Browsing by Subject "LINKAGE MAP"

Sort by: Order: Results:

Now showing items 1-6 of 6
  • Sirviö, Anu; Johnston, J. Spencer; Wenseleers, Tom; Pamilo, Pekka (2011)
  • Littrell, John; Tsaih, Shirng-Wern; Baud, Amelie; Rastas, Pasi; Solberg-Woods, Leah; Flister, Michael J. (2018)
    An accurate and high-resolution genetic map is critical for mapping complex traits, yet the resolution of the current rat genetic map is far lower than human and mouse, and has not been updated since the original Jensen-Seaman map in 2004. For the first time, we have refined the rat genetic map to sub-centimorgan (cM) resolution (
  • Whitaker, Vance M.; Knapp, Steven J.; Hardigan, Michael A.; Edger, Patrick P.; Slovin, Janet P.; Bassil, Nahla V.; Hytönen, Timo; Mackenzie, Kathryn K.; Lee, Seonghee; Jung, Sook; Main, Dorrie; Barbey, Christopher R.; Verma, Sujeet (2020)
    The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant–pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.
  • Samad, Samia; Kurokura, Takeshi; Koskela, Elli; Toivainen, Tuomas; Patel, Vipul; Mouhu, Katriina; Sargent, Daniel James; Hytonen, Timo (2017)
    Flowering time is an important trait that affects survival, reproduction and yield in both wild and cultivated plants. Therefore, many studies have focused on the identification of flowering time quantitative trait locus (QTLs) in different crops, and molecular control of this trait has been extensively investigated in model species. Here we report the mapping of QTLs for flowering time and vegetative traits in a large woodland strawberry mapping population that was phenotyped both under field conditions and in a greenhouse after flower induction in the field. The greenhouse experiment revealed additive QTLs in three linkage groups (LG), two on both LG4 and LG7, and one on LG6 that explain about half of the flowering time variance in the population. Three of the QTLs were newly identified in this study, and one co-localized with the previously characterized FvTFL1 gene. An additional strong QTL corresponding to previously mapped PFRU was detected in both field and greenhouse experiments indicating that gene(s) in this locus can control the timing of flowering in different environments in addition to the duration of flowering and axillary bud differentiation to runners and branch crowns. Several putative flowering time genes were identified in these QTL regions that await functional validation. Our results indicate that a few major QTLs may control flowering time and axillary bud differentiation in strawberries. We suggest that the identification of causal genes in the diploid strawberry may enable fine tuning of flowering time and vegetative growth in the closely related octoploid cultivated strawberry.
  • Shao, Changwei; Niu, Yongchao; Rastas, Pasi; Liu, Yang; Xie, Zhiyuan; Li, Hengde; Wang, Lei; Jiang, Yong; Tai, Shuaishuai; Tian, Yongsheng; Sakamoto, Takashi; Chen, Songlin (2015)
    High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.
  • Jin, Long; Liao, Wen Bo; Merilä, Juha (2022)
    Aim Amphibians require both terrestrial and aquatic environments to complete their life cycles. Thus, they are subject to complex selection pressures stemming from different environments, and these selection pressures are likely to vary geographically with variation in temperature and precipitation. Studies of genetic differentiation along geographical clines allow identification of footprints of these selection pressures. Location China. Methods To identify possible signatures of local adaptation to particular environmental conditions, we conducted a genome-scan with 20,572 single-nucleotide polymorphisms (SNPs) obtained with restriction site-associated DNA sequencing of pooled samples from 10 Microhyla fissipes populations spanning a 1,398 km long latitudinal gradient in China. Results The results revealed significant genetic differentiation among populations (F-ST =0.090). Numerous outlier SNPs associated with variation in both annual average temperature (n = 69) and precipitation (n = 248) were detected. Main conclusions The degree and pattern of population differentiation in the SNPs supported the hypothesis that these SNPs have been subject to directional natural selection associated with temperature and precipitation and, hence, are reflective of geographically varying local adaptation. Hence, conservation and management plans for Microhyla fissipes should take into account this heterogeneity in genetic constitution in its populations.