Dataset Information

Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS.

ABSTRACT: Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS® . Based on 99 085 high-quality SNPs, landraces were classified into three sub-populations which exhibit geographical genetic differentiation. Clustering was inferred from STRUCTURE, principal component analyses and neighbour-joining tree analyses. Using phenotypic data collected at two locations separated by 10 degrees of latitude, 17 trait-associated SNPs (TASs) for flowering time were identified, including a stable locus Chr12:5914898 and previously undetected candidate QTL/genes for flowering time in the vicinity of the previously cloned flowering genes, E1 and E2. Using passport data associated with the collection sites of the landraces, 27 SNPs associated with adaptation to three bioclimatic variables (temperature, daylength, and precipitation) were identified. A series of candidate flowering genes were detected within linkage disequilibrium (LD) blocks surrounding 12 bioclimatic TASs. Nine of these TASs exhibit significant differences in flowering time between alleles within one or more of the three individual sub-populations. Signals of selection during domestication and/or subsequent landrace diversification and adaptation were detected at 38 of the 44 flowering and bioclimatic TASs. Hence, this study lays the groundwork to begin breeding for novel environments predicted to arise following global climate change.

SUBMITTER: Li YH

PROVIDER: S-EPMC6953199 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS.

Li Ying-Hui YH Li Delin D Jiao Yong-Qing YQ Schnable James C JC Li Yan-Fei YF Li Hui-Hui HH Chen Huai-Zhu HZ Hong Hui-Long HL Zhang Ting T Liu Bin B Liu Zhang-Xiong ZX You Qing-Bo QB Tian Yu Y Guo Yong Y Guan Rong-Xia RX Zhang Li-Juan LJ Chang Ru-Zhen RZ Zhang Zhiwu Z Reif Jochen J Zhou Xin-An XA Schnable Patrick S PS Qiu Li-Juan LJ

Plant biotechnology journal 20190724 2

Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS<sup>®</sup> . Based on 99 085 high-quality SNPs, landraces were classified into three sub-populations ...[more]

PMID: 31278885

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Project description:The aim of this experiment was to explore transcriptomic changes in the distal gut of Altantic salmon fed five experimental and two control diets. The experimental diets were isonitrogenous, isolipidic and isocaloric. They had similar content of fish meal (~22%) and similar total plant protein content (~45%), but differed in the contents of soya protein concentrate (SPC) and bean protein concentrate (BPC). These two ingredients were used to replace each other (either partially or fully) at the levels of incorporation ranging from 0 to 45%, with ~11% increments. As a result, the experimental diets contained either 45% SPC and 0% BPC (S45), 34% SPC and 11% BPC (S34B11), 22% SPC and 22% BPC (S22B22), 11% SPC and 34% BPC (S11B34) or 0% SPC and 45% BPC (B45). The S45 and B45 diets were single plant protein diets, while the others (S34B11, S22B22 and S11B34) were mixed plant protein diets. The control diets were enriched with fish meal (FM diet) or soybean meal (SBM diet) to provide negative and positive controls for gut inflammation (enteritis), respectively. The study was conducted at EWOS Innovation Research Facility in Dirdal (Norway) Atlantic salmon (Salmo salar L.) of the SalmoBreed strain were supplied as fertilized eggs and hatched on site. Mixed-sex juvenile salmon in groups of ~150 fish were transferred to 26 indoor tanks (0.6 x 0.6 x 0.6 m), with ~60 L of freshwater flowing at a rate of 3.9 L/min and continuous aeration. The temperature of water was regulated at 13°C and all animals were exposed to a constant light regime (24 h light/day). Fish were fed a commercial EWOS Start 1 diet and acclimated to the experimental conditions for 2 weeks, after which (at body mass ~1.5 g) they were subjected to a 56-day feeding trial. Tanks were randomly assigned to the dietary treatments, with 4 replicate tanks per each experimental diet (S45, S34B11, S22B22, S11B34 and B45) and 3 replicate tanks per each control diet (FM and SBM diets). Fish were fed to satiation prior to the feeding trial and during the dietary manipulation using automatic band feeders (Holland Technology, Norway). During the feeding trial, all fish in each tank had their biomass recorded on days 0 (start of experiment), 14, 28, 42 and 56 (end of experiment) for evaluation of growth performance.

Dataset Information

Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS.

Publications

Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS.

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