The Power of QTL Mapping with RILs

QTL (quantitative trait loci) mapping is commonly used to identify genetic regions responsible to important phenotype variation. A common strategy of QTL mapping is to use recombinant inbred lines (RILs), which are usually established by several generations of inbreeding of an F1 population (usually up to F6 or F7 populations). As this inbreeding process involves a large amount of labor, we are particularly interested in the effect of the number of inbreeding generations on the power of QTL mapping; a part of the labor could be saved if a smaller number of inbreeding provides sufficient power. By using simulations, we investigated the performance of QTL mapping with recombinant inbred lines (RILs). As expected, we found that the power of F4 population could be almost comparable to that of F6 and F7 populations. A potential problem in using F4 population is that a large proportion of RILs are heterozygotes. We here introduced a new method to partly relax this problem. The performance of this method was verified by simulations with a wide range of parameters including the size of the segregation population, recombination rate, genome size and the density of markers. We found our method works better than the commonly used standard method especially when there are a number of heterozygous markers. Our results imply that in most cases, QTL mapping does not necessarily require RILs at F6 or F7 generations; rather, F4 (or even F3) populations would be almost as useful as F6 or F7 populations. Because the cost to establish a number of RILs for many generations is enormous, this finding will cause a reduction in the cost of QTL mapping, thereby accelerating gene mapping in many species

The Pattern of Polymorphism on Human Chromosome 21

Polymorphism data from 20 partially resequenced copies of human chromosome 21—more than 20,000 polymorphic sites—were analyzed. The allele-frequency distribution shows no deviation from the simplest population genetic model with a constant population size (although we show that our analysis has no power to detect population growth). The average rate of recombination per site is estimated to be roughly one-half of the rate of mutation per site, again in agreement with simple model predictions. However, sliding-window analyses of the amount of polymorphism and the extent of linkage disequilibrium (LD) show significant deviations from standard models. This could be due to the history of selection or demographic change, but it is impossible to draw strong conclusions without much better knowledge of variation in the relationship between genetic and physical distance along the chromosome

ゲノムの脆弱部位を利用した適応進化

2015～2017研究成果の概要（和文）：本研究では、バクテリアから高等生物まで、複数のゲノムを調べることによって、ゲノムの進化速度は一様ではなく、脆弱な速い進化を示す部分と、そうでない部分が存在することを示した。特に、寄生植物とウマを対象にした研究が成果をあげた。寄生植物は（特に完全寄生植物）、宿主ゲノムから柔軟に遺伝子を取り込み、自分のゲノムを進化させていることがわかった。その取り込んだ遺伝子は、ゲノム中に一様に分布しているのではなく、偏りが見られた。おそらく、脆弱性の高い部位に多く取り込まれたのであろう。ウマゲノムにおいても、家畜化において激しく変化したゲノム領域と、そうでない領域を特定した。研究成果の学術的意義や社会的意義脆弱部位は突然変異のホットスポットであるため、基本的には有害な物である。したがって、進化的に一時的に存在するだけで、すぐに淘汰され消滅するものであると考えられている。しかし、この概念は必ずしも正しくない。本研究では、バクテリアから高等生物まで、複数のゲノムを調べることによって、ゲノムの進化速度は一様ではなく、脆弱な速い進化を示す部分と、そうでない部分が存在するこを示した。研究成果の概要（英文）：We aim to demonstrate the evolutionary importance of fragile sites. Fragilesites are hot spots of mutation, which are usually selected against. In this sense, they areevolutionary useless. Here, we hypothesized that a genome has some benefit if it has fragile sites,especially when the host species face environmental changes and has to adapt in a short time. Todemonstrate this, we investigated genomes of various species. For example, we found a number ofgenes have been integrated in the genome of parasite plants, and there seem to be hotspots ofintegration, where multiple genes are integrated (Kado Inann 2018 Genome Biol. Evol.). We alsoinvestigated the genome of domesticated horse, from which we found a number of regions that havechanged dramatically in the domestication process

Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea

忘れられた作物「えどどころ」の起原 --ゲノム解析が明らかにする青森県三八上北地域に残る栽培イモの歴史--. 京都大学プレスリリース. 2022-08-10.A rhizomatous Dioscorea crop “Edo-dokoro” was described in old records of Japan, but its botanical identify has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of Aomori Prefecture, Japan. Rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, D. tokoro and D. tenuipes. Genome analysis revealed that Edo-dokoro is likely originated by hybridization of a male D. tokoro to a female D. tenuipes, followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten from the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information

Population genomics of the fission yeast Schizosaccharomyces pombe.

The fission yeast Schizosaccharomyces pombe has been widely used as a model eukaryote to study a diverse range of biological processes. However, population genetic studies of this species have been limited to date, and we know very little about the evolutionary processes and selective pressures that are shaping its genome. Here, we sequenced the genomes of 32 worldwide S. pombe strains and examined the pattern of polymorphisms across their genomes. In addition to introns and untranslated regions (UTRs), intergenic regions also exhibited lower levels of nucleotide diversity than synonymous sites, suggesting that a considerable amount of noncoding DNA is under selective constraint and thus likely to be functional. A number of genomic regions showed a reduction of nucleotide diversity probably caused by selective sweeps. We also identified a region close to the end of chromosome 3 where an extremely high level of divergence was observed between 5 of the 32 strains and the remain 27, possibly due to introgression, strong positive selection, or that region being responsible for reproductive isolation. Our study should serve as an important starting point in using a population genomics approach to further elucidate the biology of this important model organism

Genome analyses reveal the hybrid origin of the staple crop white Guinea yam (Dioscorea rotundata)

西アフリカの主食作物ギニアヤムの起源を解明 --ギニアヤムはサバンナと熱帯雨林に生育する野生種の雑種起源--. 京都大学プレスリリース. 2020-12-11.White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata. In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica. We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding