Genomic Analyses Reveal Genetic Adaptations to Tropical Climates in Chickens

Tian, Shilin; Zhou, Xuming; Phuntsok, Tashi; Zhao, Ning; Zhang, Dejing; Ning, Chunyou; Li, Diyan; Zhao, Huabin

doi:10.1016/j.isci.2020.101644

Cited by 33 publications

(28 citation statements)

References 84 publications

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“…Heat tolerance causes excessive oxygen consumption in organisms, which lead to optimized oxygen delivery by increasing blood flow in circulation [ 48 ]. Most recently, the potential roles of this gene in the MAPK signaling pathway, which is an upstream regulator of melanogenesis and melanoma angiogenesis, was described in detail in one experimental study on local chickens that live in tropical climates [ 98 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens

2022

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Background Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved genetic adaptations to their local environmental conditions, such as hot and arid regions. In the present study, we provide a population genome landscape of genetic variations in 72 chickens representing nine Iranian indigenous ecotypes (Creeper, Isfahan, Lari, Marand, Mashhad, Naked neck, Sari, Shiraz and Yazd) and two commercial lines (White Leghorn and Arian). We further performed comparative population genomics to evaluate the genetic basis underlying variation in the adaptation to hot climate and immune response in indigenous chicken ecotypes. To detect genomic signatures of adaptation, we applied nucleotide diversity (θπ) and FST statistical measurements, and further analyzed the results to find genomic regions under selection for hot adaptation and immune response-related traits. Results By generating whole-genome data, we assessed the relationship between the genetic diversity of indigenous chicken ecotypes and their genetic distances to two different commercial lines. The results of genetic structure analysis revealed clustering of indigenous chickens in agreement with their geographic origin. Among all studied chicken groups, the highest level of linkage disequilibrium (LD) (~ 0.70) was observed in White Leghorn group at marker pairs distance of 1 Kb. The results from admixture analysis demonstrated evidence of shared ancestry between Arian individuals and indigenous chickens, especially those from the north of the country. Our search for potential genomic regions under selection in indigenous chicken ecotypes revealed several immune response and heat shock protein-related genes, such as HSP70, HSPA9, HSPH1, HSP90AB1 and PLCB4 that have been previously unknown to be involved in environmental-adaptive traits. In addition, we found some other candidate loci on different chromosomes probably related with hot adaptation and immune response-related traits. Conclusions The work provides crucial insights into the structural variation in the genome of Iranian indigenous chicken ecotypes, which up to now has not been genetically investigated. Several genes were identified as candidates for drought, heat tolerance, immune response and other phenotypic traits. These candidate genes may be helpful targets for understanding of the molecular basis of adaptation to hot environmental climate and as such they should be used in chicken breeding programs to select more efficient breeds for desert climate.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens

2022

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“…However, the domestication, expansion and improvement are consecutive evolutionary processes. So, we designed a method to detect stepwise and directional increase or decrease of allele frequencies across multiple evolutionary stages ( 50, 51 ), which provides insights into the evolutionary dynamics of soybean genomes under the combination of both natural and artificial selection. Given the importance of flowering time in the spread and adaptation of soybean, we evaluated candidate genes in the flowering time pathway.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, the three methods are compatible and complementary. As the three methods are good at detecting different selective events, we observed a low overlap of selected molecular markers (25,26,74,75). Therefore, we took the candidates with support from at least one statistic.…”

Section: Genome-wide Selective Sweep Scanningmentioning

confidence: 99%

Genome-wide signatures of geographic expansion and breeding process in soybean

Qin

Wang

et al. 2022

Preprint

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The clarification of genomic signatures left during evolutionary histories of crops is crucial for breeding varieties adapting to changing climate. Soybean, a leguminous crop, provides both plant oil and protein. Here, we analyzed genome sequences of 2,214 soybeans and proposed its evolutionary route, which includes four geographic paths, expansion of annual wild soybean (Glycine soja Sieb. & Zucc.) from Southern China, domestication in Central China, expansion of landrace (G. max (L.) Merr.), and local breeding. We observed that local adaptation of the wild and cultivated soybeans was largely independent, and that genetic introgression was mostly derived from sympatric rather than allopatric wild populations during the range expansion of soybean landraces. Range expansion and breeding processes were accompanied with positive selection of flowering-time genes including GmSPA3c as validated by knock-out mutants. Our study shed lights on the evolutionary history of soybean and provides valuable genetic resources for future breeding.

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“…The libraries were constructed and sequenced by Novogene (Beijing, China) (Tian et al, 2020). Briefly, a total amount of 20 ng RNA per sample was used as the RNA sample for preparation.…”

Section: Library Construction and Sequencingmentioning

confidence: 99%

Novel Insights into the Potential Diagnostic Value of Circulating Exosomal IncRNA-Related Networks in Large Artery Atherosclerotic Stroke

Zhang

Wang

et al. 2021

Front. Mol. Biosci.

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Exosomes show diagnostic and therapeutic promise as carriers of ncRNAs in diseases. LncRNAs in exosomes have been identified as being stable and avoided degradation by nucleolytic enzymes. Although lncRNAs have been confirmed to be important in cancers, no studies for exo-lncRNAs have been reported in LAA stroke. High-throughput sequencing was performed to detect the differential expression profiles of lncRNAs in five paired plasma-derived exosome samples from patients with LAA stroke and controls (matched on vascular risk factors). Exo-lncRNA-associated networks were predicted with a combination of multiple databases. The expression of the selected genes in the networks was confirmed by qRT-PCR in a validation set (LAA vs. controls = 30:30). Furthermore, ROC analysis was used to evaluate the diagnostic performance of the lncRNA-related networks. A total of 1,020 differentially expressed lncRNAs were identified in LAA stroke patients. GO and KEGG pathway analyses indicated that their target genes are involved in atherosclerosis-related pathways, including inflammation, cell adhesion, and cell migration. qRT-PCR confirmed that the expression trend of differential expressed genes was consistent with RNA-seq. Furthermore, the AUCs of the lnc_002015-related network and lnc_001350-related network were 0.959 and 0.97, respectively, in LAA stroke. Our study showed the differential expression of lncRNAs in plasma exosomes and presented related diagnostic networks for LAA stroke for the first time. The results suggested that exosomal lncRNA-related networks could be potential diagnostic tools in LAA stroke.

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Genomic Analyses Reveal Genetic Adaptations to Tropical Climates in Chickens

Cited by 33 publications

References 84 publications

Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens

Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens

Genome-wide signatures of geographic expansion and breeding process in soybean

Novel Insights into the Potential Diagnostic Value of Circulating Exosomal IncRNA-Related Networks in Large Artery Atherosclerotic Stroke

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