Genetic Diversity And Association Analysis Of Major Agronomic Traits In Foxtail Millet[Setaria Italica(L.)P.Beauv.]of Shanxi Province

Foxtail millet [Setaria italica(L.)p.breauv.] originates in China,with the characteristics of drought resistance,poverty tolerance and short growth period.As a kind of grain & grass crop,it is widely planted in the Yellow River basin and still exists in the arid and semi-arid areas in northern China.As is an important birthplace of Chinese agricultural civilization and a major foxtail millet growing province,Shanxi mainly engages in dry farming with stretching across 6 latitudes(34°34 '--40°44').Because of an originating area between 17,000 and 24,000 years ago,Shanxi holds rich foxtail millet resources,accounting for 1/5 of the national ones.And there are many famous and excellent millet varieties with excellent genes in Shanxi.Based on the analysis of the database information of millet resources in Shanxi,the core collection of foxtail millet was constructed in this study.The genetic diversity and genetic structure were analyzed through field unified phenotype and SSR marker genotype identification,and materials with excellent allelic variation were discovered by the molecular markers associated with important traits.Simplified genome sequencing was used to find QTLs controlling major breeding traits in linkage populations.The main research results are as follows:1.The germplasm resources of Shanxi foxtail millet are rich and diverse.Local varieties of foxtail millet are mainly distributed in Datong,Xinzhou,Lvliang,Jinzhong and Changzhi by analysis of the geographical origin accounting for 75.7% of the province's resources.90% of resources are japonica.The phenotypic genetic diversity in Yuncheng and Jincheng was the largest with the genetic diversity index 1.8580 and 1.7793,respectively.They are abundant in seedling colors,spike types and grain color types,covering the basic types of foxtail millet resources in China.The genetic diversity is large and the types are rich,which is the important material basis of foxtail millet germplasm innovation.2.The core collection of Shanxi foxtail millet was constructed.The primary core collection retaining 10.57% of original germplasm was constructed by clustering random sampling of phenotypic data system.The results of representative test showed that the average difference percentage of phenotypic traits between core germplasm and original germplasm was 5.9%,and the coincidence rate of extreme difference was 87.4%.The difference of diversity index t test of 14 phenotypic traits was not significant.These result could indicate the primary core germplasm could represent the genetic diversity of original germplasm.3.Comprehensive evaluation of core germplasm were carried out.The 18 characters of Shanxi millet core resources were evaluated by principal component analysis,and the comprehensive score F was calculated after the principal component score was normalized.The average F value of the core germplasms of the millet was 0.5227.The comprehensive performance of each germplasm was compared by a quantitative value,and the better phenotypic comprehensive traits such as H160(Sanbianlian,0.6663),H174(Gouchangruangu,0.6881),H180(zhuhanchangruangu,0.75235)were screened out.4.Genetic diversity of core germplasm was analyzed.On the basis of unified identification and evaluation of phenotypic traits of core germplasm,genetic diversity of core resources was analyzed by SSR molecular marker technique.A total of 828 polymorphism bands were detected by 96 pairs of SSR primers,the average number of primers per pair was 8.625,and the number of allelic variation was between 2 and 26.The loci with frequency distribution between 0 and 0.2 accounted for 85.14% of the total loci,and most of them were small,indicating that there were great differences in loci among millet materials and rich genetic variation.5.Genetic structure of the core collection found: by using Structure 2.3.4,the millets are divided into three subpopulations.Combined with the geographical characteristics of Shanxi,it is found that the three subsets are roughly distinguished according to latitude,which are divided into three parts: northern,central and southern.With the geographical and ecotype differentiation of the millet resources from the molecular level,the two types of the spring and the summer millets exist at the same time,provided the molecular evidence for the division of the millet ecological region and the selection of the breeding parents in Shanxi.5.Phenotypic and genotypic association analysis found: linkage disequilibrium existed in collinear or non-collinear site combinations,indicating that the core resource population was conducive to association analysis and excellent allelic variation mining.The GLM method detected 23 markers associated with node number,plant height,peduncle length,panicle length,leaf length,stem diameter,panicle diameter,primary branch number per panicle,spikelet number per primary branch and protein content of 10 traits.At the same time,the increasing(decreasing)effects of different allelic variation of association markers were clarified,and excellent allelic variation and its carrier materials were found.In this study,the allelic variation of the positive potential for the protein content,b153-152,p14-240,and the typical materials,Xiaohonggu,Huanggu,were found.That for panicle length,B153-190,and the typical material,Sheergu,were found.That of the negative potential for plant height,B223-149?B223-145,and the typical materials,Wucharuangu,Xiaohuanggu,were found.These materials containing excellent allelic variation can be used in the selection of excellent parent combinations.6.QTL positioning: t GBS simplified genome sequencing was carried out in 238 RIL populations of "Yugu 1 × Red Seedling Dabaigu".A linkage map covering 4377 SNP markers was constructed.The total genetic distance was 1069 c M,the average distance was 0.24 c M and the maximum distance between adjacent markers was 12.1c M.IM-ADD algorithm(Interregion mapping)was used to map the QTL loci of 12 traits in 5 environments.189 QTL loci controlling agronomic traits were located on 9 chromosomes.The phenotypic variation rates explained by a single QTL varied from 2.3% to 11.4%.The number of QTL detected on chromosomes 6 and 9 was higher with 43 and 40,respectively.137(72.5%)of 189 QTLs could be detected in two or more environments.Among them,the QTL locis from scaffold₉-36540173 to scaffold₉-40248082 on chromosome 9 could be mapped to six traits,including heading date,node number and plant height,which were detected in more than 3 environments.