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1. A high-resolution consensus linkage map for barley based on GBS-derived genotypes

Author:
Amina Abed; Ana Badea; Aaron Beattie; Raja Khanal; James Tucker; François Belzile
Source:
Genome 2022 v.65 no.2 pp. 83-94
ISSN:
1480-3321
Subject:
genotyping by sequencing,   etc   ; barley; chromosome mapping; genetic recombination; genomics;     Show all 5 Subjects
Abstract:
... As genotyping-by-sequencing (GBS) is widely used in barley genetic studies, the translation of the physical position of GBS-derived SNPs into accurate genetic positions has become relevant. The main aim of this study was to develop a high-resolution consensus linkage map based on GBS-derived SNPs. The construction of this integrated map involved 11 bi-parental populations composed of 3743 segregat ...
DOI:
10.1139/gen-2021-0055

2. Genetic Diversity and Pedigree Analysis of Red Currant Germplasm

Author:
Anna Pikunova; Svetlana Goryunova; Denis Goryunov; Olga Golyaeva; Maria Dolzhikova; Anna Pavlenko
Source:
Plants 2022 v.11 no.13 pp. -
ISSN:
2223-7747
Subject:
genotyping by sequencing,   etc   ; cultivars; currants; genetic variation; genome; germplasm; pedigree; progeny;     Show all 8 Subjects
Abstract:
... This represents the first report on the genetic diversity of red currant germplasm collections based on genotyping-by-sequencing (GBS) data. Genotypes of 75 individuals of different origin were assessed in more than 7.5K genome positions. Multidimensional scaling (MDS) analysis has been performed. There are five accessions that are significantly isolated from each other and from the rest of the an ...
DOI:
10.3390/plants11131623

3. A new species of Crocus ser. Verni (Iridaceae) with 2n = 12 chromosomes from the Balkans

Author:
Irena Raca; Dörte Harpke; Lulëzim Shuka; Vladimir Ranđelović
Source:
Plant biosystems 2022 v.156 no.1 pp. 36-42
ISSN:
1724-5575
Subject:
genotyping by sequencing,   etc   ; Crocus; leaf anatomy; new species; phylogeny; single nucleotide polymorphism;     Show all 6 Subjects
Abstract:
... A Crocus population in the Northern Albanian Alps obviously belonging to C. ser. Verni was referred to C. heuffelianus, but closer field investigations revealed that it could not be identified with this or any other Verni species. The detailed description of a new species, Crocus bertiscensis, including morphology, leaf anatomy, cytology, and phylogenetic relationship is provided and illustrated. ...
DOI:
10.1080/11263504.2020.1829735

4. Population-tailored mock genome enables genomic studies in species without a reference genome

Author:
Felipe Sabadin; Humberto Fanelli Carvalho; Giovanni Galli; Roberto Fritsche-Neto
Source:
Molecular genetics and genomics 2022 v.297 no.1 pp. 33-46
ISSN:
1617-4615
Subject:
genotyping by sequencing,   etc   ; genome; genomics; marker-assisted selection; prediction; single nucleotide polymorphism; variance;     Show all 7 Subjects
Abstract:
... Based on molecular markers, genomic prediction enables us to speed up breeding schemes and increase the response to selection. There are several high-throughput genotyping platforms able to deliver thousands of molecular markers for genomic study purposes. However, even though its widely applied in plant breeding, species without a reference genome cannot fully benefit from genomic tools and moder ...
DOI:
10.1007/s00438-021-01831-9

5. The ‘Minibulk’ system for advancing winter cereal breeding populations

Author:
Eric Olson; Gina Brown‐Guedira; Amanda Noble; Jared Smith; Lance Forsberg; Elizabeth Brisco; Linda Brown
Source:
Crop science 2022 v.62 no.3 pp. 1011-1023
ISSN:
0011-183X
Subject:
genotyping by sequencing,   etc   ; Triticum aestivum; doubled haploids; greenhouses; population size; vegetative growth; vernalization; winter wheat;     Show all 8 Subjects
Abstract:
... Conventional selected‐bulk breeding is a low cost means of advancing populations but requires years of selection in the field to generate fixed lines. Doubled haploid (DH) methods produce fixed lines quickly but without selection and at high cost. The ‘Minibulk’ system was developed to combine the speed of DHs with the population size and crossover opportunities of selected‐bulk breeding. Breeding ...
DOI:
10.1002/csc2.20718

6. Genome-wide diversity in native populations of Croton grewioides Baill., a future crop with fungicidal and antioxidant activity, using SNP markers

Author:
S. D. S. Oliveira; I. B. Gois; A. F. Blank; M. F. Arrigoni-Blank; M. I. Zucchi; J. B. Pinheiro; C. E. Batista; A. Alves-Pereira
Source:
Genetic resources and crop evolution 2022 v.69 no.5 pp. 1965-1978
ISSN:
0925-9864
Subject:
genotyping by sequencing,   etc   ; Croton; antioxidant activity; discriminant analysis; evolution; genetic distance; genetic variation; germplasm; variance; Brazil;     Show all 10 Subjects
Abstract:
... Croton grewioides Baill. is a medicinal and aromatic species with proven biological activity. Considering the economic potential of the species, the use of molecular markers for genetic diversity studies is of utmost importance to develop viable strategies for its management, conservation, and use. Thus, the aim of this study was to evaluate the genetic diversity and structure of natural populatio ...
DOI:
10.1007/s10722-022-01357-y

7. Genotyping-by-sequencing based SNP discovery in a non-model rodent, the endangered hazel dormouse

Author:
Johanna Leyhausen; Berardino Cocchiararo; Carsten Nowak; Hermann Ansorge; Sandro Bertolino; Sven Büchner; Joanna Fietz; Ruud Foppen; Rimvydas Juškaitis; Maurice La Haye; Johannes Lang; Johan Michaux; Goedele Verbeylen; Alina von Thaden; Sarah A. Mueller
Source:
Conservation genetics resources 2022 v.14 no.2 pp. 195-201
ISSN:
1877-7260
Subject:
genotyping by sequencing,   etc   ; Muscardinus avellanarius; alleles; conservation genetics; genetic variation; population structure; rodents; single nucleotide polymorphism;     Show all 8 Subjects
Abstract:
... The hazel dormouse Muscardinus avellanarius presents an exemplary non-model species that is both locally threatened and whose genetic status is not fully understood owing to insufficient resolution of the currently available molecular tools. We performed normalized Genotyping-by-Sequencing (nGBS) on 48 hazel dormouse samples collected across the species European distribution, aiming at discovering ...
DOI:
10.1007/s12686-022-01253-8

8. Robust and efficient software for reference‐free genomic diversity analysis of genotyping‐by‐sequencing data on diploid and polyploid species

Author:
Andrea Parra‐Salazar; Jorge Gomez; Daniela Lozano‐Arce; Paula H. Reyes‐Herrera; Jorge Duitama
Source:
Molecular ecology resources 2022 v.22 no.1 pp. 439-454
ISSN:
1755-098X
Subject:
genotyping by sequencing,   etc   ; algorithms; computer software; cost effectiveness; diploidy; ecology; genetic variation; genome; polyploidy; population genetics;     Show all 10 Subjects
Abstract:
... Genotyping‐by‐sequencing (GBS) is a widely used and cost‐effective technique for obtaining large numbers of genetic markers from populations by sequencing regions adjacent to restriction cut sites. Although a standard reference‐based pipeline can be followed to analyse GBS reads, a reference genome is still not available for a large number of species. Hence, reference‐free approaches are required ...
DOI:
10.1111/1755-0998.13477

9. Co-dispersal of symbionts in the lichen Cladonia stellaris inferred from genomic data

Author:
Marta Alonso-García; Raquel Pino-Bodas; Juan Carlos Villarreal A
Source:
Fungal ecology 2022 v.60 pp. 101165
ISSN:
1754-5048
Subject:
genotyping by sequencing,   etc   ; Cladonia stellaris; fungi; genetic structure; genetic variation; genomics; lichens; population structure; symbionts; thallus; Canada;     Show all 11 Subjects
Abstract:
... We tested the congruence in dispersal patterns of the two main symbionts of the lichen Cladonia stellaris using genotyping-by-sequencing data. Based on 122 samples from eastern Canada, we recovered more than 21000 loci from the photobiont of C. stellaris. We described the population structure and estimate genetic diversity of the photobiont and identified the factors that contribute to explain gen ...
DOI:
10.1016/j.funeco.2022.101165

10. Molecular Characterization of Genomic Regions for Adult Plant Resistance to Stem Rust in a Spring Wheat Mapping Population

Author:
Yahya Rauf; Prabin Bajgain; Matthew N. Rouse; Khalil A. Khanzada; Sridhar Bhavani; Julio Huerta-Espino; Ravi P. Singh; Muhammad Imtiaz; James A. Anderson
Source:
Plant disease 2022 v.106 no.2 pp. 439-450
ISSN:
0191-2917
Subject:
genotyping by sequencing,   etc   ; Puccinia graminis; evolution; genomics; mature plants; quantitative traits; resistance genes; spring wheat; stem rust;     Show all 9 Subjects
Abstract:
... Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line ‘Copio’. A total of 176 recombinant inbred lines (RILs) from the cross of susceptible parent ‘Apav’ with Copio were phenotyped ...
DOI:
10.1094/PDIS-03-21-0672-RE

11. A genome-wide assessment of the genetic diversity, evolution and relationships with allied species of the clonally propagated crop Vanilla planifolia Jacks. ex Andrews

Author:
Félicien Favre; Cyril Jourda; Michel Grisoni; Quentin Piet; Ronan Rivallan; Jean-Bernard Dijoux; Jérémy Hascoat; Sandra Lepers-Andrzejewski; Pascale Besse; Carine Charron
Source:
Genetic resources and crop evolution 2022 v.69 no.6 pp. 2125-2139
ISSN:
0925-9864
Subject:
genotyping by sequencing,   etc   ; Bayesian theory; Vanilla planifolia; asexual reproduction; cultivars; domestication; evolution; genetic variation; heterozygosity; kinship; polyploidy;     Show all 11 Subjects
Abstract:
... The Vanilla genus is a complex taxonomic group characterized by a vegetative reproduction mode combined with intra- and inter-specific hybridizations, and polyploidy events. These factors strongly impact the diversification of the genus and complicate the delimitation of taxa. Among the hundred Vanilla species, Vanilla planifolia Jacks. ex Andrews and Vanilla × tahitensis J. W. Moore are the main ...
DOI:
10.1007/s10722-022-01362-1

12. Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity

Author:
J. Lucas Boatwright; Sirjan Sapkota; Hongyu Jin; James C. Schnable; Zachary Brenton; Richard Boyles; Stephen Kresovich
Source:
plant journal 2022 v.111 no.3 pp. 888-904
ISSN:
0960-7412
Subject:
genotyping by sequencing,   etc   ; Sorghum bicolor; divergent evolution; domestication; genetic markers; genetic variation; genome; genomics; phenotypic variation; plant height;     Show all 10 Subjects
Abstract:
... Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole‐genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabl ...
DOI:
10.1111/tpj.15853

13. Identification of Putative SNP Markers Associated with Resistance to Egyptian Loose Smut Race(s) in Spring Barley

Author:
Kamal A. M. Abo-Elyousr; Amira M. I. Mourad; P. Stephen Baenziger; Abdelaal H. A. Shehata; Peter E. Eckstein; Aaron D. Beattie; Ahmed Sallam
Source:
Genes 2022 v.13 no.6 pp. -
ISSN:
2073-4425
Subject:
genotyping by sequencing,   etc   ; cultivars; genetic improvement; genetic variation; genotype; heritability; models; protein kinases; resistance genes; smut diseases; spring barley;     Show all 11 Subjects
Abstract:
... Loose smut (LS) disease is a serious problem that affects barley yield. Breeding of resistant cultivars and identifying new genes controlling LS has received very little attention. Therefore, it is important to understand the genetic basis of LS control in order to genetically improve LS resistance. To address this challenge, a set of 57 highly diverse barley genotypes were inoculated with Egyptia ...
DOI:
10.3390/genes13061075

14. In‐field genetic stock identification of overwintering coho salmon in the Gulf of Alaska: Evaluation of Nanopore sequencing for remote real‐time deployment

Author:
Christoph M. Deeg; Ben J. G. Sutherland; Tobi J. Ming; Colin Wallace; Kim Jonsen; Kelsey L. Flynn; Eric B. Rondeau; Terry D. Beacham; Kristina M. Miller
Source:
Molecular ecology resources 2022 v.22 no.5 pp. 1824-1835
ISSN:
1755-098X
Subject:
genotyping by sequencing,   etc   ; Oncorhynchus kisutch; data collection; ecology; nanopores; overwintering; polymers; salmon; single nucleotide polymorphism; stakeholders; Gulf of Alaska;     Show all 11 Subjects
Abstract:
... Genetic stock identification (GSI) from genotyping‐by‐sequencing of single nucleotide polymorphism (SNP) loci has become the gold standard for stock of origin identification in Pacific salmon. The sequencing platforms currently applied require large batch sizes and multiday processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third‐generation sin ...
DOI:
10.1111/1755-0998.13595

15. Molecular mapping of CLCuD resistance introgressed from synthetic cotton polyploid in upland cotton

Author:
Suruchi Vij; Dharminder Pathak; Pankaj Rathore; Harish Kumar; P. S. Sekhon; Dharminder Bhatia; Parveen Chhuneja; Kuldeep Singh
Source:
Journal of genetics 2022 v.101 no.1 pp. 25
ISSN:
0022-1333
Subject:
genotyping by sequencing,   etc   ; Geminiviridae; Gossypium hirsutum; backcrossing; cotton; cultivars; fiber quality; introgression; leaf curling; polyploidy; resistance genes; India; Pakistan;     Show all 13 Subjects
Abstract:
... Cotton leaf curl disease (CLCuD), caused by a geminivirus complex, is the most serious disease of upland cotton in northwest India and Pakistan. It results in substantial losses in cotton yield and fibre quality. Due to continuous appearance of new viral strains, all the established CLCuD resistant stocks, extant and obsolete cultivars of upland cotton have become susceptible. Therefore, it became ...
DOI:
10.1007/s12041-022-01365-y

16. A Preliminary Study for Identifying Quantitative Trait Loci Associated with Seed Production in Radish Using Genotyping-by-Sequencing

Author:
Jinhee Kim; Suhyoung Park; Junho Lee; Koeun Han; Yoonah Jang; Wonbyoung Chae
Source:
Horticulturae 2022 v.8 no.3 pp. -
ISSN:
2311-7524
Subject:
genotyping by sequencing,   etc   ; Arabidopsis thaliana; chromosome mapping; cultivars; embryo sac; pollen; quantitative traits; radishes; seed development; seed yield; siliques;     Show all 11 Subjects
Abstract:
... The high yield of seeds can reduce the cost of seed production for parental lines, as well as F₁ cultivars in radish. The number of seeds per silique and silique length are two important traits among traits determining seed yield, but no study has been conducted on their quantitative trait loci (QTLs) in radish. A high-density linkage map was constructed, based on genotyping-by-sequencing (GBS) of ...
DOI:
10.3390/horticulturae8030268

17. Perspectives and recent progress of genome-wide association studies (GWAS) in fruits

Author:
Ghassan Zahid; Yıldız Aka Kaçar; Dicle Dönmez; Ayzin Küden; Tommaso Giordani
Source:
Molecular biology reports 2022 v.49 no.6 pp. 5341-5352
ISSN:
0301-4851
Subject:
genotyping by sequencing,   etc   ; fruit growing; fruits; genes; genetic selection; genetic traits; genotype; germplasm; marker-assisted selection; molecular biology; phenotype;     Show all 11 Subjects
Abstract:
... BACKGROUND: Earlier next-generation sequencing technologies are being vastly used to explore, administer, and investigate the gene space with accurate profiling of nucleotide variations in the germplasm. OVERVIEW AND PROGRESS: Recently, novel advancements in high-throughput sequencing technologies allow a genotyping-by-sequencing approach that has opened up new horizons for extensive genotyping ex ...
DOI:
10.1007/s11033-021-07055-9

18. Resistance in lentil (Lens culinaris) genetic resources to the pea aphid (Acyrthosiphon pisum)

Author:
Shimul Das; Lyndon D. Porter; Yu Ma; Clarice J. Coyne; Bernardo Chaves‐Cordoba; Rayapati A. Naidu
Source:
Entomologia experimentalis et applicata 2022 v.170 no.8 pp. 755-769
ISSN:
0013-8703
Subject:
genotyping by sequencing,   etc   ; Acyrthosiphon pisum; Lens culinaris; USDA; antibiotics; cluster analysis; cultivars; genomics; integrated pest management; lentils; quantitative traits; Iran;     Show all 12 Subjects
Abstract:
... The pea aphid (PA), Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae), can cause complete yield loss in lentil, Lens culinaris Medik. (Fabaceae, Leguminosae), if not managed properly. Determining lentil genetic resources with resistance to PA is important for integrated pest management (IPM) in production areas worldwide. The objectives of this study were to identify genetic resources and genes ...
Handle:
10113/7831299
DOI:
10.1111/eea.13202

19. Genomic insights into Sclerotinia basal stalk rot resistance introgressed from wild Helianthus praecox into cultivated sunflower (Helianthus annuus L.)

Author:
Talukder Zahirul I.; Underwood William; Misar Christopher G.; Seiler Gerald J.; Cai Xiwen; Li Xuehui; Qi Lili
Source:
Frontiers in plant science 2022 v.13 no. pp. 840954
ISSN:
1664-462X
Subject:
genotyping by sequencing,   etc   ; Helianthus annuus; Sclerotinia sclerotiorum; backcrossing; chromosome mapping; fungi; genomics; genotype; greenhouses; heritability; phenotypic variation; progeny; quantitative traits; spring;     Show all 14 Subjects
Abstract:
... Crop wild relatives of the cultivated sunflower (Helianthus annuus L.) are a valuable resource for its sustainable production. Helianthus praecox ssp. runyonii is a wild sunflower known for its resistance against diseases caused by the fungus, Sclerotinia sclerotiorum (Lib.) de Bary, which infects over 400 broadleaf hosts including many important food crops. The objective of this research was to d ...
Handle:
10113/7802870
DOI:
10.3389/fpls.2022.840954

20. Quantitative trait loci mapping of stem sugar content and stem diameter in sorghum recombinant inbred lines using genotyping-by-sequencing

Author:
Abera Takele; Tileye Feyissa; Tesfaye Disasa
Source:
Molecular biology reports 2022 v.49 no.4 pp. 3045-3054
ISSN:
0301-4851
Subject:
genotyping by sequencing,   etc   ; biofuels; chromosome mapping; forage; germplasm; molecular biology; phenotype; phenotypic variation; quantitative traits; sugar content; sweet sorghum; syrups; Ethiopia;     Show all 13 Subjects
Abstract:
... BACKGROUND: Sweet sorghum is an important crop with sugary stem that can mainly be used for syrup, fodder and bio-fuel. Many sugar content QTLs have been discovered from different sources through breeding worldwide. Most of these QTLs are detected using exotic germplasm as a mapping population. This study aimed to detect and map QTLs for stem sugar content and stem diameter targeting Ethiopian rec ...
DOI:
10.1007/s11033-022-07131-8