Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing. On average, 10.4 M SNPs were shared amongst the three cattle breeds, whereas, 3.0 M, 4.9 M and 5.8 M were specific to LQ, WN and WS breeds, respectively. Gene ontology (GO)analysis revealed four immune response-related GO terms were over represented in all samples, while two immune signaling pathways were significantly over-represented in WS cattle. Altogether, we found immune related genes (PGLYRP2, ROMO1, FYB2, CD46, TSC1) in the three cattle breeds. Our study provides insights into the genetic basis of Chinese indicine adaptation to the tropic and subtropical environment, and provides a valuable resource for further investigations of genetic characteristics of the three breeds.

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Genomic Patterns of Homozygosity in Chinese Local Cattle

Scientific Reports ◽

10.1038/s41598-019-53274-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 8

Author(s):

Lingyang Xu ◽

Guoyao Zhao ◽

Liu Yang ◽

Bo Zhu ◽

Yan Chen ◽

...

Keyword(s):

Genetic Basis ◽

Average Length ◽

Nucleotide Polymorphism ◽

Adaptive Traits ◽

Single Nucleotide ◽

Cattle Breeds ◽

Chinese Cattle ◽

Genome Wide ◽

Average Proportion ◽

Genomic Patterns

AbstractGenome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5–1 Mb, Medium 1–5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.

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Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

BMC Genomics ◽

10.1186/s12864-020-07014-x ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Wei-Jun Li ◽

Yu-Jia Song ◽

Hong-Liang Han ◽

Hui-Qian Xu ◽

Dong Wei ◽

...

Keyword(s):

Melon Fly ◽

Genome Wide Analysis ◽

Adult Tissues ◽

Genome Wide ◽

Non Coding Rnas

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On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Genetics Selection Evolution ◽

10.1186/s12711-021-00639-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Gabriele Senczuk ◽

Salvatore Mastrangelo ◽

Paolo Ajmone-Marsan ◽

Zsolt Becskei ◽

Paolo Colangelo ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Melting Pot ◽

Cattle Breeds ◽

Snp Data ◽

Early Migration ◽

Genome Wide ◽

European Colonization ◽

Approximate Bayesian ◽

European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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Genome-Wide Identification and Functional Analysis of Long Non-coding RNAs in Sesame Response to Salt Stress

Journal of Plant Biology ◽

10.1007/s12374-021-09324-3 ◽

2021 ◽

Author(s):

Huihui Gong ◽

Jun You ◽

Xiurong Zhang ◽

Yanzhong Liu ◽

Fengtao Zhao ◽

...

Keyword(s):

Functional Analysis ◽

Salt Stress ◽

Genome Wide ◽

Non Coding Rnas

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Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

Plant Molecular Biology ◽

10.1007/s11103-021-01121-3 ◽

2021 ◽

Author(s):

Xiaoping Huang ◽

Hongyu Zhang ◽

Qiang Wang ◽

Rong Guo ◽

Lingxia Wei ◽

...

Keyword(s):

Transcription Factors ◽

Leaf Senescence ◽

Flag Leaf ◽

Reduction Process ◽

Sequencing Analysis ◽

Biological Processes ◽

Genome Wide ◽

A Genome ◽

Non Coding Rnas ◽

Systematic Identification

Abstract Key message This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. Abstract LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation–reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

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Genome-wide linkage disequilibrium in two Japanese beef cattle breeds

Animal Genetics ◽

10.1111/j.1365-2052.2005.01400.x ◽

2006 ◽

Vol 37 (2) ◽

pp. 139-144 ◽

Cited By ~ 17

Author(s):

M. Odani ◽

A. Narita ◽

T. Watanabe ◽

K. Yokouchi ◽

Y. Sugimoto ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Beef Cattle ◽

Cattle Breeds ◽

Genome Wide ◽

Beef Cattle Breeds ◽

Genome Wide Linkage Disequilibrium

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Genome‐wide SNP analysis clearly distinguished the Belarusian Red cattle from other European cattle breeds

Animal Genetics ◽

10.1111/age.13102 ◽

2021 ◽

Author(s):

N. A. Zinovieva ◽

I. P. Sheiko ◽

A. V. Dotsev ◽

R. I. Sheiko ◽

M. E. Mikhailova ◽

...

Keyword(s):

Snp Analysis ◽

Cattle Breeds ◽

Genome Wide ◽

European Cattle

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Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation

BMC Genomics ◽

10.1186/s12864-021-07750-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jinyu Zhang ◽

Huanqing Xu ◽

Yuming Yang ◽

Xiangqian Zhang ◽

Zhongwen Huang ◽

...

Keyword(s):

Growth And Yield ◽

Biological Processes ◽

Rna Seq ◽

Plant Growth And Development ◽

P Deficiency ◽

Genome Wide ◽

Low Phosphorus ◽

Soybean Genotypes ◽

Non Coding Rnas ◽

Sensitive Genotype

Abstract Background Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear. Results In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress. Conclusions These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.

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