A Study On Geographic Differentiation,Genetic Dissection And Phylogenetic Relationship Of The World Soybean

It is generally accepted that soybean(Glycine max(L.)Merr.)originated in China,and is planted widely in world as one of the most important economic crops.The ecological diversity of soybean varieties have been developed as a result of adapting to different ecological conditions.In fact the diversity is a comprehensive reflection of the local ecological conditions(mainly light and temperature)during growth and development of different varieties.And the growth period is closely related to the geographical latitude,photoperiod and temperature.In the high latitude region,long day and low temperature delay soybean flowering,pod beginning and maturing;in the low latitude region,short day and high temperature promote soybean flowering,pod beginning and maturing.And the time of flowering and maturity decide the state of plant height,main stem nodes and other growth traits.Beeause of the sensitivity to the light and temperature,the adaptation range of different varieties is different.The maturity group was proposed by North American,it was a method to divide the soybean varieties according to the growth period length.This soybean maturity group system has been applied in many countries,because it can greatly improve the efficiency of the new varieties extension.Due to Chinese complicated climatic conditions and cropping system,initially according to early maturing,medium maturing and late maturing to divide soybean,there didn,t established a unified standard.And researchers classified Chinese soybean varieties referring to the method of North American classification and according to the characteristics of growth period in 2001,established the base for classifying soybean varieties in the future.In the past,the researches mapped QTLs of growth period by materials in MG 000??,no paper reported about the genetic difference of growth period among early maturity groups and late maturity groups.The world soybean not only have various ecological types,but also the genetic structure have changed great,formed population specificity and genetic differentiation among different populations.To study the genetic diversity and phylogenetic relationship among different geographic populations,in favor of understanding the evolutionary relationship between geographic populations.This study selected a representative sample with 371 world soybean varieties from 27 countries,and according to the geographical origin and succession of introduce,13 geographic populations were grouped:O-HCHN,O-SCHN,A-NCHN,Al-RUFE,A2-SSWE,B-KORP,B-JPAN,Bl-SEAS,B2-SASI,B3-AFRI,C-NNAM,C-SNAM and C1-CSAM(no Australian varieties).We planted 371 soybean varieties at Nanjing(32°N)in spring for two years(1 INJSp and 12 NJSp),in summer for one year(11NJSu),at Jining(35ON)in spring for two years(11JNSp and 12 JNSp),and investigated their flowering time,pod beginning,maturity,plant height,main stem node,100-seed weight,protein content and oil content,and analyzed differentiation and relationship of phenotypic characteristic in five environments(1 INJSp,11NJSu,11JN,12NJSp and 12JN).Used“RTM-GWAS”method to perform GWAS of flowering time,Pod beginning,maturity,Plant height and 100-seed weight in 371 varieties.According to the positioning result,we obtained the effects of QTL alleles and constructed QTL-allele matrices.These can help us to understand the genetic structure differences of growth period traits in different maturity groups.Finally,referring to the paths of soybean disseminated from China to global,evaluated the genetic diversity,population structure and phylogenetic relationship of different geographic populations by using 371 varieties and 20,701 SNPLDBs.Added 141 soybean varieties for studying the maturity groups classification of world soybean,according to the characteristics of-growth period with different geographic populations,except sping sowing for two years in Nanjing and Jining respectively,the early-maturing varieties were planted in Heihe(50°N)and Mudanjiang(45°N),and late-maturiting varieties were planted at Nanjing in 2013.According to the main results of Nanjing spring maturity classification and supplementary results of some varieties identified in Heihe,Mudanjiang,Jining additionally,comprehensively divided all the varieties into appropriate maturity groups.The main results are as follows:1 Variation of growth period related traits in different geographic populations of world soybeanThe variation of agronomic traits among 371 world soybean varieties was very extensive,their average days to flowering ranged from 27 to 110 days,days to pod beginning ranged from 34 to 123 days,days to maturity ranged from 74 to 172 days,plant height ranged from 19 to 169 cm,number of nodes on main stem ranged from 5 to 36 nodes,100-seed weight ranged from 4.48 to 36.47 g,protein content ranged from 38.32%to 49.78%,and oil content ranged from 15.72%to 24.02%under fiver environments.The range of days to flowering,pod beginning and maturity were large in O-HCHN and O-SCHN.The days of each growth period stages were short in A.NCHN,A1-RUFE and A2-SSWE,and the range of days to flowering,pod beginning and maturity were small.And they had lower plant height and protein content,higher oil content.The performance of growth period related traits in B-KORP and B-JPAN was similar with O-HCHN and O-SCHN.The days of each growth period stages were longer in B1-SEAS,B2-SASI and B3-AFRI,and the range of days to flowering,pod beginning and maturity were large too.And they had higher plant height,more main stem nodes,but their 100-seed weight,protein and oil content were lower.The range of days to flowering,pod beginning and maturity were the largest in C-NNAM,C-SNAM and C1-CSAM,and they had higher oil content.A cluster analysis was earried out for the photo-thermal sensitive traits(flowering time,maturity and main stem node).Generally,A-NCHN,Al-RUFE,A2-SSWE and C-NNAM are in the most photo-thermal insensitive group,O-HCHN,O-SCHN,B-KORP and B-JPAN in a less photo-thermal sensitive group,Bl-SEAS,B2-SASI,B3-AFRI,C-SNAM and C1-CSAM in a photo-thermal sensitive group.2 Maturity group classification of world soybeanBy the method of Gai et al.proposed to divide Chinese soybean varieties into maturity groups,firstly we divide world soybeans into ??? groups aceording to the growth period performance of 48 MG standard varieties at Nanjing in spring for two years.Because the growth period difference of early MG standard varieties was not great in Nanjing,these early maturing varieties were identified in Jining,Mudanjiang and Heihe respectively,and divided into ??? groups,0 and ? groups,000?0 groups respectively.Due to the differences within groups of MG ??? were too smaller in Nanjing spring,we were unable to identify the criterion of the two groups,and the two groups were classified into ?/? groups.Therefore we divided 464 varieties into 000??/? groups mainly according to the classification result of Nanjing spring,supplemented by the classification results of Jining,Mudanjiang and Heihe.Gai et al.(2001)found that Chinese soybean landraces from 0??I groups varied in days to flowering,and they further divided the four groups into eight sub-groups according to the different number of days to flowering.In this study besides the four groups,we found the variation of flowering was great in ?,?,? and ? groups.And according to the indicator of "the percent of days to flowering in the whole growth period",divided the four groups into eight sub-groups.There was no necessary to further divided MG ? and MG?/? into sub-groups,because they showed less variation in days to flowering,which distributed in a narrow region.The classification of sub-groups associated with multiple cropping system,the days to flowering of spring sowing types were short and summer-autumn sowing types were long.Finally these world soybean cultivars were classified into 12 maturity groups in which 6 groups further were divided into 12 sub-groups,000,00,01,?1,?1,?2,?1,?2,?1,?2,???1,?2,?1:,?2,?1,?2,?/?.There showed different MG typical accessions distributed different geographie regions,for example,the A2-SSWE were MG 000 types;the Al.RUFE were almost MG 01??1 types;the A-NCHN were between MG 000??1 types;the O-HCHN were MG ?1??1 types;the O-SCHN accessions were MG ?1??2 types;the B-KORP and B-JPAN were MG 01??1 types;the B1-SEAS and B2-SAS I were MG ?1?IX/X types;the C-NNAM were MG 00??1 types;the C-SNAM and C1-CSAM were MG ???1 types;the B3-AFRI were MG ?2??/? types.When the accessions were identified to which maturity group in Heihe,we found that Dengke 2(N27419),Hujiao 07-2479(N27298)and Hujiao 07-2123(N27299)matured earlier 7?13 days than MG 000 standard accessions Maple Presto(PI 548594)and OAC Vision(PI 567787).It implied that the Chinese accessions had developed the more matured trend.3 The genome-wide genetic constitution of growth period relatedto traits among world soybeanUsed of GWAS(Genome-Wide Association Studies),in 371 soybeans we obtained 38 loci of flowering time,explaining 82.80%of phenotypic variation;42 loci of pod beginning,explaining 83.10%of phenotypic variation;45 loci of maturity time,explaining 72.70%of phenotypic variation.The origin of the mater:ials used in this study were extensive and the variation of growth period was great,the result explained most phenotypic variation.There were five flowering time QTLs(qFt-a-04-029 qFt-a-11-01,qFt-a-13-02,qFt-a-18-04 and qFt-a-20-03)9 five pod beginning QTLs(qPb-a-04-02,qPb-a-06-03,qPb-a-11-03,qPb-a-12-01 and qPb-a-18-02)and four maturity QTLs(qMt-a-03-01,qMt-a-03-02,qMt-a-06-03 and qMt-a-11-02).they belong to the great contribution of QTLs(R2)5%).Compared to the growth period QTLs of Soybase data published,there were 16 flowering QTLs in the overlap with 32 of 66 publised flowering QTLs,3 pod beginning QTLs in the overlap with 3 of 6 published pod beginning QTLs and 26 maturity QTLs in the overlap with 64 of 138 published maturity QTLs.There 22 new flowering QTLs,39 new pod beginning QTLs and 19 new maturity QTLs were found in 371 world soybean varieties,therefore the genetic basis of growth period traits remains to be further revealed.Respectively established the QTL-allele matrix of flowering time,pod beginning and maturity according to the 204 flowering time allele effects,229 pod beginning allele effects and 211 maturity allele effects.We found 5 specific-present alleles(SPAs)in flowering time QTLs(qFt-a-01-01(G),qFt-a-08-01(A),qFt-a-13-01(6),qFt-a-13-02(10)qFt-a-20-01(C)),2 SPAs in pod beginning QTLs(qPb-a-07-02(3)and qPb-a-11-02(7))and 3 SPAs in maturity QTLs(qMt-a-07-02(4),qMt-a-11-02(5)and qMt-a-18-01(A)),and these SPAs only appeared in ???/? groups.One pod beginning SPA were found in 000??groups.Compared the genetic differentiation and the QTL-allele matrixes of growth period related traits among 12 maturity groups,we found that the genetic difference of early maturing-maturity groups were caused by accumulation of small negative-allele effect.The genetic difference of late maturing-maturity groups were caused by accumulation of small positive-allele effect,and existed the specific present allele with great positive-allele effect.According to the genomic information of Williams 82,annotated gene function for 34 QTLs of flowering time,32 QTLs of pod beginning and 30 QTLs of maturity.Some candidate genes were directly related to the development of flower organs,pollen development(Glyma05g02470),petal formation(Glyma18g44391),floral organ morphogenesis(Glyma13g26820);and the light reaction,anthocyanin accumulation in tissues in response to UV light(Glyma08g20700),photomorphogenesis(Glyma06g41500),long-day photoperiodism(Glyma13g24970),short-day photoperiodism(Glyma07g06420).4 Geographic differentiation,phylogenetic relationship and validated the disseminated route of the world soybeanUsing the genomic haplotype marker SNPLDB(SNP linkage-disequilibrium block)featured with multiple alleles,more allele richness and dispersion were found in original and early-formed populations/centers,accounting for more than 74%of the total alleles of the world soybean population,but the SPAs was not many,only 8,11,and 2.While the genetic diversity of newly-formed derived centers was less,but there were more SPAs,for example in C-NNAM,A1-RUFE,A2-SSWE,B2-SASI,the SPA was as many as 28,41,41,and 67,respectively.There was very small differentiation coefficient between O-HCHN and O-SCHN(Fst=0.054),the similar result was obtained between the two populations within the secondary center B(Fst=0.053),but not between the two populations within the third-stage center in North America(Fst=0.153).The original center O differentiated no large with the secondary center B(Fst=0.110?0.136),but larger with the secondary center A,the Northeast China population(Fst=0.158?0.0196)and especially with the third.stage center C,the North America population(Fst=0.196?0.233).In the past A-NCHN was included in the original center but nominated as one of the two secondary centers in this study.In addition to the European A2-SSWE was quite different from all the other populations,the American centers were of larger differentiation from Asian and African populations.Here the decay distances in the old centers were less than those in the new centers,which indicates more out-crossing happened in the long history in the old centers than in the new centers even strong hybridization breeding happened in the new centers.From both the genetic clustering among geographic populations and among the 371 varieties,the genetic cluster constitutions were somewhat but not well match those of the phenotypic cluster constitutions.It indicated the genetic adaptation not necessary due to only the major ecological environment factors but depending on the comprehensive breeding efforts.The original center populations,O-HCHN and O-SCHN had close relationship with Asian populations,especially with B1-SEAS,B2-SASI and B3-AFRI,but B-KORP and B-JPAN had formed independent geneic basis.The A-NCHN had part similar genetic basis with A1-RUFE and A2-SSWE,and had close relationship with C-NNAM.The C-NNAM,C-SNAM and C1-CSAM populations clustered one group,of which C-SNAM and C1-CSAM had a closer genetic relationship.In this study,using SNPLDB of the whole genome demonstrated that the soybean disseminated from the original center in China through four paths to Northeast China further north to Russia Far East and southern Sweden,to Korea Peninsula and Japan islands,to Southeast Asia,South Asia,further to Africa,and to North America then to South America.