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Environmental versus geographical effects on genomic variation in wild soybean ( Glycine soja ) across its native range in northeast Asia

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ABSTRACT

A fundamental goal in evolutionary biology is to understand how various evolutionary factors interact to affect the population structure of diverse species, especially those of ecological and/or agricultural importance such as wild soybean (Glycine soja). G. soja, from which domesticated soybeans (Glycine max) were derived, is widely distributed throughout diverse habitats in East Asia (Russia, Japan, Korea, and China). Here, we utilize over 39,000 single nucleotide polymorphisms genotyped in 99 ecotypes of wild soybean sampled across their native geographic range in northeast Asia, to understand population structure and the relative contribution of environment versus geography to population differentiation in this species. A STRUCTURE analysis identified four genetic groups that largely corresponded to the geographic regions of central China, northern China, Korea, and Japan, with high levels of admixture between genetic groups. A canonical correlation and redundancy analysis showed that environmental factors contributed 23.6% to population differentiation, much more than that for geographic factors (6.6%). Precipitation variables largely explained divergence of the groups along longitudinal axes, whereas temperature variables contributed more to latitudinal divergence. This study provides a foundation for further understanding of the genetic basis of climatic adaptation in this ecologically and agriculturally important species.

No MeSH data available.


Collection sites of the 99 wild soybean ecotypes sampled across northeastern Asia. The wild soybean ecotypes locations are color‐coded by the genetic cluster to which they were assigned by the STRUCTURE procedure. The four genetic clusters are as follows: Red: GROUP 1; Blue: GROUP 2; Green: GROUP 3; Purple: GROUP 4. Individuals assigned at a probability of <70% were shown on the map with a color Pie indicating the composition of the genome. The plant picture on the top‐left corner is Glycine soja.
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ece32351-fig-0001: Collection sites of the 99 wild soybean ecotypes sampled across northeastern Asia. The wild soybean ecotypes locations are color‐coded by the genetic cluster to which they were assigned by the STRUCTURE procedure. The four genetic clusters are as follows: Red: GROUP 1; Blue: GROUP 2; Green: GROUP 3; Purple: GROUP 4. Individuals assigned at a probability of <70% were shown on the map with a color Pie indicating the composition of the genome. The plant picture on the top‐left corner is Glycine soja.

Mentions: Contemporary genetic distribution patterns in species are shaped and maintained by their population history and evolutionary factors such as natural selection, gene flow and genetic drift. Understanding the interaction of these factors in natural populations is a long‐standing goal in ecological and evolutionary biology. Currently, there is much interest in assessing the relative contribution of environmental versus geographic factors in shaping population structure, with a number of studies suggesting that environmental adaptation may play an important role in population divergence (Manel et al. 2010; Lee and Mitchell‐Olds 2013; Leamy et al. 2014). Natural selection acts to foster adaptation in local populations and thus also to maintain genetic variation among populations (Mitchell‐Olds and Schmitt 2006). Whether a particular species will adapt to a changing environment, however, depends on the nature and extent of its genetic variation. With current and projected trends in climatic change, it is crucial that we better understand the effects of environmental and geographic factors that shape genetic variation and the adaptation process (Reusch and Wood 2007). This is especially the case for species of both agricultural and ecological significance, such as Glycine soja (Fig 1).


Environmental versus geographical effects on genomic variation in wild soybean ( Glycine soja ) across its native range in northeast Asia
Collection sites of the 99 wild soybean ecotypes sampled across northeastern Asia. The wild soybean ecotypes locations are color‐coded by the genetic cluster to which they were assigned by the STRUCTURE procedure. The four genetic clusters are as follows: Red: GROUP 1; Blue: GROUP 2; Green: GROUP 3; Purple: GROUP 4. Individuals assigned at a probability of <70% were shown on the map with a color Pie indicating the composition of the genome. The plant picture on the top‐left corner is Glycine soja.
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Related In: Results  -  Collection

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ece32351-fig-0001: Collection sites of the 99 wild soybean ecotypes sampled across northeastern Asia. The wild soybean ecotypes locations are color‐coded by the genetic cluster to which they were assigned by the STRUCTURE procedure. The four genetic clusters are as follows: Red: GROUP 1; Blue: GROUP 2; Green: GROUP 3; Purple: GROUP 4. Individuals assigned at a probability of <70% were shown on the map with a color Pie indicating the composition of the genome. The plant picture on the top‐left corner is Glycine soja.
Mentions: Contemporary genetic distribution patterns in species are shaped and maintained by their population history and evolutionary factors such as natural selection, gene flow and genetic drift. Understanding the interaction of these factors in natural populations is a long‐standing goal in ecological and evolutionary biology. Currently, there is much interest in assessing the relative contribution of environmental versus geographic factors in shaping population structure, with a number of studies suggesting that environmental adaptation may play an important role in population divergence (Manel et al. 2010; Lee and Mitchell‐Olds 2013; Leamy et al. 2014). Natural selection acts to foster adaptation in local populations and thus also to maintain genetic variation among populations (Mitchell‐Olds and Schmitt 2006). Whether a particular species will adapt to a changing environment, however, depends on the nature and extent of its genetic variation. With current and projected trends in climatic change, it is crucial that we better understand the effects of environmental and geographic factors that shape genetic variation and the adaptation process (Reusch and Wood 2007). This is especially the case for species of both agricultural and ecological significance, such as Glycine soja (Fig 1).

View Article: PubMed Central - PubMed

ABSTRACT

A fundamental goal in evolutionary biology is to understand how various evolutionary factors interact to affect the population structure of diverse species, especially those of ecological and/or agricultural importance such as wild soybean (Glycine soja). G. soja, from which domesticated soybeans (Glycine max) were derived, is widely distributed throughout diverse habitats in East Asia (Russia, Japan, Korea, and China). Here, we utilize over 39,000 single nucleotide polymorphisms genotyped in 99 ecotypes of wild soybean sampled across their native geographic range in northeast Asia, to understand population structure and the relative contribution of environment versus geography to population differentiation in this species. A STRUCTURE analysis identified four genetic groups that largely corresponded to the geographic regions of central China, northern China, Korea, and Japan, with high levels of admixture between genetic groups. A canonical correlation and redundancy analysis showed that environmental factors contributed 23.6% to population differentiation, much more than that for geographic factors (6.6%). Precipitation variables largely explained divergence of the groups along longitudinal axes, whereas temperature variables contributed more to latitudinal divergence. This study provides a foundation for further understanding of the genetic basis of climatic adaptation in this ecologically and agriculturally important species.

No MeSH data available.