Genetic Diversity, Population Differentiation And Evolution As Well As Association Analysis Of QTLs Of Breeding Target Traits In Glycine Max (L.) Merr. And Glycine Soja Sieb. Et Zucc. In China

It is well known that the cultivated soybean,Glycine max(L.) Merr.,was domesticated from its annual wild relative Glycine soja Sieb.et Zucc.in China.The study of origin and evolution of soybean have been called attention by both botanists and soybean breeders.In order to evaluate the unclear and chloroplastic genetic diversity,mechanism of differentiation and genetic relationship among different eco-types of cultivated and wild soybean,we analyzed allelic profiles at 60 nuclear simple-sequence repeat(nuSSR) markers and 11 chloroplastic SSR (cpSSR) of a representative sample with 393 cultivated soybean and 196 wild soybean accessions from the Chinese countrywide area.Moreover,based on linkage disequilibrium of pairwise loci and population structure analysis,the genotyping data of 60 simple-sequence repeat(SSR) markers with phenotypic data of 20 agronomic and quality traits were used in association mapping.Comparisons were also conducted to discriminate the different character of the alleles associated with breeding traits between the cultivated and wild soybean populations.A set of elite alleles,loci and their carrier materials were screened out.The main results were as follows:1.Genetic diversity,geo-ecotypes differentiation and evolution relationship among eco-types of Glycine max and Glycine soja in China(1) The present analysis detected relatively high level of variation at the nuSSR loci in both G.max and G.soja populations(A value was 980 and 1067 respectively).The cpSSR loci produced relatively low level of variation(A value was 44 and 57 for G.max and G. soja respectively).In comparison,the genetic diversity of G.soja was much higher than that of G.max not only at nuclear genome level but also at chloroplastic genome level,which indicates the genetic diversity obviously decreased during the domestication process.However,of the 980 nuclear alleles detected in the cultivated soybean,603 ones(61.5%) were the same as in G. soja,accounting for only 57%of the total allelic number(1067) of the wild soybean,and 377 new alleles(38.5%) emerged after domestication in the cultivated soybean.On the other hand,of the 44 chloroplastic alleles detected in the cultivated soybean,37 ones(84.1%) were the same as in G.soja, and 7 new alleles(15.9%) emerged,which showed the great contribution of artificial evolution not only subject to the nuclear but also to chloroplastic diversification of G.max.Cultivated soybean accessions from Southern China,especially from Southwest and Central south region,showed higher value in most statistics of genetic diversity than those from Northern China did except for A value.Greatest genetic diversity was detected in Lower and Middle Changjiang river G.soja population.No remarkable difference had been detected in the value of genetic diversity at chloroplastic level among different ecotypes of G.max and G.soja.All ecotypes of the cultivated accessions tested possessed common alleles(NTCP10-₁₁₇) with different frequency,which was detected in wild accessions from Lower and Middle Changjiang river,indicating that there exists cytoplasmic gene flow between this G.soja population and all eco-types of G.max.(2) There exists three evidences supporting that eco-geographic differentiation has its sound genetic bases for both Chinese cultivated and wild soybean populations:1) The results of AMOVA showed that significant portions of the variation existed either in interspecies or among the populations of the two species at both nuclear and chloroplastic level and expect for differentiation between populations of G.max at chloroplastic level.2) Theχ²-test showed significant association between the two grouping factors,namely SSR data clusters and geographic eco-types.3)There exists a plenty of geo-ecotype-specific-present alleles,geo-ecotype-specific-deficit alleles in different ecotypes of G.max and G.soja.(3) Cluster analysis of all accessions clearly showed that accessions from Lower and Middle Changjiang river and Southwest—Central south had relatively smaller genetic distance with all cultivated soybean.A UPGMA dendrogram representing relationships among ecotypes of G.max and G.soja further showed genetic distance between all eco-types of G.max and Lower and Middle Changjiang river G.soja population were closer than those between the regional population of G.max and their respective G.soja counterpart,confirmed that the primitive Lower and Middle Changjiang river G.soja population might be the common ancestor of all the cultivated soybeans.2.Association analysis of QTLs of breeding target traits in G.max and G.soja populations(4) In present study,the cultivated soybean population had more LD loci pairs than wild soybean population did,while the later had higher degree and slower attenuation of LD than the former did.Genetic structure analysis showed that both of the cultivated and wild populations was composed of nine and four subpopulations,respectively,which associated with their geographic eco-types,indicating the classification of geographic eco-types was of sound genetic bases.(5) Ninety one and thirty nine nuSSR loci,which associated with the agronomic traits and quality traits respectively,were screened out from the wild and cultivated soybean accessions.The rate of checking out for agronomic-traits-associated-loci in wild soybean was much higher than the value detected in the cultivated soybean population,however,the rate of checking out for quality-traits-associated-loci in cultivated soybean was much higher than the value detected in the wild counterpart.Twenty seven and thirty four SSR loci associated with the traits were screened out from cultivated and wild populations, respectively.The number of QTLs detected with association mapping was more than the value detected with family-based linkage mapping method.Some loci were found to associate with a same trait in both populations,and there existed both consistent and inconsistent association between the cultivated and wild populations.There were a few loci associated with two or more traits simultaneously,which might be the genetic reason of correlation among traits or pleiotropic phenomena.In addition,thirty two associated markers were in agreement with mapped QTLs from family-based linkage mapping procedure.(6) The phenotypic allele effect was estimated through comparison between the average phenotypic value over accessions with the specific allele and that of accessions with "null allele",and then the average positive(negative) allele effect(AAE) of a locus was calculated over the estimated phenotypic effects of all positive(negative) alleles.The results showed:a set of elite alleles,loci and their carrier materials were screened out.The elite alleles existed in Glycine max and Glycine soja,some were consistent,some inconsistent and some complementary.The phenotypic effects of positive(negative) alleles were different from each other,and therefore,the average positive(negative) effect of a locus were also different from each other,indicating the potential of genetic recombination for breeding purposes.A same marker locus could associate with multiple traits with its alleles performed in their own way of direction and size,and the covariation of a same allele performed in two related traits might be the genetic base of their phenotypic correlation.In summary,the results implied that association mapping could offer further genetic information complementary to the family-based linkageship mapping for the improvement of breeding procedures.