Genomic analysis reveals variant association with high altitude adaptation in native chickens

Abstract

Native chickens are endangered genetic resources that are kept by farmers for different purposes. Native chickens distributed in a wide range of altitudes, have developed adaptive mechanisms to deal with hypoxia. For the first time, we report variants associated with high-altitude adaptation in Iranian native chickens by whole genome sequencing of lowland and highland chickens. We found that these adaptive variants are involved in DNA repair, organs development, immune response and histone binding. Amazingly, signature selection analysis demonstrated that differential variants are adaptive in response to hypoxia and are not due to other evolutionary pressures. Cellular component analysis of variants showed that mitochondrion is the most important organelle for hypoxia adaptation. A total of 50 variants was detected in mtDNA for highland and lowland chickens. High-altitude associated with variant discovery highlighted the importance of COX3 , a gene involved in cell respiration, in hypoxia adaptation. The results of study suggest that MIR6644-2 is involved in hypoxia and high-altitude adaptations by regulation of embryo development. Finally, 3877 novel SNVs including the mtDNA ones, were submitted to EBI (PRJEB24944). Whole-genome sequencing and variant discovery of native chickens provided novel insights about adaptation mechanisms and highlights the importance of valuable genomic variants in chickens.

Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

“…These methods above were also used to detect candidate genes for high altitude hypoxia adaptation in plateau animals and some candidate genes for hypoxia adaptation had been detected, such as EPAS1 , EGLN1 , CTGF and AMOT , etc. [ 9 , 26 , 27 , 28 , 29 , 30 , 31 ]. Using the Hp method and RNA sequencing analysis, Zhang et al [ 9 ] identified only one believable candidate gene ( CTGF ) for chicken embryonic hypoxia adaptation, which was not an ideal result for the quantitative trait.…”

Comparative Analysis of Long Non-Coding RNA and mRNA Expression Provides Insights Into Adaptation to Hypoxia in Tibetan Sheep

“…In this study, we found that the target genes including MB, PIK3R1, CYP1A1, MMP14, and TGFB1 belong to the list of 247 hypoxia genes. In addition, the candidate genes (MMP14 44 , TUBB4B 45 , PSMD13 46 , COL3A1, COL1A2 47 , DSG3 48,49 , and ATP6 50 were also identified as candidate genes associated with high altitude adaptation by previous functional studies.…”

“…Koopaee et al found that PSMD13 gene was associated with the hypoxia by whole genome sequencing of lowland and highland chickens46 . Qi et al conducted a cross-tissue, cross-altitude, and cross-species study to characterize the transcriptomic landscape of domestic yaks.…”

Comparative Analysis of Long Non-Coding RNA and mRNA Expression Provides Insights into Adaptation to Hypoxia in Tibetan Sheep

“…In addition, the genes (TUBB4B, PSMD13, COL3A1, COL1A2, DSG3, and ATP6) were also identi ed as candidate genes associated with high altitude adaptation by previous functional studies. Kharrati-Koopaee et al found that PSMD13 gene was associated with the hypoxia by whole genome sequencing of lowland and highland chickens [26]. Qi et al conducted a cross-tissue, cross-altitude, and cross-species study to characterize the transcriptomic landscape of domestic yaks.…”

“…We also found six genes (MB, CYP2C31, CYP2B4, CYP2B5, CYP1A1, and CYCS) were functionally involved in oxygen binding, oxygen transport, and heme binding. In addition, eight candidate genes (MMP14 [24], TUBB4B [25], PSMD13 [26], COL3A1, COL1A2 [27], DSG3 [28,29], ATP6 [30] and TGFB1 [22] were also identi ed as candidate genes associated with high altitude adaptation by previous functional studies. These nding indicated that the relative genes might have played a key role in Tibetan sheep to respond to extreme hypoxic environments.…”