scholarly journals Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing

Heredity ◽  
2019 ◽  
Vol 123 (3) ◽  
pp. 371-383 ◽  
Author(s):  
Natsuki Moriguchi ◽  
Kentaro Uchiyama ◽  
Ryutaro Miyagi ◽  
Etsuko Moritsuka ◽  
Aya Takahashi ◽  
...  
Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 898 ◽  
Author(s):  
Soichiro Nagano ◽  
Tomonori Hirao ◽  
Yuya Takashima ◽  
Michinari Matsushita ◽  
Kentaro Mishima ◽  
...  

Along with progress in sequencing technology and accumulating knowledge of genome and gene sequences, molecular breeding techniques have been developed for predicting the genetic potential of individual genotypes and for selecting superior individuals. For Japanese cedar (Cryptomeria japonica (L.f.) D.Don), which is the most common coniferous species in Japanese forestry, we constructed a custom primer panel for target amplicon sequencing in order to simultaneously determine 3034 informative single nucleotide polymorphisms (SNPs). We performed primary evaluation of the custom primer panel with actual sequencing and in silico PCR. Genotyped SNPs had a distribution over almost the entire region of the C. japonica linkage map and verified the high reproducibility of genotype calls compared to SNPs obtained by genotyping arrays. Genotyping was performed for 576 individuals of the F1 population, and genomic prediction models were constructed for growth and wood property-related traits using the genotypes. Amplicon sequencing with the custom primer panel enables efficient obtaining genotype data in order to perform genomic prediction, manage clones, and advance forest tree breeding.


Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.


2021 ◽  
Vol 13 (3) ◽  
Author(s):  
J Roman Arguello ◽  
Stefan Laurent ◽  
Andrew G Clark

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yoshihiko Nanasato ◽  
Masafumi Mikami ◽  
Norihiro Futamura ◽  
Masaki Endo ◽  
Mitsuru Nishiguchi ◽  
...  

AbstractCryptomeria japonica (Japanese cedar or sugi) is one of the most important coniferous tree species in Japan and breeding programs for this species have been launched since 1950s. Genome editing technology can be used to shorten the breeding period. In this study, we performed targeted mutagenesis using the CRISPR/Cas9 system in C. japonica. First, the CRISPR/Cas9 system was tested using green fluorescent protein (GFP)-expressing transgenic embryogenic tissue lines. Knock-out efficiency of GFP ranged from 3.1 to 41.4% depending on U6 promoters and target sequences. The GFP knock-out region was mottled in many lines, indicating genome editing in individual cells. However, in 101 of 102 mutated individuals (> 99%) from 6 GFP knock-out lines, embryos had a single mutation pattern. Next, we knocked out the endogenous C. japonica magnesium chelatase subunit I (CjChlI) gene using two guide RNA targets. Green, pale green, and albino phenotypes were obtained in the gene-edited cell lines. Sequence analysis revealed random deletions, insertions, and replacements in the target region. Thus, targeted mutagenesis using the CRISPR/Cas9 system can be used to modify the C. japonica genome.


Author(s):  
Phillip A. Morin ◽  
Frederick I. Archer ◽  
Catherine D. Avila ◽  
Jennifer R. Balacco ◽  
Yury V. Bukhman ◽  
...  

2008 ◽  
Vol 4 (6) ◽  
pp. 752-754 ◽  
Author(s):  
Emma Svensson ◽  
Anders Götherström

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.


2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.


1997 ◽  
Vol 26 (1) ◽  
pp. 15-46 ◽  
Author(s):  
David Britain

ABSTRACTThis article reports on research carried out in the Fens in Eastern England, a region noted in the dialectological literature as the site of a number of important phonological transitions, most notably [] and [a – a:], which separate northern and southern varieties of British English. Recordings of 81 speakers from across the Fens were analyzed for the use of (ai), a particularly salient local variable. A “Canadian Raising” type of allophonic variation was found in the central Fenland: speakers in this area used raised onsets of (ai) before voiceless consonants but open onsets before voiced consonants, morpheme boundaries, and //. The article weighs a number of possible explanations for the emergence of this variation in the Fens. Based on compelling evidence from the demographic history of the area, it supports a view that such an allophonic distribution, previously thought not to be found in Britain, emerged as the result of dialect contact. The sociolinguistic process of koinéization that is commonly associated with post-contact speech communities (Trudgill 1986) is held responsible for the focusing of this allophonic variation from the input dialects of an initially mixed variety. The article concludes by suggesting a socially based explanatory model to account for the way that speakers implement processes of focusing and koinéization in areas of dialect contact. [English, dialects, contact, koiné, geographical linguistics, social networks, structuration theory)


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