Genetic and allelic diversity
Elite soybeans from the Northeastern spring and Northern spring regions of China and early maturity European elite soybean cultivars are genetically separated from each other as independently revealed by SNP and SSR marker analysis (Figs. 1 and 2). This clearly indicates that the two soybean sets are representing different world soybean populations as proposed by Liu et al. (2020a). In their world soybean classification based on historical dissemination patterns and phylogeographical relationships, soybean populations from the north of China, far east Russia, north of North America and north of Europe (represented by Swedish accessions only) are forming one cluster according to phenotypic data considering daylength- and temperature-sensitive adaptation traits, whereas genetically these populations are clustering differently thus confirming the present results with respect to north Chinese and European cultivars. Similarly, Chinese and American soybean cultivars were also described as having clearly distinct genetic bases (Liu et al. 2017).
The continuous reduction of genetic diversity from soybean domestication through the generation of landraces, ancestors of selective breeding and the subsequent development of present-day elite cultivars is well documented, and several genetic bottlenecks have been identified which caused the loss of rare alleles or larger structural variants (Hyten et al. 2006; Liu et al. 2020b). However, on the level of elite cultivars covered in the present study, a lower level of diversity also would have been assumed for European cultivars as compared to Chinese ones due to the much shorter growing history and lower extend of breeding as well as a rather narrow genetic base in Europe (Tavaud-Pirra et al. 2009). In contrast to this assumption, the level of overall diversity within each the European and the Chinese population appears to be rather similar (Fig.s 1, 2, Tables 3, 4) with average genetic distances suggesting slightly higher diversity in Europe for experimental groups 1 and 4 vs. higher diversity in China for groups 2 and 3, respectively (Suppl. Table 4). This finding is corroborating earlier research (Hahn and Würschum 2014) which identified significant genetic variation existing in Central European soybean germplasm. Moreover, the present results also demonstrate that genetic diversity can be maintained by breeding and selection which was similarly shown for Canadian soybean diversity (Bruce et al. 2019) or for North American ancestors vs. elite cultivars (Hyten et al. 2006).
Within the populations, soybean cultivars were grouped according to their maturity classification. This was particularly evident for the European population, which was additionally grouped according to their country of origin (Fig. 1B). In a comparable set of European cultivars, genotypes also clearly clustered according to maturity group and country of cultivar origin (Žulj Mihaljević et al. 2020). Similarly, time to maturity, geographical location of a breeding program and specific breeding decisions have been identified as major factors affecting diversity of North American public soybeans (Gizlice et al. 1996). Thus, the country-wise grouping (Fig. 1B) probably indicates different breeding programs as well as regional adaptation due to specific environmental conditions between the different European soybean growing regions. Within the Chinese elite population, however, the clustering of cultivars according to the experimental maturity grouping or according to breeding institutions was less clear. This might be due to much larger and more homogenous soybean production regions in China as compared to Europe, and a classification scheme of cultivars into primary ecotypes such as the Northeastern Spring or Northern Spring soybeans (Wang et al. 2006) rather than more narrow maturity groups. In addition, this is also supported by AMOVA results (Tables 1 and 2) indicating a larger percentage of variation attributable to geographic origin rather than to maturity group.
The number of different SSR-alleles was slightly higher in the Chinese than in the European population (Table 3). Remarkably, however, 56 private alleles were found in the European set of cultivars which were not present in the Chinese set. These alleles might have been lost during previous cycles of selection in one region, or they reveal the occurrence of new mutations developing from previous alleles. The considerable number of private alleles found both in the Chinese and European population is also indicating that the populations have been derived from clearly different gene pools with different ancestral lines (Viana et al. 2022). In addition, differences in allele distribution of particular SSR loci between populations might as well indicate signatures of selection for adaptation to particular environments (Tomicic et al. 2015). While the mean number of SSR alleles per locus was 5.5 across the two populations of the present study (Suppl. Table 3) and similar to the sets of Žulj Mihaljević et al. (2020) or Tavaud-Pirra et al. (2009), numbers of alleles were lower in Serbian (Tomicic at al. 2015) and Indian (Kumar et al. 2022) sets of elite cultivars. In contrast, the numbers of alleles were considerably higher in several sets of soybean accessions originating from Korea (Hwang et al. 2020; Lee et al. 2014; Song et al. 2013). Particular SSR loci exhibited a rather high number of alleles (e.g. Satt281 in Suppl. Table 3, also confirmed by Tavaud-Pirra et al. (2009)), whereas other polymorphic loci have two alleles only across the whole population (e.g. locus SacK149 in Suppl. Table 3, for which the two alleles are associated with low or high cadmium (Cd) uptake from soil (Vollmann et al. 2015), and additional alleles would be of interest in view of potential phenotypic effects).
Genetic structure
The clear separation between Chinese and European cultivars is also confirmed on the level of structure analysis (Fig. 3). For the European cultivars, the existence of two major ancestral lines (dark blue and green bars in Fig. 3, K = 5) was suggested in this analysis. Late maturity European soybeans as represented by Serbian cultivars (Suppl. Table 1) are roughly tracing back to northern U.S. cultivars such as Evans and Hodgson (Hrustic and Miladinovic 2011) which contain ancestral varieties such as Lincoln (pedigree: Mandarin / Manchu) and Richland in their pedigree (Allen and Bhardwaj 1987; SoyBase 2022). As a consequence, the six ancestral varieties Mandarin, Capital, Richland, Lincoln, Strain No. 18 and Mukden have been identified to make about 75% of the parental contribution to south-east European elite cultivars (Tomicic et al. 2015). In contrast, early maturity European soybean cultivars used in central and northern regions of Europe are often tracing back to extremely early germplasm developed in Sweden from germplasm obtained in Sakhalin (Fiskeby, Holmberg varieties) and early maturity Canadian (i.e. Ontario) varieties. Both Canadian and Swiss soybeans such as the widely grown cultivars Maple Arrow (pedigree: Harosoy 63 / Holmberg 840-1-3) or Ceresia (pedigree: Fiskeby V / Harosoy 107-2031-2) have been selected for chilling tolerance and adaptation to cool environments (Yamaguchi et al. 2018). Many modern Canadian, Swiss, German, Polish and Austrian cultivars are related through the use of Swedish early maturity germplasm, e.g. introgression of Fiskeby V through Bicentennial into at least nine North American cultivars, or Maple Arrow being present in the pedigree of almost 20 modern cultivars (SoyBase 2022). Therefore, Canadian, Swiss and German germplasm materials have been described as genetically similar (Hahn and Würschum 2014). Thus, the two ancestral lines structuring the European elite cultivar population (Fig. 3, K = 5) might indicate the two different breeding pathways of cultivars from south-east or central-north Europe.
The Chinese elite population is structured into three major ancestral lines which is suggesting a higher level of genetic background variation than for the European population (Fig. 3, K = 5, yellow, red and light blue bars). Despite the fact that the series of Heihe or Dongnong cultivars are earlier and Hefeng or Suinong cultivars are clearly later in maturity, the structure within each of these series is not homogenous. This appears as a clear illustration of a different breeding history between China and Europe: As discussed above, European soybean diversity is largely based on a limited number of distinct plant introductions adapted to small and separated agroecological regions. In contrast, Chinese soybean diversity in the large Northeastern Spring and Northern Spring sowing regions as represented in the present study appears to be more continuous due to multiple ancestral contributions and larger growing areas (Li et al. 2008; Liu et al. 2020b; Wang et al. 2006).
LD decay
Differences in LD decay (Bruce et al. 2019; Contreras-Soto et al. 2017; Viana et al. 2022) may have multiple reasons including size and specifics of population, breeding intensity, or maturity group. The faster LD decay in the European population (Fig. 4) as compared to the Chinese one might again indicate the lower number of ancestors in the European gene pool, because of which relatively more hybridizations per each ancestral line had been carried out thus causing higher rates of recombination; population specific differences in LD decay or greater selection strength in the Chinese population might have contributed to the overall difference as well.