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1. Parentage assignment with genotyping‐by‐sequencing data

Author:
Whalen, Andrew; Gorjanc, Gregor; Hickey, John M.
Source:
Journal of animal breeding and genetics 2019 v.136 no.2 pp. 102-112
ISSN:
0931-2668
Subject:
genotyping by sequencing,   etc   ; ecology; homozygosity; loci; parentage; parents;     Show all 6 Subjects
Abstract:
... In this paper, we evaluate using genotype‐by‐sequencing (GBS) data to perform parentage assignment in lieu of traditional array data. The use of GBS data raises two issues: First, for low‐coverage (e.g., <2×) GBS data, it may not be possible to call the genotype at many loci, a critical first step for detecting opposing homozygous markers. Second, the amount of sequencing coverage may vary across ...
DOI:
10.1111/jbg.12370

2. Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations

Author:
Wang, Xiao; Lund, Mogens Sandø; Ma, Peipei; Janss, Luc; Kadarmideen, Haja N.; Su, Guosheng
Source:
Journal of animal science and biotechnology 2019 v.10 no.1 pp. 8
ISSN:
2049-1891
Subject:
genotyping by sequencing,   etc   ; genomics; genotyping errors; homozygosity; livestock; loci; prediction; quality control; single nucleotide polymorphism;     Show all 9 Subjects
Abstract:
... BACKGROUND: Genotyping by sequencing (GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes, dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic pr ...
DOI:
10.1186/s40104-019-0315-z

3. Evaluation of genotyping by sequencing for population genetics of sibling and hybridizing birds: an example using Syrian and Great Spotted Woodpeckers

Author:
Gurgul, Artur; Miksza-Cybulska, Anna; Szmatoła, Tomasz; Semik-Gurgul, Ewelina; Jasielczuk, Igor; Bugno-Poniewierska, Monika; Figarski, Tomasz; Kajtoch, Łukasz
Source:
Journal of ornithology 2019 v.160 no.1 pp. 287-294
ISSN:
2193-7192
Subject:
genotyping by sequencing,   etc   ; genotype; introgression; nucleotide sequences; phenotype; population genetics; urban population; wild birds; woodpeckers;     Show all 9 Subjects
Abstract:
... Recent high-throughput genotyping technologies allow for comprehensive genomic analyses on an unprecedented scale. However the advantages of the most commonly used tools are strongly limited in non-model organisms, including wild birds. In this study we attempt to test the utility of genotyping by sequencing (GBS) without relying on the reference genome sequence in selected pairs of sibling bird s ...
DOI:
10.1007/s10336-018-1601-9

4. Cryptic natural hybridization between two species of Protea

Author:
Mitchell, N.; Holsinger, K.E.
Source:
South African journal of botany 2018 v.118 pp. 306-314
ISSN:
0254-6299
Subject:
genotyping by sequencing,   etc   ; Protea; introgression; mountains; seedlings; single nucleotide polymorphism;     Show all 6 Subjects
Abstract:
... Protea punctata and P. venusta are closely related, but morphologically distinct, species that naturally hybridize in the wild. Here we examined patterns of hybridization and cryptic introgression in seedlings grown from seeds collected at Blesberg Mountain in the Swartberg Mountain range. We used restriction site associated genotyping by sequencing (RAD-Seq) to identify 7185 single nucleotide pol ...
DOI:
10.1016/j.sajb.2017.12.002

5. Saffron (Crocus sativus) is an autotriploid that evolved in Attica (Greece) from wild Crocus cartwrightianus

Author:
Nemati, Zahra; Harpke, Dörte; Gemicioglu, Almila; Kerndorff, Helmut; Blattner, Frank R.
Source:
Molecular phylogenetics and evolution 2019 v.136 pp. 14-20
ISSN:
1055-7903
Subject:
genotyping by sequencing,   etc   ; Crocus sativus; DNA; alleles; chloroplast genome; chloroplasts; genotype; islands; phylogeny; saffron; triploidy; vegetative propagation; Greece;     Show all 13 Subjects
Abstract:
... Crocus sativus, the saffron crocus, is the source of saffron, which is made from the dried stigmas of the plant. It is a male-sterile triploid lineage that ever since its origin has been propagated vegetatively. Its mode of evolution and area of origin are matters of long-lasting debates. Here we analyzed chloroplast genomes and genome-wide DNA polymorphisms obtained through genotyping-by-sequenci ...
DOI:
10.1016/j.ympev.2019.03.022

6. Single Nucleotide Polymorphisms and Biochemical Markers As Complementary Tools To Characterize Hops (Humulus lupulus L.) in Brewing Practice

Author:
Van Holle, Ann; Muylle, Hilde; Ruttink, Tom; Van Landschoot, Anita; Haesaert, Geert; Naudts, Dirk; De Keukeleire, Denis; Roldán-Ruiz, Isabel
Source:
Journal of agricultural and food chemistry 2019 v.67 no.13 pp. 3761-3771
ISSN:
1520-5118
Subject:
genotyping by sequencing,   etc   ; Geographical Locations; Humulus lupulus; beers; biomarkers; brewing; brewing industry; quality control; single nucleotide polymorphism;     Show all 9 Subjects
Abstract:
... In brewing practice, the use of the appropriate hop variety is essential to produce consistent and high-quality beers. Yet, hop batches of the same variety cultivated in different geographical regions can display significant biochemical differences, resulting in specific taste- and aroma-related characteristics in beer. In this study, we illustrate the complementarity of genetic and biochemical fi ...
DOI:
10.1021/acs.jafc.9b00816

7. Genotyping-by-sequencing performance in selected livestock species

Author:
Gurgul, Artur; Miksza-Cybulska, Anna; Szmatoła, Tomasz; Jasielczuk, Igor; Piestrzyńska-Kajtoch, Agata; Fornal, Agnieszka; Semik-Gurgul, Ewelina; Bugno-Poniewierska, Monika
Source:
Genomics 2019 v.111 no.2 pp. 186-195
ISSN:
0888-7543
Subject:
genotyping by sequencing,   etc   ; cattle; cost effectiveness; genes; genetic variation; high-throughput nucleotide sequencing; horses; sheep; single nucleotide polymorphism;     Show all 9 Subjects
Abstract:
... Application of next generation sequencing for large scale genotyping in livestock is limited by high costs and challenging data analysis process. However, available restriction enzyme-based enrichment techniques like e.g. genotyping-by-sequencing (GBS) are promising tools allowing reduction of financial outlies by a high sample multiplexing and narrowing down the sequenced genome areas to the rand ...
DOI:
10.1016/j.ygeno.2018.02.002

8. Mapping kernel texture in a soft durum (Triticum turgidum subsp. durum) wheat population

Author:
Ibba, Maria Itria; Kiszonas, Alecia M.; See, Deven R.; Skinner, Daniel Z.; Morris, Craig F.
Source:
Journal of cereal science 2019 v.85 pp. 20-26
ISSN:
0733-5210
Subject:
genotyping by sequencing,   etc   ; Triticum turgidum subsp. durum; additive effect; alleles; durum wheat; genetic factors; hardness; introgression; loci; seeds; texture;     Show all 11 Subjects
Abstract:
... Kernel texture (”hardness”) is one of the major determinants of wheat quality and is primarily controlled by the Puroindoline (Pin) genes, located at the Hardness (Ha) locus. The absence of the Ha locus is responsible for the extremely hard kernels of durum wheat (T. turgidum subsp. durum). Recently, the Pin genes from a soft common wheat variety were introgressed into durum wheat through homoeolo ...
Handle:
10113/6179930
DOI:
10.1016/j.jcs.2018.10.006

9. Genome-wide association mapping of virulence gene in rice blast fungus Magnaporthe oryzae using a genotyping by sequencing approach

Author:
Korinsak, Siripar; Tangphatsornruang, Sithichoke; Pootakham, Wirulda; Wanchana, Samart; Plabpla, Anucha; Jantasuriyarat, Chatchawan; Patarapuwadol, Sujin; Vanavichit, Apichart; Toojinda, Theerayut
Source:
Genomics 2019 v.111 no.4 pp. 661-668
ISSN:
0888-7543
Subject:
genotyping by sequencing,   etc   ; Magnaporthe oryzae; Oryza sativa; blast disease; chromosome mapping; chromosomes; fungi; genes; genetic variation; pathogens; phenotype; population structure; rice; single nucleotide polymorphism; virulence;     Show all 15 Subjects
Abstract:
... Magnaporthe oryzae is a fungal pathogen causing blast disease in many plant species. In this study, seventy three isolates of M. oryzae collected from rice (Oryza sativa) in 1996–2014 were genotyped using a genotyping-by-sequencing approach to detect genetic variation. An association study was performed to identify single nucleotide polymorphisms (SNPs) associated with virulence genes using 831 se ...
DOI:
10.1016/j.ygeno.2018.05.011

10. Genetic diversity and heritability of economically important traits in captive Australasian snapper (Chrysophrys auratus)

Author:
Ashton, David T.; Hilario, Elena; Jaksons, Peter; Ritchie, Peter A.; Wellenreuther, Maren
Source:
Aquaculture 2019 v.505 pp. 190-198
ISSN:
0044-8486
Subject:
genotyping by sequencing,   etc   ; animal production; aquaculture; breeding programs; genetic variation; heritability; inbreeding; parentage; parents; pedigree; progeny; snapper; species diversity; New Zealand;     Show all 14 Subjects
Abstract:
... Aquaculture is the fastest growing animal production sector in New Zealand but low species diversity is a barrier to long-term growth. Snapper (Chrysophrys auratus) has been identified as a promising candidate for aquaculture development and an initial population has been established at the New Zealand Institute for Plant & Food Research Limited. The aim of the present study was to combine high-th ...
DOI:
10.1016/j.aquaculture.2019.02.034

11. A high‐throughput system used to determine frequency and distribution of phosphine resistance across large geographical regions

Author:
Schlipalius, David I; Tuck, Andrew G; Pavic, Hervoika; Daglish, Gregory J; Nayak, Manoj K; Ebert, Paul R
Source:
Pest management science 2019 v.75 no.4 pp. 1091-1098
ISSN:
1526-498X
Subject:
genotyping by sequencing,   etc   ; Rhyzopertha dominica; alleles; dihydrolipoyl dehydrogenase; farms; gene frequency; geographical distribution; high-throughput nucleotide sequencing; insects; pest management; phosphine; resistance management; surveys; Australia;     Show all 14 Subjects
Abstract:
... BACKGROUND: Next‐generation sequencing can enable genetic surveys of large numbers of individuals. We developed a genotyping‐by‐sequencing assay for detecting strong phosphine resistance alleles in the dihydrolipoamide dehydrogenase (dld) gene of Rhyzopertha dominica populations. The assay can estimate the distribution and frequency of resistance variants in thousands of individual insects in a si ...
DOI:
10.1002/ps.5221

12. Application of microsatellite genotyping by sequencing (SSR-GBS) to measure genetic diversity of the East African Oreochromis niloticus

Author:
Tibihika, Papius Dias; Curto, Manuel; Dornstauder-Schrammel, Eva; Winter, Silvia; Alemayehu, Esayas; Waidbacher, Herwig; Meimberg, Harald
Source:
Conservation genetics 2019 v.20 no.2 pp. 357-372
ISSN:
1566-0621
Subject:
genotyping by sequencing,   etc   ; Oreochromis niloticus; alleles; automation; bioinformatics; data collection; ecological genetics; genetic markers; genetic variation; genotype; loci; microsatellite repeats; polymerase chain reaction; population genetics;     Show all 14 Subjects
Abstract:
... Microsatellites play an important role when investigating population and ecological genetics, although high effort in development and genotyping constitute a technical constraint and remains a major bottleneck. Here we use a microsatellite genotyping approach utilizing sequences of amplicons for allele calling (SSR-GBS) based on Illumina that requires less effort and time. The approach consist of ...
DOI:
10.1007/s10592-018-1136-x

13. Experimental drought reduces genetic diversity in the grassland foundation species Bouteloua eriopoda

Author:
Whitney, Kenneth D.; Mudge, Joann; Natvig, Donald O.; Sundararajan, Anitha; Pockman, William T.; Bell, Jennifer; Collins, Scott L.; Rudgers, Jennifer A.
Source:
Oecologia 2019 v.189 no.4 pp. 1107-1120
ISSN:
0029-8549
Subject:
genotyping by sequencing,   etc   ; Bouteloua eriopoda; biomass; climate; climate change; conservation areas; drought; ecosystems; genetic variation; grasses; grasslands; growing season; sexual reproduction; shrublands; stolons; New Mexico;     Show all 16 Subjects
Abstract:
... Understanding the resistance and resilience of foundation plant species to climate change is a critical issue because the loss of these species would fundamentally reshape communities and ecosystem processes. High levels of population genetic diversity may buffer foundation species against climate disruptions, but the strong selective pressures associated with climatic shifts may also rapidly redu ...
DOI:
10.1007/s00442-019-04371-7

14. Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations

Author:
Swarm, Stephen A.; Sun, Lianjun; Wang, Xutong; Wang, Weidong; Brown, Patrick J.; Ma, Jianxin; Nelson, Randall L.
Source:
Theoretical and applied genetics 2019 v.132 no.4 pp. 1195-1209
ISSN:
0040-5752
Subject:
genotyping by sequencing,   etc   ; Glycine max; Glycine soja; chromosomes; domestication; genetic markers; genomics; germplasm; growth habit; hybrids; quantitative trait loci; seeds; single nucleotide polymorphism; soybeans; wild relatives; East Asia;     Show all 16 Subjects
Abstract:
... KEY MESSAGE: A total of 132 domestication-related QTLs, of which 41 were novel, were identified through genotyping-by-sequencing of two Glycine max × Glycine soja populations. Soybean [Glycine max (L.) Merr.] was domesticated in East Asia from the wild progenitor Glycine soja. The domestication process led to many distinct morphological changes that adapt it to cultivation. These include larger se ...
DOI:
10.1007/s00122-018-3272-6

15. Genetic modification of spikelet arrangement in wheat increases grain number without significantly affecting grain weight

Author:
Wolde, Gizaw M.; Mascher, Martin; Schnurbusch, Thorsten
Source:
Molecular genetics and genomics 2019 v.294 no.2 pp. 457-468
ISSN:
1617-4615
Subject:
genotyping by sequencing,   etc   ; alleles; backcrossing; dry matter accumulation; durum wheat; florets; genetic engineering; grain yield; introgression; isogenic lines; phenotype; seeds; spikelets;     Show all 13 Subjects
Abstract:
... Crop yield is determined by the acquisition and allocation of photoassimilates in sink organs. Therefore, genetic modification of sink size is essential for understanding the complex signaling network regulating sink strength and source activities. Sink size in wheat depends on the number of spikelets per spike, floret/grain number per spikelet as well as the grain weight or dry matter accumulatio ...
DOI:
10.1007/s00438-018-1523-5

16. Genotyping-by-sequencing (GBS), ITS and cpDNA phylogenies reveal the existence of a distinct Pyrenean/Cantabrian lineage in the European high mountain genus Homogyne (Asteraceae) and imply dual westward migration of the genus

Author:
Gerschwitz-Eidt, Michael A.; Kadereit, Joachim W.
Source:
Alpine botany 2019 v.129 no.1 pp. 21-31
ISSN:
1664-2201
Subject:
genotyping by sequencing,   etc   ; Asteraceae; alpine plants; botany; chloroplast DNA; data collection; genetic variation; geographical distribution; hybridization; internal transcribed spacers; phylogeny; species diversity; Alps region;     Show all 13 Subjects
Abstract:
... Quaternary climatic oscillations have been a major factor in shaping plant diversity and distribution in the European Alpine System (EAS). Plants responded to these oscillations with repeated changes in their abundance and geographical distribution. However, oscillating shifts in geographical distribution have only rarely been reported in molecular analyses of genetic variation across the EAS. Hom ...
DOI:
10.1007/s00035-018-0212-7

17. Introgression reshapes recombination distribution in grapevine interspecific hybrids

Author:
Delame, Marion; Prado, Emilce; Blanc, Sophie; Robert-Siegwald, Guillaume; Schneider, Christophe; Mestre, Pere; Rustenholz, Camille; Merdinoglu, Didier
Source:
Theoretical and applied genetics 2019 v.132 no.4 pp. 1073-1087
ISSN:
0040-5752
Subject:
genotyping by sequencing,   etc   ; Vitis rotundifolia; Vitis vinifera; backcrossing; chromosome mapping; chromosomes; crops; cultivars; genes; genetic recombination; genomics; grapes; hybrids; interspecific hybridization; introgression; meiosis; parents; single nucleotide polymorphism;     Show all 18 Subjects
Abstract:
... KEY MESSAGE: In grapevine interspecific hybrids, meiotic recombination is suppressed in homeologous regions and enhanced in homologous regions of recombined chromosomes, whereas crossover rate remains unchanged when chromosome pairs are entirely homeologous. Vitis rotundifolia, an American species related to the cultivated European grapevine Vitis vinifera, has a high level of resistance to severa ...
DOI:
10.1007/s00122-018-3260-x

18. BSA-seq mapping reveals major QTL for broomrape resistance in four sunflower lines

Author:
Imerovski, Ivana; Dedić, Boško; Cvejić, Sandra; Miladinović, Dragana; Jocić, Siniša; Owens, Gregory L.; Tubić, Nataša Kočiš; Rieseberg, Loren H.
Source:
Molecular breeding 2019 v.39 no.3 pp. 41
ISSN:
1380-3743
Subject:
genotyping by sequencing,   etc   ; Helianthus annuus; Orobanche cernua; breeding programs; chromosomes; genetic markers; genomics; parasitic plants; quantitative trait loci; races; resistance genes; virulence;     Show all 12 Subjects
Abstract:
... Broomrape (Orobanche cumana) is a parasitic weed that causes substantial yield losses in sunflower. In this study, four biparental genetic populations comprised of between 96 and 150 F₃ families were phenotyped for resistance to broomrape race G. Bulk segregant analyses (BSA) combined with genotyping-by-sequencing (GBS) technology was used to verify previously identified genes and map new resistan ...
DOI:
10.1007/s11032-019-0948-9

19. Genome-wide association studies of molybdenum and selenium concentrations in C. arietinum and C. reticulatum seeds

Author:
Ozkuru, Esin; Ates, Duygu; Nemli, Seda; Erdogmus, Semih; Karaca, Nur; Yilmaz, Hasan; Yagmur, Bulent; Kartal, Canan; Tosun, Muzaffer; Ocak, Ozgul Ozdestan; Otles, Semih; Kahriman, Abdullah; Tanyolac, Muhammed Bahattin
Source:
Molecular breeding 2019 v.39 no.3 pp. 46
ISSN:
1380-3743
Subject:
genotyping by sequencing,   etc   ; Cicer arietinum; Cicer reticulatum; agronomic traits; chickpeas; chromosomes; crops; genetic variation; genome-wide association study; human nutrition; molybdenum; population structure; seeds; selenium; single nucleotide polymorphism;     Show all 15 Subjects
Abstract:
... Chickpea is the second most important and ancient pulse crop with its use in human diet for approximately 7500 years as one of the Neolithic founder crops. Previous studies on chickpea have predominantly focused on agronomic traits, with only limited research being dedicated to developing micronutrient-rich crops over the last half century. The objectives of this study were to identify genetic var ...
DOI:
10.1007/s11032-019-0947-x

20. Genome-wide association study of the level of blood components in Pekin ducks

Author:
Zhu, Feng; Cui, Qian-Qian; Yang, Yu-ze; Hao, Jin-Ping; Yang, Fang-Xi; Hou, Zhuo-Cheng
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
genotyping by sequencing,   etc   ; Pekin; alkaline phosphatase; blood serum; breeding programs; calcium; cholinesterase; ducks; genes; genome-wide association study; humans; metabolism; quantitative trait loci; single nucleotide polymorphism;     Show all 14 Subjects
Abstract:
... Blood components are considered to reflect nutrient metabolism and immune activity in both humans and animals. In this study, we measured 12 blood components in Pekin ducks and performed genome-wide association analysis to identify the QTLs (quantitative trait locus) using a genotyping-by-sequencing strategy. A total of 54 QTLs were identified for blood components. One genome-wide significant QTL ...
DOI:
10.1016/j.ygeno.2019.02.017