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Genetica

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https://www.readbyqxmd.com/read/29143284/development-and-characterization-of-79-nuclear-markers-amplifying-in-viviparous-and-oviparous-clades-of-the-european-common-lizard
#1
J L Horreo, M L Peláez, T Suárez, P S Fitze
The European common lizard (Zootoca vivipara) is a widely distributed species across Europe and Asia exhibiting two reproductive modes (oviparity/viviparity), six major lineages and several sublineages. It has been used to tackle a large variety of research questions, nevertheless, few nuclear DNA sequence markers have been developed for this species. Here we developed 79 new nuclear DNA sequence markers using a clonation protocol. These markers were amplified in several oviparous and viviparous specimens including samples of all extant clades, to test the amplification success and their diversity...
November 15, 2017: Genetica
https://www.readbyqxmd.com/read/29119314/trait-specific-long-term-consequences-of-genomic-selection-in-beef-cattle
#2
Haroldo Henrique de Rezende Neves, Roberto Carvalheiro, Sandra Aidar de Queiroz
Simulation studies allow addressing consequences of selection schemes, helping to identify effective strategies to enable genetic gain and maintain genetic diversity. The aim of this study was to evaluate the long-term impact of genomic selection (GS) in genetic progress and genetic diversity of beef cattle. Forward-in-time simulation generated a population with pattern of linkage disequilibrium close to that previously reported for real beef cattle populations. Different scenarios of GS and traditional pedigree-based BLUP (PBLUP) selection were simulated for 15 generations, mimicking selection for female reproduction and meat quality...
November 8, 2017: Genetica
https://www.readbyqxmd.com/read/29101627/genetic-mapping-reveals-a-dominant-awn-inhibiting-gene-related-to-differentiation-of-the-variety-anathera-in-the-wild-diploid-wheat-aegilops-tauschii
#3
Ryo Nishijima, Tatsuya M Ikeda, Shigeo Takumi
Aegilops tauschii, a wild wheat relative, is the D-genome donor of common wheat. Subspecies and varieties of Ae. tauschii are traditionally classified based on differences in their inflorescence architecture. However, the genetic information for their diversification has been quite limited in the wild wheat relatives. The variety anathera has no awn on the lemma, but the genetic basis for this diagnostic character is unknown. Wide variations in awn length traits at the top and middle spikes were found in the Ae...
November 3, 2017: Genetica
https://www.readbyqxmd.com/read/29071446/sequence-requirement-of-the-ade6-4095-meiotic-recombination-hotspot-in-schizosaccharomyces-pombe
#4
Steven J Foulis, Kyle R Fowler, Walter W Steiner
Homologous recombination occurs at a greatly elevated frequency in meiosis compared to mitosis and is initiated by programmed double-strand DNA breaks (DSBs). DSBs do not occur at uniform frequency throughout the genome in most organisms, but occur preferentially at a limited number of sites referred to as hotspots. The location of hotspots have been determined at nucleotide-level resolution in both the budding and fission yeasts, and while several patterns have emerged regarding preferred locations for DSB hotspots, it remains unclear why particular sites experience DSBs at much higher frequency than other sites with seemingly similar properties...
October 25, 2017: Genetica
https://www.readbyqxmd.com/read/29032466/codon-usage-and-amino-acid-usage-influence-genes-expression-level
#5
Prosenjit Paul, Arup Kumar Malakar, Supriyo Chakraborty
Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes...
October 14, 2017: Genetica
https://www.readbyqxmd.com/read/29030763/conservation-and-genetic-characterisation-of-common-bean-landraces-from-cilento-region-southern-italy-high-differentiation-in-spite-of-low-genetic-diversity
#6
Daniele De Luca, Paola Cennamo, Emanuele Del Guacchio, Riccardo Di Novella, Paolo Caputo
Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction...
October 13, 2017: Genetica
https://www.readbyqxmd.com/read/29030762/genetic-diversity-of-avenin-like-b-genes-in-aegilops-tauschii-coss
#7
Dong Cao, Hongxia Wang, Bo Zhang, Baolong Liu, Dengcai Liu, Wenjie Chen, Huaigang Zhang
Avenin-like storage proteins influence the rheological properties and processing quality in common wheat, and the discovery of new alleles will benefit wheat quality improvement. In this study, 13 avenin-like b alleles (TaALPb7D-A-M) were discovered in 108 Aegilops tauschii Coss. accessions. Ten alleles were reported for the first time, while the remaining three alleles were the same as alleles in other species. A total of 15 nucleotide changes were detected in the 13 alleles, resulting in only 11 amino acid changes because of synonymous mutations...
October 13, 2017: Genetica
https://www.readbyqxmd.com/read/28921302/comparative-evolutionary-genomics-of-corynebacterium-with-special-reference-to-codon-and-amino-acid-usage-diversities
#8
Shilpee Pal, Indrani Sarkar, Ayan Roy, Pradeep K Das Mohapatra, Keshab C Mondal, Arnab Sen
The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium...
September 18, 2017: Genetica
https://www.readbyqxmd.com/read/28916874/development-of-cacta-transposon-derived-scar-markers-and-their-use-in-population-structure-analysis-in-zea-mays
#9
Neha Samir Roy, Kyong-Cheul Park, Sung-Il Lee, Min-Ji Im, Rahul Vasudeo Ramekar, Nam-Soo Kim
Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population...
September 15, 2017: Genetica
https://www.readbyqxmd.com/read/29103106/tracing-the-spatio-temporal-dynamics-of-endangered-fin-whales-balaenoptera-physalus-within-baleen-whale-mysticeti-lineages-a-mitogenomic-perspective
#10
Jihyun Yu, Bo-Hye Nam, Joon Yoon, Eun Bae Kim, Jung Youn Park, Heebal Kim, Sook Hee Yoon
To explore the spatio-temporal dynamics of endangered fin whales (Balaenoptera physalus) within the baleen whale (Mysticeti) lineages, we analyzed 148 published mitochondrial genome sequences of baleen whales. We used a Bayesian coalescent approach as well as Bayesian inferences and maximum likelihood methods. The results showed that the fin whales had a single maternal origin, and that there is a significant correlation between geographic location and evolution of global fin whales. The most recent common female ancestor of this species lived approximately 9...
December 2017: Genetica
https://www.readbyqxmd.com/read/28942569/buzz-in-paris-flower-production-and-plant-pollinator-interactions-in-plants-from-contrasted-urban-and-rural-origins
#11
James Desaegher, Sophie Nadot, Isabelle Dajoz, Bruno Colas
Urbanisation, associated with habitat fragmentation, affects pollinator communities and insect foraging behaviour. These biotic changes are likely to select for modified traits in insect-pollinated plants from urban populations compared to rural populations. To test this hypothesis, we conducted an experiment involving four plant species commonly found in both urban and rural landscapes of the Île-de-France region (France): Cymbalaria muralis, Geranium robertianum, Geum urbanum and Prunella vulgaris. The four species were grown in four urban and four rural experimental sites in 2015...
December 2017: Genetica
https://www.readbyqxmd.com/read/28942468/complete-mitochondrial-genome-of-porzana-fusca-and-porzana-pusilla-and-phylogenetic-relationship-of-16-rallidae-species
#12
Peng Chen, Yuqing Han, Chaoying Zhu, Bin Gao, Luzhang Ruan
The complete mitochondrial genome sequences of Porzana fusca and Porzana pusilla were determined. The two avian species share a high degree of homology in terms of mitochondrial genome organization and gene arrangement. Their corresponding mitochondrial genomes are 16,935 and 16,978 bp and consist of 37 genes and a control region. Their PCGs were both 11,365 bp long and have similar structure. Their tRNA gene sequences could be folded into canonical cloverleaf secondary structure, except for tRNA(Ser (AGY)), which lost its "DHU" arm...
December 2017: Genetica
https://www.readbyqxmd.com/read/28940104/an-american-termite-in-paris-temporal-colony-dynamics
#13
Guillaume Baudouin, Franck Dedeine, Nicolas Bech, Stéphanie Bankhead-Dronnet, Simon Dupont, Anne-Geneviève Bagnères
Termites of the genus Reticulitermes are widespread invaders, particularly in urban habitats. Their cryptic and subterranean lifestyle makes them difficult to detect, and we know little about their colony dynamics over time. In this study we examined the persistence of Reticulitermes flavipes (Kollar) colonies in the city of Paris over a period of 15 years. The aim was (1) to define the boundaries of colonies sampled within the same four areas over two sampling periods, (2) to determine whether the colonies identified during the first sampling period persisted to the second sampling period, and (3) to compare the results obtained when colonies were delineated using a standard population genetic approach versus a Bayesian clustering method that combined both spatial and genetic information...
December 2017: Genetica
https://www.readbyqxmd.com/read/28939989/the-cotesia-sesamiae-story-insight-into-host-range-evolution-in-a-hymenoptera-parasitoid-and-implication-for-its-use-in-biological-control-programs
#14
REVIEW
L Kaiser, S Dupas, A Branca, E A Herniou, C W Clarke, C Capdevielle Dulac, J Obonyo, R Benoist, J Gauthier, P A Calatayud, J F Silvain, B P Le Ru
This review covers nearly 20 years of studies on the ecology, physiology and genetics of the Hymenoptera Cotesia sesamiae, an African parasitoid of Lepidoptera that reduces populations of common maize borers in East and South Africa. The first part of the review presents studies based on sampling of C. sesamiae from maize crops in Kenya. From this agrosystem including one host plant and three main host borer species, studies revealed two genetically differentiated populations of C. sesamiae species adapted to their local host community, and showed that their differentiation involved the joint evolution of virulence genes and sensory mechanisms of host acceptance, reinforced by reproductive incompatibility due to Wolbachia infection status and natural inbreeding...
December 2017: Genetica
https://www.readbyqxmd.com/read/28939979/relationship-between-oviposition-virulence-gene-expression-and-parasitism-success-in-cotesia-typhae-nov-sp-parasitoid-strains
#15
R Benoist, C Chantre, C Capdevielle-Dulac, M Bodet, F Mougel, P A Calatayud, S Dupas, E Huguet, R Jeannette, J Obonyo, C Odorico, J F Silvain, B Le Ru, L Kaiser
Studying mechanisms that drive host adaptation in parasitoids is crucial for the efficient use of parasitoids in biocontrol programs. Cotesia typhae nov. sp. (Fernández-Triana) (Hymenoptera: Braconidae) is a newly described parasitoid of the Mediterranean corn borer Sesamia nonagrioides (Lefebvre) (Lepidoptera: Noctuidae). Braconidae are known for their domesticated bracovirus, which is injected with eggs in the host larva to overcome its resistance. In this context, we compared reproductive success traits of four Kenyan strains of C...
December 2017: Genetica
https://www.readbyqxmd.com/read/28932936/is-induction-ability-of-seed-germination-of-phelipanche-ramosa-phylogenetically-structured-among-hosts-a-case-study-on-fabaceae-species
#16
Rémi Perronne, Stéphanie Gibot-Leclerc, Fabrice Dessaint, Carole Reibel, Valérie Le Corre
Phelipanche ramosa is a major root-holoparasitic damaging weed characterized by a broad host range, including numerous Fabaceae species. In France, the agricultural threat posed by P. ramosa has increased over two decades due to the appearance of a genetically differentiated pathovar presenting a clear host specificity for oilseed rape. The new pathovar has led to a massive expansion of P. ramosa in oilseed rape fields. The germination rate of P. ramosa seeds is currently known to vary among P. ramosa pathovars and host species...
December 2017: Genetica
https://www.readbyqxmd.com/read/28932924/when-gis-zooms-in-spatio-genetic-maps-of-multipaternity-in-armadillidium-vulgare
#17
Nicolas Bech, Charlotte Depeux, Sylvine Durand, Catherine Debenest, Alexandra Lafitte, Sophie Beltran-Bech
Geographic information system (GIS) tools are designed to illustrate, analyse and integrate geographic or spatial data, usually on a macroscopic scale. By contrast, genetic tools focus on a microscopic scale. Because in reality, landscapes have no predefined scale, our original study aims to develop a new approach, combining both cartographic and genetic approaches to explore microscopic landscapes. For this, we focused on Armadillidium vulgare, a terrestrial isopod model in which evolutionary pressures imposed by terrestrial life have led to the development of internal fertilisation and, consequently, to associated physiological changes...
December 2017: Genetica
https://www.readbyqxmd.com/read/28913775/complete-mitochondrial-genome-of-taharana-fasciana-insecta-hemiptera-cicadellidae-and-comparison-with-other-cicadellidae-insects
#18
Jiajia Wang, Hu Li, Renhuai Dai
Here, we describe the first complete mitochondrial genome (mitogenome) sequence of the leafhopper Taharana fasciana (Coelidiinae). The mitogenome sequence contains 15,161 bp with an A + T content of 77.9%. It includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding (A + T-rich) region; in addition, a repeat region is also present (GenBank accession no. KY886913). These genes/regions are in the same order as in the inferred insect ancestral mitogenome. All protein-coding genes have ATN as the start codon, and TAA or single T as the stop codons, except the gene ND3, which ends with TAG...
December 2017: Genetica
https://www.readbyqxmd.com/read/28905157/landscape-genetics-in-the-subterranean-rodent-ctenomys-chasiquensis-associated-with-highly-disturbed-habitats-from-the-southeastern-pampas-region-argentina
#19
Matías Sebastián Mora, Fernando J Mapelli, Aldana López, María Jimena Gómez Fernández, Patricia M Mirol, Marcelo J Kittlein
Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci...
December 2017: Genetica
https://www.readbyqxmd.com/read/28875394/genomic-based-breeding-tools-for-tropical-maize-improvement
#20
REVIEW
Thammineni Chakradhar, Vemuri Hindu, Palakolanu Sudhakar Reddy
Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions...
December 2017: Genetica
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