scholarly journals Genetic characterization of buckwheat accessions through genome-wide allele frequency fingerprints / Genetska karakterizacija vzorcev ajde z odtisi frekvence alelov v genomu

2020 ◽  
Vol 61 (1) ◽  
pp. 17-23
Author(s):  
Michelle M. Nay ◽  
Stephen L. Byrne ◽  
Eduardo A. Pérez ◽  
Achim Walter ◽  
Bruno Studer
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Genotyping By Sequencing ◽  
Allele Frequencies ◽  
Fagopyrum Esculentum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Fagopyrum Esculentum Moench

Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat. Key words: Buckwheat (Fagopyrum esculentum Moench), genotyping by sequencing (GBS), population genomics, genome-wide allele frequency fingerprints (GWAFFs)   Izvleček Genomsko podprto žlahtnjenje ajde (Fagopyrum esculentum Moench) je odvisno od robustnih metod genotipiziranja. Genotipiziranje s spremljanjem sekvenc (genotyping by sequencing, GBS) se je razvilo kot fleksibilna in razmeroma poceni metoda, ki se jo uporablja pri žlahtnjenju rastlin. Uporabnih je več virov GBS za genetsko karakterizacijo posamičnih genotipov, toda te metode niso primerne za predstavitev genetske raznolikosti vzorcev ajde, ki jih vzdržujemo v heterozigotni obliki, kar velja za odprto oplodne populacije. Tu poročamo o razvoju GBS metode, ki, namesto prikazovanja bi-alelnega polimorfizma posameznih nukleotidov (single nucleotide polymorphisms, SNPs), pokaže frekvence alelov v populaciji na nivoju genoma. Ta prikaz frekvence alelov na nivoju genoma (genome-wide allele frequency fingerprints, GWAFFs) z združenimi sto posameznimi rastlinami vsakega vzorca se je pokazal kot visoko ponovljiv in je prikazal genetsko podobnost 20 različnih vzorcev ajde, ki smo jih analizirali v naši raziskavi. Metoda GWAFFs ni uporabna samo kot učinkovito orodje za natančen opis materiala za žlahtnjenje ajde, ponuja tudi možnosti raziskave  genetskih razlik med različnimi vzorci ajde in omogoča zbirke podatkov. Nadalje, metoda GWAFFs omogoča povezovanje frekvenc alelov s fenotipskimi lastnostmi in kvalitativnih parametrov, ki so najbolj zanesljivo opisani na nivoju populacij. To je ključ za praktično uporabo z genomiko podprtega žlahtnjenja, kot je z genskimi markerji podprta selekcija in genomska selekcija z GWAFFs. Ključne besede: ajda (Fagopyrum esculentum Moench), genotipizacija s sekvenciranjem (GBS), populacijska genomika, GWAFFs

scholarly journals Genetic diversity and genetic origin of Lanping black-boned sheep investigated by genome-wide single-nucleotide polymorphisms (SNPs)

2020 ◽  
Vol 63 (1) ◽  
pp. 193-201
Author(s):  
Heli Xiong ◽  
Xiaoming He ◽  
Jing Li ◽  
Xingneng Liu ◽  
Chaochao Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Structure Analysis ◽  
Genetic Background ◽  
Nucleotide Polymorphisms ◽  
Genetic Origin ◽  
Single Nucleotide ◽  
Sheep Breeds ◽  
Genome Wide ◽  
Nj Tree

Abstract. Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population FST, which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.

scholarly journals Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 822 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Myoung-Jae Shin ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Differentiation ◽  
Principal Components ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.

scholarly journals Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1074
Author(s):  
Joanna Grzegorczyk ◽  
Artur Gurgul ◽  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Agnieszka Fornal ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Read Depth ◽  
Model Organisms ◽  
Single Nucleotide Polymorphism Discovery ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polymorphism Discovery ◽  
Genome Wide ◽  
Plumage Development ◽  
Edar Gene

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

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