D. DEPARTMENT OF POPULATION GENETICS
D-a. Division of Population Genetics - Toshiyuki Takano Group

RESEARCH ACTIVITIES

(1) Inter-locus nonrandom association of polymorphisms in Drosophila chemoreceptor genes

Toshiyuki Takano-Shimizu, Yuriko Ishii, Akira Kawabe¹, Masanobu Itoh², Nobuyuki Inomata³, Rumi Kondo⁴ and Yutaka Inoue⁵ (¹University of Edinburgh, ²Kyoto Institute of Technology, ³Kyushu University, ⁴Ochanomizu University, ⁵Osaka University of Foreign Studies)

--Some forms of multilocus selection with epistasis, such as truncation selection, can effectively reduce the mutation load. Many quantitative characters, including complex genetic diseases, are likely to be subject to these types of selection. However, direct measurement of selection in natural populations is difficult and the effect of epistasis on within-species variations remains unclear. Epistatic interaction in the fitness effect can generate linkage disequilibrium (LD). Therefore, we may detect the action of natural selection from its amount and pattern. We found a large number of inter-locus nonrandom associations between polymorphisms in 98 Drosophila chemoreceptor genes. LD was examined in two fly samples collected at the same location, but in different seasons. The amount of LD was much larger in the spring sample than in the autumn one. This between-sample difference was much more striking for the replacement polymorphisms than for the silent polymorphisms. The difference between the replacement and silent polymorphisms could not be attributed to differences in the mean marker distances. We also found a significant excess of associations between one frequent and one less common allele for the replacement polymorphisms, but not for the silent polymorphisms. It is unlikely that a simple seasonal bottleneck could explain all these differences in the scale of LD between the samples and between the replacement and silent polymorphisms. Natural selection is suggested to play a significant role in shaping the pattern of LD observed in this study. For details, see Paper 4.

(2) A high frequency null mutant of an odorant-binding protein, Obp57e, in Drosophila melanogaster

Aya Takahashi and Toshiyuki Takano-Shimizu

--We have found a null mutant of an odorant-binding protein, Obp57e, in Drosophila melanogaster. This frameshift mutation, which is a 10 bp deletion in the coding region, is at a high frequency in the Kyoto population, and is also present in Taiwan and Africa. We have sequenced an about 1.5kb region including the tandemly duplicated gene, Obp57d, from 16 inbred lines sampled in Kyoto, Japan. The analyses showed a peak of nucleotide diversity and strong linkage disequilibrium around this mutation. This pattern suggests an elevated mutation rate or an influence of balancing selection in this region. The level of nucleotide divergence between D. melanogaster and D. simulans does not support the former possibility. Thus, this presence/absence polymorphism may be due to balancing selection, which takes advantage of the relatively weak functional constraint in members of a large gene family. In addition, the Obp57d gene region showed an excess of high frequency derived mutants that is consistent with a pattern predicted under positive natural selection.

(3) Analyses of the mechanism and genetics of mate choice by Drosophila melanogaster males

Aya Takahashi and Toshiyuki Takano-Shimizu

--We surveyed multiple strains of D. melanogaster and D. simulans for differences in heterospecific copulation frequencies, and identified two D. melanogaster inbred lines between which mating frequencies of males against D. simulans females differ by a large extent. One line was originated in West Africa and the other was collected in Taiwan. We also performed an intraspecific mating experiment and found that males from these two lines have different mating preference against conspecific females of different lines. A cuticular hydrocarbon transfer experiment revealed that this preference is likely to be affected by the differences in cuticular hydrocarbon components of the females. These two lines have been subjected to over 20 generations of sib-mating, and are suitable materials for genetic mapping. Our genetic analyses showed that the third chromosome has a major effect on these behavioral differences of males.

(4) Null alleles at Drosophila chemoreceptor genes

Akira Kawabe¹, Yuriko Ishii and Toshiyuki Takano-Shimizu (¹University of Edinburgh)

--We determined a total of about 85-kb sequence of 110 chemoreceptor genes of seven D. melanogaster strains and found 16 putative null alleles at 13 loci: 4 nonsense mutations, 7 small insertions/deletions causing frame shifts, and 5 long deletions encompassing parts of coding sequence. The seven strains analyzed in the present study had at least one null allele and, in total, 27 null alleles. Because we determined only one-half of the coding sequences, there might be eight null alleles per haploid genome of D. melanogaster. Importantly, the ratio (π_R/π_S) of the average nucleotide diversity (π) at the replacement sites to that at the synonymous sites suggested that the null alleles did not necessarily appear only in very low constraint loci, although the Or85e seems to be a pseudogene. On the other hand, the frequencies of most of these putative null alleles in a natural population are not very low: 36% of a deletion in Or98b, 30% of an insertion in Gr2a, 1% of a nonsense mutation in Gr22b, 10% of a nonsense mutation in Gr36c, 39% of a deletion in Gr39aA, 8% of a nonsense mutation in Gr47a, 12% of a nonsense mutation in Gr58a and 4% of a deletion in Gr85a. Then, the frequencies of null homozygotes are not expected to be very low. In sum, the results suggested that selection is weak but not completely relaxed in the Or and Gr genes. This condition may allow rapid evolution of the chemoreceptor genes. We found a single putative null mutation in 54 loci of a single D. simulans strain, which did not include Or85e. The expected number of null alleles at the chemoreceptor genes in D. simulans was comparable to that in D. melanogaster.

(5) Genetic and molecular basis of sex-comb-tooth-number variation in Drosophila

Haruki Tatsuta¹, Yuriko Ishii and Toshiyuki Takano-Shimizu (¹National Institute of Environmental Studies)

--The sex comb on the forelegs of Drosophila males is a secondary sexual trait, and the number of teeth on these combs varies greatly within and between species. To understand the relationship between the intra- and interspecific variations, we did quantitative trait loci (QTL) analyses of intra-specific sex-comb-tooth-number variations in five mapping populations with two inbred Drosophila simulans strains of large and small numbers of sex-comb teeth (whole-genome F₂, two second-chromosome substitution strains, and two third-chromosome congenic strains). From these mapping studies, we identified three major QTLs on the third chromosome and one of them likely matched the QTL responsible for the simulans-mauritiana differences. We focused our analyses on this region. Linkage disequilibrium survey for association study is now under way.

PUBLICATIONS

Papers
1. Kobayashi, S., Noro, Y., Nagano, H., Yoshida, K., Takano-Shimizu, T., Kishima, Y. and Sano, Y. Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer. Gene (in press).
2. Takahashi, A., Liu, Y.-H. and Saitou, N. (2004). Genetic variation versus recombination rate in a structured population of mice. Mol. Biol. Evol. 21, 404-409.
3. Takahashi, A. and Ting, C.-T. (2004). Genetic basis of sexual isolation in Drosophila melanogaster. Genetica 120, 273-284.
4. Takano-Shimizu, T., Kawabe, A., Inomata, N., Nanba, N., Kondo, R., Inoue, Y. and Itoh, M. (2004). Inter-locus nonrandom association of polymorphisms in Drosophila chemoreceptor genes. Proc. Natl. Acad. Sci. USA 101, 14156-14161.

ORAL PRESENTATIONS

1. Itoh, M., Kawabe, A., Inomata, N., Nanba, N., Kondo, R., Inoue, Y. and Takano-Shimizu, T. Linkage disequilibrium analysis as a new approach for understanding the functional network of the olfactory and gustatory receptor genes in Drosophila. International Symposium on Chemical Sense and Insect Behavior, Kyoto, July, 2004.
2. 高橋文「ショウジョウバエにおける交尾前生殖隔離の分子機構とその進化」第6回日本進化学会、東京、2004年8月
3. 高橋文、高野敏行「キイロショウジョウバエ雄による雌選好性のメカニズムとその遺伝的解析」日本遺伝学会第76回大会、吹田市、2004年9月
4. 高野敏行、猪股伸幸、難波紀子、近藤るみ、河邊昭、井上寛、伊藤雅信「ショウジョウバエ嗅覚・味覚受容体遺伝子のアミノ酸変異に働く自然淘汰」日本遺伝学会第76回大会、吹田市、2004年9月
5. 難波紀子、伊藤雅信、猪股伸幸、近藤るみ、高野敏行「ショウジョウバエX連鎖遺伝子の連鎖不平衡の集団間比較」日本遺伝学会第76回大会、吹田市、2004年9月

POSTER PRESENTATIONS

1. Takano-Shimizu, T., Kawabe, A., Inomata, N., Nanba, N., Kondo, R., Inoue, Y. and Itoh, M. Linkage disequilibrium between polymorphisms at Drosophila chemoreceptor genes. 45th Annual Drosophila Research Conference, Washington, DC, March, 2004.
2. Takahashi, A. and Takano-Shimizu, T. A high frequency null mutant of an odorant-binding protein, Obp57e. Genomes & Evolution 2004. University Park, U.S.A., June, 2004

EDUCATION

1. Dr. T. Takano gave a lecture at The Graduate University for Advanced Studies, April, 2004 (in Japanese).
2. Dr. T. Takano was invited to give a lecture in “Shonan Lecture: Diversity and Evolution of Populations" at The Graduate University for Advanced Studies, August, 2004.
3. Dr. T. Takano organized a Collaborative Research Meeting at the National Institute of Genetics, Mishima, June, 2004.
4. Dr. T. Takano gave a two-day training course for Mishima Kita Junior High School students, October, 2004.

SOCIAL CONTRIBUTIONS AND OTHERS

1. Dr. T. Takano served as a member of the steering committee of National Bio-Resource Project“DROSOPHILA".
2. Drs. T. Takano and A. Takahashi served as members of the election administration committee of the Genetics Society of Japan.
3. Dr. T. Takano served as a member of the examination specialist committee for National Personnel Authority.