Genetic Background Analysis and Elite Genes Identification in Soybean Cultivar Suinong 14
|School||Agricultural University of Hebei|
|Course||Crop Genetics and Breeding|
|Keywords||Soybean Suinong 14 Pedigree analysis SSR Genetic relationship in silico mpping QTL Linkage disequilibrium|
Suinong14 was one of the largest-scale grown soybean (Glycine max L.) variety and the typical elite cultivar in China. Tracing its breeding pedigree, it had been found that Suinong14 was derived from five generations of recombination between 17 genotypes which included 5 well-known domestic cultivars and 2 oversea ones. Molecular database and phenotype database on Suinong14 pedigree obtained from different planting areas have been constructed. With in silico mapping method, the QTLs related to agronomic traits were detected in the pedigree of Suinong 14. Trancing of gene transmission in the pedigree elucidates the heredity pattern of exotic genes in typical elite cultivars and explores the utilization of exotic germplasm in soybean breeding program. Some economic traits used to present in a complex inheritance pattern. Association study of these complex traits based on linkage disequilibrium (LD) originally used in human genetics would help to reveal their genetic pattern and offer useful information in soybean breeding.1 Construction of soybean Molecular datebase. Based on the public integreted map, a total of 550 SSR markers distributed on 20 linkage groups were chosen and analyzed, of which 477 markers performed polymorphic among 14 inbreeding lines in the pedigree of Suinong14. The Percentage of polymorphic locus was 86.72% and the percent of the locus whose PIC was over 70% was 10.18%.2 Construction of soybean agronomic traits datebase. 50 agronomic traits were chosen and analyzed. According to nature of every trait, the 50 agricultural traits were adivided into 6 groups, Growth traits, Yield traits, Quality traits, Resistance traits, Nodule traits and salt tolerance traits. PH, PHB and L of Growth traits decreased with the generation, Y and SW of Suinong14 and Hefeng25 were significantly improved compared with cultivars developed earlier. There were no significant difference in Resistance traits and Quality traits between different generations.3 Analysis of Genetic Relationship among Parents of Elite Soybean Cultivars Suinong14 Pedigree Revealed by SSR Markers. 550 SSR loci, distributed on 20 linkage groups were analyzed to explain evolvement and genetic relationship of Suinong 14 and its pedigree. Three methods, including similarity coefficient (SC), genetic contribution (GC) and coefficient (Neighbour-jioning method), were used to reveale genetic relationship in Suinong14 pedigree parents. The accessions clustered result were different because of the different of parental original and mating types. The characteristics of the times and mating types leaded to diversity of genetic structure of Suinong 14 pedigree. GC should be the index in a study of the genetic relationship with known pedigree information, SC should be the index in a study of the genetic relationship with unknown pedigree information.4. Genetic contribution of foreign germplasm to elite Chinese soybean cultivars revealed by SSR markers. SSR analysis, combined with pedigree analysis, was used to trace the genetic constitutes of Suinong 14 and Hefeng 25, so as to clarify the contribution of foreign germplasm to those elite cultivars, and to provide instruction for further utilization of foreign germplasm effectively in Chinese soybean breeding. SSR clustering results indicated that the genetic base of elite Chinese soybean cultivars, including Suinong 14 and Hefeng 25, was broaden due to the introduction of Amsoy from America and Shishengchangye from Japan during soybean genetic improvment. Among the special alleles of foreign parents, 12 special loci in Amsoy were transferred to Suinong 14, and 14 loci from Shishengchangye to Suinong 14. Some SSR loci had been proved to be correlated with phenotypes, indicating that the two foreign parents might have important contribution in developing Suinong14 and Hefeng 25.5. A total of 477 SSR polymorphic loci consisted of 113764bps had been identified, LD was significant at a comparison-wise 0.01 level in nearly 0.149%o of SSR marker pairs when all cultivars were included. According to linkage distance of SSR loci, all tested loci could be evaluated as tightly linked (<1.5cM), loosely linked(<1.5cM within one LG) and unlinked loci. The number of SSR loci of each LD type was one, three and 13, respectively. Seven of 116 specific SSR loci shared by Suinong14 and Hefeng25 showed LD. Association analysis of 6 SSR loci with LD and agronomic traits showed that significant correlation could be observed between two pair of LD loci and agronomic traits (p<0.01). which indicated the existence of LD in genes related to agronomic traits.6 We extended in silico mapping for single trait to mapping peiotropic QTL for multiple traits by defining new statistic to measure the correlation between multiple traits and the markers. Data included phenotypes of 32 agronomic traits extracted from Northern Spring soybean ecotypes area and genotyped 477 polymorphic markers on public integrated genetic map, on 14 inbreeding lines in the pedigree of Suinong14. With in silico mapping, a total of 141 markers distributing on 18 linkage groups were identified as QTL, no QTL are found for SII, N3SP, K. The mean of QTL was 4.86. Tracing the transmission of functional genes in the pedigree, it was found that 15 genes were capable to explain the genetic mechanism for the contribution of exotic germplasm to soybean cultivars in the improvement of the performance and quality.7 Gene discovery and transmission of functional genes in the pedigree of an elite soybean cultivar Suinong 14. In this study, we performed in silico mapping for single trait to analyze data from multiple environments by calculating inter-correlations and to mapping peiotropic QTL for multiple traits by defining new statistic to measure the correlation between multiple traits and the marker. Data include phenotypes of 8 agronomic traits obtained from 6 different ecological environments and years, and genotyped 477 polymorphic markers on public integrated genetic map, on 14 inbreeding lines in the pedigree of Suinong14. With in silico mapping, a total of 49 markers distributing on 14 linkage groups were detected separately as QTL responsible for 8 agronomic traits and 10 QTL were precisely identified as pleiotrpic ones. Tracing the transmission of functional genes in the pedigree found that some genes explain the genetic mechanism for the contribution of exotic germplasm and domestic founders in the improvement of the performance and quality of soybean cultivars.8 In silico mapping QTL for multiple traits in the pedigree of soybean cultivars. In silico mapping for single trait is performed to analyze many agronomic traits in the pedigree of soybean. Twenty six agronomic traits are measured and 477 polymorphic markers chosen on public genetic map are genotyped on 14 inbreeding lines in the pedigree of Suinong14. We determined 6 principal components from 26 agronomic traits using the principal component analysis and constructed 6 "super traits" by the multiplication of the vector of the standardized original traits by the eigenvectors corresponding to the principle components. With in silico mapping, a total of 24 markers distributing on 13 linkage groups are detected separately as quantitative trait loci (QTL) responsible for 6 "super traits", of which 14 QTL performed pleiotropy. Tracing the transmission of functional genes in the pedigree found that some genes are capable to explain the genetic mechanism for the contribution of exotic germplasm and domestic founders in the improvement of the performance and quality of soybean cultivars.