei Xu ◽  
Tingting Hu ◽  
Yuejian Yang ◽  
Xiaohua Wu ◽  
Baogen Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Simple Sequence Repeat ◽  
Recombinant Inbred Lines ◽  
Flower Color ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Asparagus Bean ◽  
Simple Sequence ◽  
T Locus

Colors of flower and seedcoat are interesting traits of asparagus bean, a cultivated subspecies of cowpea grown throughout Asia for its tender, long green pods. Little is known about the inheritance of these traits including their genome location. We report here the genetic analysis and mapping of the genes governing flower and seedcoat color in asparagus bean based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. Analysis of the F1 and F7:8 generation of recombinant inbred lines (RILs) population showed a monogenetic inheritance of both traits. Purple flower and brown seedcoat are dominant over white flower and cream seedcoat, respectively. We further show that genes governing flower color and seedcoat color are tightly linked on LG8, ≈0.4 cM apart. Synteny analysis showed that the gene controlling seedcoat color in our study is syntenic to the soybean T locus. The use of the mapping information in asparagus bean breeding is discussed.

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