Alleles at plasma alpha-amylase locus(Amy-1) of the house musk shrew(Suncus murinus): frequency distribution and new variants in laboratory lines and local Asian populations

Among nine laboratory shrew lines originating from the Japanese islands (Nag, Tok, TKU, Ize, Tr and OKI lines), West Java (Bog), Bangladesh (BAN) and Sri Lanka (SRI), Nag, Tr and Bog were fixed with Amy-1b and SRI with Amy-1a. The remaining lines were still highly polymorphic with the two alleles. A new electrophoretic band C was found in the BAN line and concluded to be expressed by a codominant allele, Amy-1c, which was carried by a single heterozygous female from among eleven wild shrews of the original breeding stock. In most local populations of the Asian shrews surveyed, Amy-1b was more common than Amy-1a. The Sri Lanka population was clearly distinguishable from the others, being nearly fixed with Amy-1a. The C band was found in eleven (one homozygous) of 86 wild shrews caught in Bangladesh. Of a total of 234 wild shrews collected from four Japanese and two Indonesian islands, Bangladesh, and Sri Lanka, only two showed different AMY-bands from AMY-A, -B and -C, and such bands were not found in the laboratory-bred shrews examined.     

Polymorphism of mitochondrial DNA in pigs based on restriction endonuclease cleavage patterns

Restriction endonuclease cleavage patterns of mitochondrial DNA (mtDNA) of pigs and Japanese wild boars were analyzed using 17 enzymes which recognize six nucleotides. The map of cleavage sites was made by double-digestion methods. Polymophism of mtDNA was detected in the digestion by BglII, EcoRV, ScaI, and StuI. The restriction cleavage patterns were identical among the breeds of Landrace, Hampshire, Duroc I, and Large White I (A type). The patterns of Large White II were the same as those of Japanese wild boars (B type). A difference between the A type and the B type of mtDNA was found in the case of three restriction enzymes, BglII, ScaI, and StuI, and the nucleotide alterations between them were estimated as more than six. On the other hand, a difference between mtDNA from almost all pigs and mtDNA from Duroc II was detected using EcoRV. We suggest that the difference of mtDNA between the A type and the B type of mtDNA could result from the different origin of boars, that is, whether they were of European or Asian origin.     

Pig mitochondrial DNA: Polymorphism,restriction map orientation,and sequence data

Restriction endonuclease cleavage patterns of mitochondrial DNA (mtDNA) in pigs were analyzed using 18 enzymes which recognize six nucleotides and 1 four-nucleotide-recognizing enzyme. Pigs including Taiwan native breeds and miniature strains maintained in Japan were examined in this study; four commercial breeds of pigs and Japanese wild boars have been investigated earlier [Watanabe, T., et al. (1985). Biochem. Genet. 23:105]. mtDNA polymorphisms were observed in the cleavage patterns of five restriction enzymes, Bg1II, EcoRV, ScaI, StuI, and TaqI. The results support the previous hypothesis that pigs must be derived from two different maternal origins, European and Asian wild boars, and that a breed, Large White, arises from both European and Asian pigs. Two HindIII cleavage fragments were cloned into the HindIII site of M13mp10 and were partially sequenced by the dideoxynucleotide-chain termination method. Furthermore, DraI and StuI cleavage sites were newly determined on the restriction endonuclease map. On the basis of these results, the restriction endonuclease cleavage map of pig mtDNA was rewritten. Comparing sequence data of pig mtDNA at 237 positions with those of cow, human, mouse, and rat mtDNA, the sequence difference, silent and replacement changes, and transitions and transversions among mammalian species were estimated. The relationships among them are discussed.     

Mitochondrial DNA polymorphism in native Philippine cattle based on restriction endonuclease cleavage patterns

An analysis of patterns of cleavage of mtDNA by restriction endonucleases was performed for nine individuals from the Philippine population of native cattle. MtDNA polymorphisms were detected in the restriction patterns generated by the following six enzymes,BamHI,BglII,EcoRV,HindIII,PstI, andScaI. The restriction patterns showing polymorphisms were distributed nonrandomly among the nine individuals examined from the Philippine population of native cattle, indicating the existence of two separate types of mtDNA. These two types of mtDNA are very different from each other, at the level of subspecies. Since the native Philippine cattle are considered to represent an admixture of European and Indian cattle, the two types of mtDNA must be derived from the mtDNAs of both varieties. The polymorphic sites in mtDNA have been located on a restriction map, and the nucleotide substitutions at some of the sites have also been estimated.     

Morphological and reproductive characteristics of musk shrews (Suncus murinus) collected in Bangladesh, and development of the laboratory line (BAN line) derived from them

To establish a unique laboratory line of the musk shrew with different genetic properties from previously developed laboratory lines, 49 male and 49 female shrews were captured in the campus of Bangladesh Agricultural University from October through November in 1983 and from December in 1985 to January in 1986. The shrews collected were of various ages. They had light gray coats, with slight variations in color. Except for the 12 shrews introduced into our laboratory, the total length and body weight of the shrews ranged from 17.2 to 31.9 cm and 32.5 to 147.0 g in males, and 21.1 to 26.6 cm and 40.8 to 110.0 g in females, respectively. Pregnant females were found throughout the trapping period, and the average fetal litter size was 3.54 (11 cases). Five males and 7 females of the shrews captured in 1983 were transported to our laboratory. After more than 100 days of laboratory rearing, their total length and body weight averaged 27.6 cm and 147.3 g in males, and 24.6 cm and 81.7 g in females. Their body weight was more than double that of Japanese shrews. The shrews introduced (except for one male) produced a total of 59 offspring, which were regarded as the first generation of the laboratory line (BAN Line). Gestation period and average litter size were between 28 and 30 days (10 cases) and 3.47 (17 cases), respectively. The BAN line has consisted of about 60 individuals at each generation and has been maintained as a closed breeding colony.     

Cytoplasmic male sterility and nuclear restorer genes in a natural population of Beta maritima: genetical and molecular aspects

Summary One natural population (F₀ generation) of Beta maritima situated on the French Atlantic coast has been analysed. It was composed of 62% female, 30% hermaphrodite and 8% intermediate plants. The analysis of half-sib progeny (F₁ generation) obtained from in situ open pollination demonstrates the cytoplasmic determination of male sterility in Beta maritima and the restoration of fertility by nuclear genes. The mitochondrial DNA (mtDNA) and the chloroplast DNA (ctDNA) of sixteen F₁ plants, extracted from offspring of the three sexual phenotypes, were analysed using the restriction enzymes Sal I and Bam HI, respectively. Two cytoplasmic lines with their own peculiar genetic characteristics were distinguished using the restriction enzyme patterns of mtDNA: (i) the S cytoplasmic line was found in segregating progeny of two F₀ plants; all three phenotypes were produced (that is, progeny including hermaphrodite, female and intermediate plants); (ii) the N cytoplasmic line was found in the progeny of one F₀ hermaphrodite plant; this produced only hermaphrodites. Thus, segregating and non-segregating hermaphrodite F₀ plants can be distinguished. The nuclear genes maintaining sterility or restoring fertility are expressed in line S. At the same time the analysis of Beta vulgaris material has been carried out at the molecular level: N cytoplasmic lines of B. vulgaris and B. maritima differed only by 3 fragments of mtDNA; but the S cytoplasmic line of B. maritima was very different from Owen's cytoplasmic male sterile line of B. vulgaris. No variation in the ctDNA pattern was detected within and between the two taxa.     

Development of a laboratory line (SRI line) derived from the wild house musk shrew, Suncus murinus, indigenous to Sri Lanka

Five male and 9 female house musk shrews (Suncus murinus) captured in Koralawella, Sri Lanka were acquired by our laboratory. One male and 3 females alone contributed to the development of a new laboratory line (SRI line). The SRI line has been maintained as a closed breeding colony consisting of more than 40 shrews. Gestation period and litter size at birth averaged 31.2 days (43 cases) and 2.4 (43 litters), respectively. The SRI line shrews were uniformly covered with light gray fur. The body weight and total length of adult shrews averaged 72.9 g and 23.9 cm in males, and 49.6 g and 21.0 cm in females. These data indicate a body size intermediate between BAN line shrews originating from Bangladesh and Nag or OKI line shrews from Japan. The SRI shrews are also characterized by having 30 chromosomes in diploid, being the smallest number in the entire species, whereas the otherlines (Nag, OKI and BAN) all have 40 chromosomes.     

A unique cytoplasmic male sterility (CMS) determinant is present in three Phaseolus species characterized by different mitochondrial genomes

Previous results have shown that cytoplasmic male sterility (CMS) in lines from Phaseolus coccineus and Phaseolus vulgaris contain the same CMS-specific sequence, raising the question of whether this sequence rearrangement arose before divergence of the two species or afterward with subsequent transfer by introgression. Hybridization patterns of total DNA from eight P. vulgaris lines with cytoplasm from P. coccineus and three P. vulgaris lines were examined in order to analyze the mitochondrial DNA (mtDNA) diversity within each species and to determine differences between CMS lines derived from the two species. Three restriction enzymes and 17 heterologous mtDNA sequences were used. The analysis of the different hybridization patterns revealed a considerable diversity in mtDNA organization particularly within P. coccineus. We obtained distinctive hybridization patterns for the five CMS lines tested. The resulting classification showed that mitochondrial genomes from P. coccineus CMS lines group with those of fertile P. coccineus but not with CMS lines from P. vulgaris. The groupings concur with the taxonomic classification of these lines. The results support the hypothesis of a single ancient origin of the CMS determinant and exclude the transfer of cytoplasm by introgression from P. vulgaris to P. coccineus and P. coccineus ssp polyanthus.     

Genetic relationship among the musk shrews,Suncus murinus insectivora,inhabiting islands and the continent based on mitochondrial DNA types

Cleavage patterns of mitochondrial DNA (mtDNA) by restriction endonucleases were examined in musk shrews collected at six trapping sites on two Japanese and two Indonesian islands, on Sri Lanka, situated close to the Indian subcontinent, and on the mainland of East Bengal in Bangladesh. No variation of mtDNAs was found among the Japanese and Indonesian shrews, despite their geographical isolation by the sea. In contrast, at least six mtDNA types were present in the Sri Lanka and the Bangladesh populations (three types for each), and these two populations seemed to be differentiated to the extent, which could be compared to the mice-intersubspecific differences. These populations were also differentiated from the Japanese-Indonesian type. Furthermore, a similar level of differentiation was also estimated between two mtDNA types within these respective populations. This feral species might be considered unique because of its high emigration rate caused by human movements and its high rate of subspecific hybridization.     

RFLP analysis of mitochondrial DNA from cytoplasmic male-sterile lines of pearl millet

Mitochondrial DNA (mtDNA) from 13 cytoplasmic male-sterile (cms) lines from diverse sources were characterized by Southern blot hybridization to pearl millet and maize mtDNA probes. Hybridization patterns of mtDNA digested with PstI, BamHI, SmaI or XhoI and probed with 13.6-, 10.9-, 9.7- or 4.7-kb pearl millet mtDNA clones revealed similarities among the cms lines 5141 A and ICMA 1 (classified as the S-A1 type of cytoplasm based on fertility restoration patterns), PMC 30A and ICMA 2. The remaining cms lines formed a distinct group, within which three subgroups were evident. Among the maize mitochondiral gene clones used, the coxI probe revealed two distinct groups of cytoplasms similar to the pearl millet mtDNA clones. The atp9 probe differentiated the cms line 81 A4, derived from P. glaucum subsp. monodii, while the coxII gene probe did not detect any polymorphism among the cms lines studied. MtDNA digested with BamHI, PstI or XhoI and hybridized to the atp6 probe revealed distinct differences among the cms lines. The maize atp6 gene clone identified four distinct cytoplasmic groups and four subgroups within a main group. The mtDNA fragments hybridized to the atp6 gene probe with differing intensities, suggesting the presence of more than one copy of the gene in different stoichiometries. Rearrangements involving the coxI and/or rrn18-rrn5 genes (mapped within the pearl millet clones) probably resulted in the S-A1 type of sterility. Rearrangements involving the atp6 gene (probably resulting in chimeric form) may be responsible for male sterility in other cms lines of pearl millet.     

Identification of cytoplasmically transferred mitochondrial DNA in female germlines of Drosophila and its propagation in the progeny

Summary The composition of mitochondrial DNA (mtDNA) was analyzed in single female flies that developed from fertilized Drosophila melanogaster eggs, into which germ plasm of D. simulans had been introduced. HpaII cleavage patterns showed that all 12 individual female flies examined had developed from eggs in which 37%–71% of the total mtDNA was D. simulans mtDNA (Ds mtDNA) and the rest was D. melanogaster mtDNA (Dm mtDNA). The stability of this heteroplasmic state in these isofemale lines was monitored for seven generations at both individual and population levels. Results showed that the heteroplasmy of Dm and Ds mtDNAs was stably transmitted for at least three generations at the population level, but showed stochastic segregation at the individual level. After 4–6 generations, all individuals lost Ds mtDNA. The mechanisms of preferential loss of Ds mtDNA and of transmission of heteroplasmic mtDNA to descendants are discussed.     

Molecular analysis of organelle DNA of different subspecies of rice and the genomic stability of mtDNA in tissue cultured cells of rice

Summary Chloroplast (ct) and mitochondrial (mt) DNAs were isolated from two subspecies of rice (Oryza sativa), japonica (Calrose 76) and indica (PI353705) and compared by restriction endonuclease fragment pattern analysis. Similarly, PI353705 (A5) mtDNA was also compared with the mtDNA of its long term tissue cultured line, BL2. Variation in the ctDNA of the 2 subspecies was detected with two (AvaI and BglI) of the 11 restriction endonucleases tested, whereas their mtDNAs showed considerable variation when restricted by PstI, BamHI, HindIII and XhoI endonucleases. Thus, the chloroplast DNA was more highly conserved than the mtDNA in the subspecies comparisons. Only minor variation was observed between the restriction endonuclease patterns of the mtDNAs of BL2 and A5. Southern blots of mtDNA were hybridized with heterologous probes from maize and spinach organelle genes. Differences were found in the hybridization patterns of the two subspecies for six of the eight (mitochondrial and chloroplast) probes tested. Two of the seven (mitochondrial) probes (coxII and 26S rRNA) detected tissue culture generated variation in mtDNA. The relative values of restriction endonuclease and hybridization patterns for studying phylogenetic and genetic relationships in rice are discussed.Florida Agricultural Experiment Station Journal Series No. 8807. Mention of a trademark or proprietary product does not constitute a guarantee or warranty of the product by the USDA, and does not imply its approval to the exclusion of other products that may also be suitable     

Polymorphism of mitochondrial DNA (mtDNA) in cattle and buffaloes

Mitochondrial DNA (mtDNA) from two breeds of cattle, viz., [Hariana (Bos indicus), Holstein (Bos taurus)] and Indian water buffalo (Bubalis bubalus), was analyzed using 13 restriction endonucleases which recognized an average of about 40 six-base sites. Polymorphism among cattle was detected with six of these enzymes. The two Holstein differed at six sites, whereas the Hariana breed (Bos indicus) did not show any site polymorphism. Surprisingly, the Hariana type differed by only one site from one of the Holstein types. The total size of buffalo mtDNA was estimated to be 16.4 kb. Polymorphism within the Murrah buffalo breed was observed with respect to aBglI site. Scarcely any of the restriction fragments of buffalo mtDNA matched those of cattle mtDNA.     

Concerted evolution of sequence repeats inDrosophila mitochondrial DNA

Summary In the eightDrosophila species of themelanogaster subgroup, the mitochondrial DNA (mtDNA) contains an A+T-rich region in which replication originates. The length of this region, in contrast with that of the coding part of the genome, varies extensively among these species. The A+T-rich region ranges from about 1kbp inD. yakuba, D. teissieri, D. erecta, andD. orena to 5 kbp inD. melanogaster, D. simulans, D. mauritiana, andD. sechellia. The difference in size is due in part to the amplification, in the species with long genomes, of a 470-bp sequence that is present only once in each of the four species with short genomes.Usually three to six repeats of this sequence occur in direct tandem repetition in the species with long genomes. The sequence is characterized by the relative positions of the Hpa I and Acc I cleavage sites. Comparative study of the genomes found in the species with long mtDNA molecules reveals relative homogeneity of the repeat units within a given genome, which contrasts with the variability found among the repeats of different genomes. This result is suggestive of a process of a concerted evolution.The examination of heteroplasmic flies of three species (D. simulans, D. mauritiana, andD. sechellia) has shed light on this process. In most cases the molecular types of mtDNA present in a heteroplasmic individual differ by one repeat unit. Addition or deletion of this sequence appears to be the original mutational event generating transient heteroplasmy. Cycles of addition or deletion may consequently maintain the intragenomic homogeneity of the repeats.Finally, we have analyzed an exceptional isofemale line in which three molecular lengths of mtDNA are found (molecules with four, five, and six repeats, respectively). Individual offspring of this line carry from one to three of the molecular types, in all combinations. This indicates that the remodeling of the mitochondrial genome occurs through a mechanism that is at present unknown, but that is site specific and rather frequent.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

Genetic and geographical differentiation of <Emphasis Type="Italic">Pandaka</Emphasis> gobies in Japan

The mitochondrial DNA (mtDNA) phylogeny of Japanese Pandaka species (Perciformes: Gobiidae) was inferred from partial nucleotide sequences of the mitochondrial 12S and 16S rRNA genes (1083bp). The resultant mtDNA tree showed two major clades (clade I and clade II), which were inconsistent with the present taxonomic classification. One of the major clades was further divided into two geographical groups, distributed on the Japanese Major Islands (clade I-A) and from Amami-oshima Island to Iriomote Island (clade I-B). The mtDNA haplotypes in clade II were found only on Iriomote Island. The mtDNA divergences in clade I indicated that the Japanese Major Island (clade I-A) and Ryukyu (clade I-B) groups have been geographically isolated from each other for millions of years, based on the putative molecular divergence rate. The geographical distributions of mtDNA haplotypes in clade I-A and clade I-B also suggested that Pandaka gobies had not dispersed to distant offshore islands, indicating that their geographical differentiation may be closely associated with the geological history of the Japanese and Ryukyu Archipelagos.This revised version was published online in January 2005 with corrections to the repetition of the 1st authors name.     

Mitochondrial DNA polymorphism in Japanese

Summary The mitochondrial DNA (mtDNA) from 120 Japanese was analysed with 15 restriction enzymes that recognize six base pairs, of which 11 enzymes showed at least one atypical cleavage pattern. Digestion patterns with HincII and HaeII were highly polymorphic. The observed restriction enzyme morphs were classified into 22 types of distinct cleavage patterns. By pairwise comparison of each restriction type, the average number of nucleotide substitutions per nucleotide site () was estimated at 0.00417, which agreed with the values obtained from other human populations in previous studies. There were 11 site gains, of which seven were transitions and four were transversions. Phylogenetic analysis of the present data suggested that the Japanese population conceals a considerably high degree of mtDNA diversity.     

Cytoplasmic male sterility in hybrids of sterile wild beet (Beta vulgaris ssp. maritima) and O-type fertile sugar beet (Beta vulgaris L.): molecular analysis of mitochondrial and nuclear genomes

The organization of the mitochondrial genome of B3, B4 and B5generations of hybrids created by backcrossing sterile wild beet Betamaritima with a fertile O-type sugar beet line was studied usingrestriction fragment length polymorphism (RFLP) analysis. Random amplifiedpolymorphic DNA (RAPD) analysis was used to study restoration of the fertile(O-type) sugar beet genotype in hybrids after multiple backcrossings.Restriction of mtDNAs from the cytoplasm of B. maritimaandhybrids revealed BamHI, EcoRI andXhoI restriction patterns different from those for sterileand fertile sugar beet lines. The most conspicuous feature of our accession ofsterile wild beet mtDNA was the absence of the 10.7-kbEcoRI fragment detected in the cytoplasm of S-type sterileB. maritima and sugar beet. The hybridization of digestedmtDNAs with coxII, atpA andatp6 homologous probes revealed alterations within thesegene loci that distinguished wild beet and hybrids from sugar beets.Characteristic hybridization profiles for the wild beet and B3, B4 and B5hybrids were observed for all probes regardless of the restrictase used todigest mtDNA. Notable changes in atpA andatp6 genes resulted when probes that comprised the5flanking sequences of these genes and a small part of the coding sequences wereused. RFLP analysis of the sterile B. maritimamitochondrial genome further supported the unique character of this source ofwild beet sterility. The genotypic differences between hybrids and parentalaccessions were determined by scoring PCR-RAPD reaction products for nineselected primers. The diversity of the B. maritimagenotyperesulted in a lower genetic similarity index in comparison with hybrids,sterileand fertile lines of sugar beet. The dendrogram obtained after cluster analysisdistinguished hybrids as a group that differed from wild beet and themaintainersugar beet line used for backcrossing. These results may indicate incompleterestoration of the fertile sugar beet genotype in hybrids.     

Asymmetric protoplast fusion aimed at intraspecific transfer of cytoplasmic male sterility (CMS) in Lolium perenne L.

Summary Techniques have been developed for the production of cybrids in Lolium perenne (perennial ryegrass). Gamma-irradiated protoplasts of a cytoplasmically male-sterile breeding line of perennial ryegrass (B200) were fused with iodoacetamide-treated protoplasts of a fertile breeding line (Jon 401). After fusion 25 putative cybrid calli were characterized to determine mitochondrion type and composition of the nuclear genome. Analysis of phosphoglucoisomerase isozyme profiles and determination of the ploidy level by flow cytometry indicated that all of the calli tested essentially contained the nuclear DNA of the fertile line. However, the presence of parts of the nuclear DNA from the sterile line could not be excluded. Southern blotting of total DNA isolated from the parental lines and putative cybrids combined with hybridizations using the mitochondrial probes cox1 and atp6 revealed that the mitochondria of the calli originated from the fertile line (5 calli), the sterile line (5 calli) or from both parental lines (15 calli). The hybridization patterns of the mtDNA from the cybrid calli showed extensive quantitative and qualitative variation, suggesting that fusion-induced inter- or intramolecular mitochondrial recombination had taken place.     

Polymorphism of Mitochondrial DNAs of Yunnan Domestic Water Buffaloes, Bubalus bubalis, in China, Based on Restriction Endonuclease Cleavage Patterns

Restriction endonuclease cleavage patterns of mitochondrial DNA(mtDNA) of three local types of Yunnan native water buffalo were analyzed using 18 enzymes which recognize six nucleotides. Among the 12 animals analyzed, 3 of 18 enzymes, BamHI, EcoRI, and ScaI, revealed polymorphisms. Three mtDNA types were identified. The results indicate that a relatively low level of mtDNA variation exists in Yunnan domestic water buffaloes. The origin of Chinese buffalo derived from Yunnan province of China is discussed.