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Fitness benefits of male dominance behaviours depend on the degree of individual inbreeding in a polyandrous lizard

May 2020 | Piza-Roca C, Schoeman D, Frere C,
Proceedings of the Royal Society B. 287(1927) 20200097
DOI: 10.1098/rspb.2020.0097 | Show abstract ...

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Discovery of thermophilic Bacillales using reduced-representation genotyping for identification

May 2020 | Talamantes-Becerra B, Carling J, Kilian A, Georges A,
BMC Microbiology volume. 2020. 20 : 1-16.
DOI: 10.1186/s12866-020-01800-z | Show abstract ...

Background

This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin. Genomic DNA was double-digested with two combinations of restriction enzymes followed by PCR amplification, using a commercial provider of DArTseq™, Diversity Arrays Technology Pty Ltd. (Canberra, Australia). The resulting fragments which formed a reduced-representation of approximately 2.3% of the genome were sequenced. The sequence tags obtained were aligned against all available RefSeq bacterial genome assemblies by BLASTn to identify the nearest reference genome.

Results

Based on the preliminary identifications, a total of 99 bacterial isolates were identified to species level, from which 8 isolates were selected for whole-genome sequencing to assess the identification results. Novel species and strains were discovered within this set of isolates. The preliminary identifications obtained by reduced-representation genotyping, as well as identifications obtained by BLASTn alignment of the 16S rRNA gene sequence, were compared with those derived from the whole-genome sequence data, using the same RefSeq sequence database for the three methods. Identifications obtained with reduced-representation sequencing agreed with the identifications provided by whole-genome sequencing in 100% of cases. The identifications produced by BLASTn alignment of 16S rRNA gene sequence to the same database differed from those provided by whole-genome sequencing in 37.5% of cases, and produced ambiguous identifications in 50% of cases.

Conclusions

Previously, this method has been successfully demonstrated for use in bacterial identification for medical microbiology. This study demonstrates the first successful use of DArTseq™ for preliminary identification of thermophilic bacterial isolates, providing results in complete agreement with those obtained from whole-genome sequencing of the same isolates. The growing database of bacterial genome sequences provides an excellent resource for alignment of reduced-representation sequence data for identification purposes, and as the available sequenced genomes continue to grow, the technique will become more effective.

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Genetic diversity of coffee (Coffea spp.) in Mexico evaluated by using DArTseq and SNP markers

Apr 2020 | Spinoso-Castillo J L, Escamilla-Prado E, Aguilar-Rincón V H, Ramos V M, Santos G G d l, Pérez-Rodríguez P, Corona-Torres T,
Genetic Resources and Crop Evolution. 2020. 67(7) : 1795-1806.
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Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin (Kajikia audax), a broadly distributed and highly migratory pelagic species

Apr 2020 | Mamoozadeh N R, Graves J E, McDowell J R,
Evolutionary applications. 2020. 13(4) : 677-698.
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Genomic methodologies offer unprecedented opportunities for statistically robust studies of species broadly distributed in environments conducive to high gene flow, providing valuable information for wildlife conservation and management. Here, we sequence restriction site-associated DNA to characterize genome-wide single nucleotide polymorphisms (SNPs) in a broadly distributed and highly migratory large pelagic fish, striped marlin (Kajikia audax). Assessment of over 4,000 SNPs resolved spatiotemporal patterns of genetic connectivity throughout the species range in the Pacific and, for the first time, Indian oceans. Individual-based cluster analyses identified six genetically distinct populations corresponding with the western Indian, eastern Indian, western South Pacific, and eastern central Pacific oceans, as well as two populations in the North Pacific Ocean (F_ST = 0.0137–0.0819). F_ST outlier analyses identified a subset of SNPs (n = 59) putatively under the influence of natural selection and capable of resolving populations separated by comparatively high degrees of genetic differentiation. Temporal collections available for some regions demonstrated the stability of allele frequencies over three to five generations of striped marlin. Relative migration rates reflected lower levels of genetic connectivity between Indian Ocean populations (m_R ≤ 0.37) compared with most populations in the Pacific Ocean (m_R ≥ 0.57) and highlight the importance of the western South Pacific in facilitating gene flow between ocean basins. Collectively, our results provide novel insights into rangewide population structure for striped marlin and highlight substantial inconsistencies between genetically distinct populations and stocks currently recognized for fisheries management. More broadly, we demonstrate that species capable of long-distance dispersal in environments lacking obvious physical barriers to movement can display substantial population subdivision that persists over multiple generations and that may be facilitated by both neutral and adaptive processes. Importantly, surveys of genome-wide markers enable inference of population-level relationships using sample sizes practical for large pelagic fishes of conservation concern.

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Genomic prediction for disease resistance to Hepatopancreatic parvovirus and growth, carcass and quality traits in Banana shrimp Fenneropenaeus merguiensis

Mar 2020 | Nguyen N H, Phuthaworn C, Knibb W,
Genomics. 2020. 111(2) : 2021-2027.
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In-depth genome diversity, population structure and linkage disequilibrium analysis of worldwide diverse safflower (Carthamus tinctorius L.) accessions using NGS data generated by DArTseq technology

Feb 2020 | Hassani S M R, Talebi R, Pourdad S S, Naji A M, Fayaz F,
Mol Biol Rep. 2020. 47 : 2123–2135.
DOI: 10.1007/s11033-020-05312-x | Show abstract ...

Safflower (Carthamus tinctorius L.) is one of the most important oilseed crops for its seed oil rich in unsaturated fatty acids. Precise utilization of diverse genetic resources is fundamental in breeding programs to improve high yield genotypes with desirable traits. In this study, for the first time we report successful application of DArTseq technology; an efficient genotyping-by-sequencing (NGS); to analysis genetic diversity and population structure of 89 safflower accessions from worldwide origins. Totally, 19,639 DArTseq markers (10,130 SilicoDArTs and 9509 SNPs) generated through DArTseq genotyping. After filtering the data, 3431 polymorphic DArTseq markers (1136 SilicoDArTs and 2295 SNPs) used for genetic diversity, population structure and linkage disequilibrium analysis in safflower genotypes. All the SilicoDArT and SNP markers showed high reproducibility and call rate. Polymorphism information content (PIC) values ranged from 0.1 to 0.5, while ≥ 0.50% of SilicoDArTs and ≥ 0.64% SNPs showed PIC values more than median. Genotypes grouping using DArTseq markers resulted in three distinct clusters. Results showed weak correlation between safflower diversity pattern and origins. Analysis of molecular variance revealed that the majority of genetic variation was attributed to the differences among varieties within cluster populations and there was no significant molecular variance between origins. However, safflower of accessions belonged to Iran, Turkey, Pakistan and India indeed appear to be genetically similar and grouped close in referred cluster, while the accessions from Near East (Afghanistan, China) being distinct. Our results were in agreement with hypothesis that safflower domesticated in somewhere west of Fertile Crescent and then expanded through Africa and Europe. Present study using a panel of globally diverse safflower accessions and large number of DArTseq markers set the stage for future analysis of safflower domestication using large germplasm from proposed domestication centers. Also, studied germplasm in this study can be used as a valuable source for future genomic studies in safflower for mapping desirable traits through genome-wide association mapping studies.

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Global gene flow releases invasive plants from environmental constraints on genetic diversity

Feb 2020 | Smitha A L, Hodkinsonc T R, Villellasd J, Catforde J A, Csergo A M, Blombergh S P, Cronei E E, Ehrlénj J, Garciak M B, Lainel A, Roachn D A, Salguero-Gómezo R, Wardlep G M, Childsq D Z, Elderdr B D, Finna A, Munné-Boschs S, Baudraza M E A, Bódisu J, Brearleyv F Q, Bucharovaw A, Carusoy C M, Duncanz R P, Dwyerh J M, Goodenbb B, Groentemandd R, Hamreee L N, Helmff A, Kellya R, Laanistogg L, Lonatihh M, Mooreii J L, Moraless M, Olsenkk S L, Pärtelff M, Petryll W K, Ramulamm S, Rasmussenj P U, Enrihh S R, Roederoo A, Roscheroo C, Saastamoinenqq M, Tackj A J M, Töpperss J P, Vosett G E, Wandragz E M, Winglervv A, Buckleya Y M,
PNAS. 2020. 117(8) : 4218-4227.
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Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Feb 2020 | Pascual L, Ruiz M, López-Fernández M, Pérez-Peña H, Benavente E, Vázquez J F, Sansaloni C, Giraldo P,
BMC Genomics. 2020. 21 : 122.
DOI: 10.1186/s12864-020-6536-x | Show abstract ...

Background

One of the main goals of the plant breeding in the twenty-first century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping.

Results

The DArTseq GBS approach generated 10 K SNPs and 40 K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsp. durum, turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin.

Conclusions

The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties, and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

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DArTseq Molecular Markers Associated with the Spiny-Tip Leaf Margin in Pineapple (Ananas comosus L.)

Jan 2020 | Sanewski G M,
Tropical Plant Biol.. 2020. 13 : 91-116.
DOI: 10.1007/s12042-019-09245-z | Show abstract ...

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Mapping Agronomic and Quality Traits in Elite Durum Wheat Lines under Differing Water Regimes

Jan 2020 | Mérida-García R, Bentley A R, Gálvez S, Dorado G, Solís I, Ammar K, Hernandez P,
Agronomy. 2020. 10(1) : 144.
DOI: 10.3390/agronomy10010144 | Show abstract ...

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