Genetic Diversity and Differentiation of MHC Class I Genes in Red-Crowned Crane Populations

Abstract

The red-crowned crane (Grus japonensis) has been demoted to “vulnerable species” because its populations have apparently stabilized in Japan and Korea. Low variation and genetic drift may cause damage to the nascent recovery of the G. japonensis population. The major histocompatibility complex (MHC) is one of the most polymorphic gene families in the vertebrate genome and can reflect information on the adaptive evolution of endangered species. In this study, variations in MHC I exon 3 of captive G. japonensis in China were assessed and compared with those in cranes from Japan. Forty MHC alleles of 274 base pairs were isolated from 32 individuals from two captive populations in China. There was high variability in the nucleotide and amino acid composition, showing the proportion of polymorphic sites of 18.98 and 32.97%, respectively. Comparative analyses of the Chinese and Japanese populations based on 222 base pair sequences revealed more alleles and higher variation in the Chinese population. The lack of significant geographical differentiation of G. japonensis was supported by the genetic differentiation coefficient (0.04506) between the Chinese and Japanese populations. Positive selection of antigen-binding sites was observed, which contributed to maintaining the diversity of MHC class I genes. Phylogenetic analysis suggested the persistence of trans-species polymorphisms among MHC class I genes in Gruidae species. Our results may contribute to optimizing the management of G. japonensis populations and population recovery of this threatened species.

Possible Shifts in the Genetic Diversity of Red-crowned Cranes (Grus japonensis) in Hokkaido, Japan: Indications of Continental Gene Flow

“…A total of 33 MHC types (amino acid sequences) were detected in a total of 89 samples from both northern and southeastern Hokkaido ( Table S3 ), including blood relatives. A total of 10 of the 46 MHC (AA) types reported by Xu et al [ 17 ] were confirmed in this study. These were all continent-specific (Grja-UA*27, 28, 33, 38, 44) or common to the continent and Japan (Grja-UA*47, 50, 51, 54, 55).…”

“…While MHC sequences of 150 bp or 274 bp were reported previously [17,18], our study using the new high-throughput sequencing (HTS) system was able to achieve sequence reads up to 420 bp (140 AA).…”

“…We used high throughput sequencing of amplicons in our evaluation. To detect major histocompatibility complex (MHC) type, the same primer set flanking, MHC Class I Exon 3, as that used in a previous report [ 17 ] was employed here (MHC I-E3-F: 5′-TCAGCCCCRTCTCCCTGGTC-3′, MHC I-E3-R: 5′-GTAGAAGCCGTAAGCGCGGCA-3′). The first-round PCR was carried out with a DNA sample prepared as described in the previous section using Tks Gflex DNA Polymerase (Takara Bio, Kusatsu, Japan).…”

“…Then, AmpliSAS was applied to the read file after the filtering. The parameter “maximum number of alleles per amplicon” was set to 15, based on the recommendations of Akiyama et al [ 18 ] and Xu et al [ 17 ], who detected a maximum of 11 variants per individual. The parameter “minimum amplicon depth” was set to 20, based on the results of AmpliCHECK, in which variants with a depth less than 20 were detected in only one sample, likely due to artifacts.…”

“…The high polymorphism of MHC genes among individuals makes them a valuable tool for studies of genetic diversity [ 15 , 16 ]. Within the red-crowned crane population, Akiyama et al and Xu et al performed population analyses by sequencing the MHC class I exon 3 region [ 17 , 18 ]. Xu et al identified 30 amino acid (AA) types of MHC specific for the continental population and 10 types belonging to the Hokkaido population [ 17 ].…”