Genome-wide diversity analysis for signatures of selection of Bos indicus adaptability under extreme agro-climatic conditions of temperate and tropical ecosystems

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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Potential for Aquifer Storage and Recovery (ASR) in South Bihar, India

Sustainability ◽

10.3390/su13063502 ◽

2021 ◽

Vol 13 (6) ◽

pp. 3502

Author(s):

Somnath Bandyopadhyay ◽

Aviram Sharma ◽

Satiprasad Sahoo ◽

Kishore Dhavala ◽

Prabhakar Sharma

Keyword(s):

Pilot Study ◽

Environmental Sustainability ◽

Hard Rock ◽

Climatic Conditions ◽

Aquifer Storage And Recovery ◽

Aquifer Recharge ◽

Aquifer Storage ◽

Cropping Season ◽

Selection Of ◽

Surface Technique

Among the several options of managed aquifer recharge (MAR) techniques, the aquifer storage and recovery (ASR) is a well-known sub-surface technique to replenish depleted aquifers, which is contingent upon the selection of appropriate sites. This paper explores the potential of ASR for groundwater recharge in the hydrological, hydrogeological, social, and economic context of South Bihar in India. Based on the water samples from more than 137 wells and socio-economic surveys, ASR installations were piloted through seven selected entrepreneurial farmers in two villages of South Bihar. The feasibility of ASR in both hard rock and deep alluvial aquifers was demonstrated for the prominent aquifer types in the marginal alluvial plains of South Bihar and elsewhere. It was postulated through this pilot study that a successful spread of ASR in South Bihar can augment usable water resources for agriculture during the winter cropping season. More importantly, ASR can adapt to local circumstances and challenges under changing climatic conditions. The flexible and participatory approach in this pilot study also allowed the farmers to creatively engage with the design and governance aspects of the recharge pit. The entrepreneurial farmers-led model builds local accountability, creates avenues for private investments, and opens up the space for continued innovation in technology and management, while also committing to resource distributive justice and environmental sustainability.

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A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species

Genetics Selection Evolution ◽

10.1186/s12711-020-00599-7 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Wim Gorssen ◽

Roel Meyermans ◽

Steven Janssens ◽

Nadine Buys

Keyword(s):

Association Studies ◽

Genome Wide Association Studies ◽

Single Nucleotide ◽

Future Studies ◽

Snp Data ◽

Animal Populations ◽

Genome Wide ◽

Starting Point ◽

Different Populations ◽

Signatures Of Selection

Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). Conclusions We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.

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Analysis of yield and oil from a series of canola breeding trials. Part II. Exploring variety by environment interaction using factor analysisThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-080 ◽

2010 ◽

Vol 53 (11) ◽

pp. 1002-1016 ◽

Cited By ~ 59

Author(s):

B.R. Cullis ◽

A.B. Smith ◽

C.P. Beeck ◽

W.A. Cowling

Keyword(s):

Pedigree Information ◽

Environment Interaction ◽

Correlation Matrices ◽

New Approach ◽

Genome Wide ◽

Selection Indices ◽

New Varieties ◽

Oilseed Brassicas ◽

Analytic Models ◽

Selection Of

Exploring and exploiting variety by environment (V × E) interaction is one of the major challenges facing plant breeders. In paper I of this series, we presented an approach to modelling V × E interaction in the analysis of complex multi-environment trials using factor analytic models. In this paper, we develop a range of statistical tools which explore V × E interaction in this context. These tools include graphical displays such as heat-maps of genetic correlation matrices as well as so-called E-scaled uniplots that are a more informative alternative to the classical biplot for large plant breeding multi-environment trials. We also present a new approach to prediction for multi-environment trials that include pedigree information. This approach allows meaningful selection indices to be formed either for potential new varieties or potential parents.

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Genome wide simple sequence repeats development and their application in genetic diversity analysis in wax gourd ( Benincasa hispida )

Plant Breeding ◽

10.1111/pbr.12990 ◽

2022 ◽

Author(s):

Qianmei Hu ◽

Haiping Wang ◽

Biao Jiang ◽

Huayu Zhu ◽

Xiaoming He ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Genome Wide ◽

Benincasa Hispida ◽

Wax Gourd ◽

Simple Sequence

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A Robust Rerank Approach for Feature Selection and Its Application to Pooling-Based GWA Studies

Computational and Mathematical Methods in Medicine ◽

10.1155/2013/860673 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Jia-Rou Liu ◽

Po-Hsiu Kuo ◽

Hung Hung

Keyword(s):

Characteristic Curve ◽

Real Data ◽

Tuning Parameter ◽

Practical Implementation ◽

Tuning Parameters ◽

Genome Wide ◽

Feature Based ◽

The Difference ◽

Gwa Studies ◽

Selection Of

Large-p-small-ndatasets are commonly encountered in modern biomedical studies. To detect the difference between two groups, conventional methods would fail to apply due to the instability in estimating variances int-test and a high proportion of tied values in AUC (area under the receiver operating characteristic curve) estimates. The significance analysis of microarrays (SAM) may also not be satisfactory, since its performance is sensitive to the tuning parameter, and its selection is not straightforward. In this work, we propose a robust rerank approach to overcome the above-mentioned diffculties. In particular, we obtain a rank-based statistic for each feature based on the concept of “rank-over-variable.” Techniques of “random subset” and “rerank” are then iteratively applied to rank features, and the leading features will be selected for further studies. The proposed re-rank approach is especially applicable for large-p-small-ndatasets. Moreover, it is insensitive to the selection of tuning parameters, which is an appealing property for practical implementation. Simulation studies and real data analysis of pooling-based genome wide association (GWA) studies demonstrate the usefulness of our method.

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ISSR marker-assisted genetic diversity analysis of Dioscorea hispida and selection of the best variety for sustainable production

Comptes Rendus Biologies ◽

10.1016/j.crvi.2017.08.003 ◽

2017 ◽

Vol 340 (8) ◽

pp. 359-366 ◽

Cited By ~ 6

Author(s):

Nur Fatihah Hasan Nudin ◽

Abdul Manaf Ali ◽

Norhayati Ngah ◽

Nor Zuhailah Mazlan ◽

Nashriyah Mat ◽

...

Keyword(s):

Genetic Diversity ◽

Sustainable Production ◽

Issr Marker ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Selection Of

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Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses

PLoS ONE ◽

10.1371/journal.pone.0171088 ◽

2017 ◽

Vol 12 (1) ◽

pp. e0171088 ◽

Cited By ~ 7

Author(s):

George Msalya ◽

Eui-Soo Kim ◽

Emmanuel L. K. Laisser ◽

Maulilio J. Kipanyula ◽

Esron D. Karimuribo ◽

...

Keyword(s):

Genetic Structure ◽

Genome Wide ◽

Signatures Of Selection ◽

Friesian Cattle

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Elk (Cervus elaphus) Seasonal Habitat Selection in a Heterogeneous Forest Structure

International Journal of Forestry Research ◽

10.1155/2013/415913 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 5

Author(s):

Jesse N. Popp ◽

David N. C. McGeachy ◽

Josef Hamr

Keyword(s):

Habitat Selection ◽

Cervus Elaphus ◽

Forest Structure ◽

Hardwood Forests ◽

Climatic Conditions ◽

White Birch ◽

Balsam Poplar ◽

Adult Females ◽

Selection Of ◽

Future Management

Seasonal habitat selection by the reintroduced Burwash elk population, approximately 30 km south of Sudbury, Ontario, has been analysed in order to assist in the development of future management. Twenty-five adult females were radio-collared and tracked 1–3 times a week for 3 years. The most prominent patterns included selection of intolerant hardwood forests (trembling aspen, white birch, and balsam poplar) during all seasons, while Great Lakes-St. Lawrence pines (white and red pine dominated stands) were used less than expected based on availability for all seasons. The selection patterns are likely associated with seasonal climatic conditions and forage preferences. Because the selection behaviours displayed here varied greatly from other elk habitat studies, it is suggested that managers consider the importance of population-specific habitat studies before developing related strategies.

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