Dataset Information

Genetic Mapping of Prince Rupprecht's Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing.

ABSTRACT: A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht's larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees.

SUBMITTER: Dong M

PROVIDER: S-EPMC6723236 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genetic Mapping of Prince Rupprecht's Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing.

Dong Mingliang M He Qingwei Q Zhao Jian J Zhang Yan Y Yuan Deshui D Zhang And Jinfeng AJ

Genes 20190731 8

A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht's larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and t ...[more]

PMID: 31370324

Similar Datasets

Project description:Elucidating the correlation between soil microbial communities and forest productivity is the focus of research in the field of forest ecology. Nonetheless, the relationship between stand age, soil quality, soil microorganisms, and their combined influence on productivity is still unclear. In this study, five development stages (14, 25, 31, 39, and >80 years) of larch (Larix principis-rupprechtii) forests were investigated in Inner Mongolia and Shanxi provinces of China. We evaluated soil quality using the Integrated Soil Quality Index (SQI) and analyzed changes in bacterial and fungal communities using high-throughput sequencing. Regression models were also established to examine the impacts of stand age, microbial diversity, and SQI on productivity. The findings revealed an ascending trend in soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), available potassium (AK), and SQI in 14, 25, 31, and 39-year-old stands. The abundance of oligotrophic bacteria Acidobacteria exhibited a gradual decline with increasing forest age, whereas copiotroph bacteria Proteobacteria displayed a progressive increase. Stands older than 80 years exhibited a higher abundance of both the saprophytic fungus Ascomycota and mycorrhizal fungus Basidiomycota. Forest age had a significant impact on microbial diversity, particularly in terms of bacterial diversity, impacting both α and β diversity. The soil bacterial community structure was influenced by AK, SOM, TN, TP, and pH. Conversely, the fungal community structure was regulated by crucial factors including SOM, TN, TP, TK, AK, and pH. Fungal diversity demonstrated a significant and positive correlation with the basal area increment (BAI) of larch. Furthermore, microbial diversity accounted for 23.6% of the variation in BAI. In summary, the findings implied a robust association between microbial composition, diversity, and soil chemical properties throughout the chronosequence of larch forests. These factors collectively played a crucial role in influencing the productivity of larch forest.

Dataset Information

Genetic Mapping of Prince Rupprecht's Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing.

Publications

Genetic Mapping of Prince Rupprecht's Larch (<i>Larix principis-rupprechtii</i> Mayr) by Specific-Locus Amplified Fragment Sequencing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets