- Genetic diversity analysis of a flax ( Linum usitatissimum L.) global collection. - To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. - Results: All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. - The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. - All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34).. - 0.25) between most of the combinations.. - 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r respectively and p <. - As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. - Full list of author information is available at the end of the article. - Different molecular marker techniques such as RAPD, AFLP, ISSR, SSR and IRAP has been used to assess the genetic diversity of flax germplasm [16–22]. - relatedness among individuals of the germplasm collection is desirable which leads to rapid LD decay and increases the power of marker detection [5].. - The objectives were (1) to explore genetic diversity and differentiation among the genotypes, (2) to investigate the potential of the collection as parental resource and (3) to assess the suitability of the collection for marker-assisted breeding.. - Sub-population wise marker diversity parameters are presented in supple- mentary Table S3.. - The whole collection was divided into seven sub- populations based on structure analysis using the Delta K approach (Fig. - The NDSU released and other Ameri- can genotypes were grouped under sub-population-5 (P5) whereas European (Hungary), Turkish and Asian (India &. - Pakistan) genotypes were under sub-population-1 (P1), sub-population-7 (P7) and sub-population-6 (P6), respect- ively. - Sub-population-2 (P2), sub-population-3 (P3) and sub-population-4 (P4) were composed of a mixture of genotypes of different origins (Fig. - All of the sub- populations consist of oil type genotypes except sub- population-2, which consists of mostly fiber type genotypes.. - Based on individual Q matrix, the proportion of pure (non- hybrid) and admixed (containing markers assigned to more than one sub-population) genotypes in each sub-population was calculated.. - The proportion of pure accessions in each sub- population ranged from 18 to 81% at a 0.7 cutoff value.. - We also performed principal coordinate analysis (PCoA) to show the genetic similar- ity among sub-populations. - The first two axes explained 18.49% of the total observed variation (Table S4). - The PCoA revealed that NDSU released and other American genotypes (P5), Turkish (P7) and Asian (P6) genotypes were well clustered and separated from rest of the geno- types (Fig. - In all sub-populations the percentage of polymorphic loci was greater than 60%. - The diversity (H) of the seven sub-populations ranged from 0.12 (P6) to 0.28 (P3) with an average of 0.22. - The mean pairwise relatedness (r) among individuals within sub-population was signifi- cant (p <. - The AMOVA revealed that variance among sub- populations covered 28% of total variation whereas the remaining 72% of total variation accounted for variance among individuals within sub-populations (Table 6) with a F st and Nm value of 0.28 and 0.64, respectively. - All pairwise F st comparisons between sub-populations were significant (p <. - Most of the combinations showed a great degree of di- vergence (F st >. - Approximately 80% of the pairwise IBS coefficients ranged from 1.12 to 1.50 (Table S8, Figure S5).. - Mantel test was performed to show the correlation between geographic and genetic distance among individ- uals within each sub-population (Table 8).. - 0.05) whereas it was not significant in other sub-populations (Figure S1).. - The linkage disequilibrium (LD) pattern was investigated across the entire collection, each sub-population and chromosome-wise. - A similar result was also found in Table 3 Number of pure and admixed individuals per sub-population. - Sub- populations. - Table 4 Sub-population wise diversity parameters. - Sub-populations Polymorphic loci. - In our study, based on the identified SNP markers, the different sub-populations exhibited moderate diversity (average H = 0.22), which is in line with our expectation as flax possesses an autogamous reproduction system. - The great homogeneity of the diversity indices of different sub- populations in the studied collection suggests that the spe- cies is durable enough to avoid the natural loss of genetic variability by drift [46]. - We also calculated the Tajima’s D value to indicate the abundance or scarcity of rare alleles in different sub-population and selection mechanism behind sub-populations [47]. - Sub-population P6 displayed a nega- tive Tajima ’ s D value indicating presence of more rare al- leles in this group or recent expansion of the group as most of the individuals of this sub-population are cultivars grown in India and Pakistan. - sub-populations showed positive Tajima’s D values indicat- ing less rare alleles in those groups or recent population contraction. - All seven sub-populations showed significant level of related- ness (r). - The negative correlation between diversity indices (H and I) and relatedness indicates that inbreeding and genetic drift play a significant role in reducing genetic vari- ability in the studied population which results in increased differentiation among sub-populations. - To enrich the paren- tal stock of the on-going program, the genetic diversity of 350 flax germplasms comprising NDSU released varieties and advanced breeding lines were analyzed in this study. - seven sub-populations based on structure, PCoA and NJ-tree analysis though cluster number was less and more [52] than ours finding in pre- vious studies. - In the studied collection of 350 lines, we identified limited gene flow as one of the determi- nants of genetic differentiation as Nm value was less than one [54]. - It was also supported by the relatively large separation of P6 (Indian and Pakistani genotypes) and P7 (Turkish genotypes) from other sub-populations as extensive geographic distance hinders the gene flow.. - Sub-population P1, P2 and P3 contained European Table 5 Mean pairwise relatedness (r) values within sub-population. - Sub-populations P1 P2 P3 P4 P5 P6 P7. - Among sub-populations Fst: 0.28 0.64. - The presence of fiber type genotypes in P2 is likely one of the reasons for separation of P2 with other European groups P1 and P3. - As per our expectation, all NDSU released var- ieties and advanced breeding lines, Canadian genotypes were grouped under the same sub-population (P5) as advanced breeding lines shared ancestors and historical germplasm exchanged occurred between USA and Canada [16]. - The re- sults of the mantel test indicated non-significant correlation between genetic and geographic distances of the studied populations. - Pairwise F st is a good indication of the degree of divergence among populations. - To develop high yielding and high oil content varieties we will choose breeding parents from divergent sub- population pairs such as P5 and P6, P7 and P6 as pair- wise F st between them is highest (F st >. - 0.50) These sub- populations also contain different released varieties. - Within sub-populations, crossing among geno- types will also be useful as AMOVA reveals variance among individuals within sub-population covered a lar- ger portion of total variation than variance among sub- population. - All sub- populations contained both pure (non-hybrid) as well as admixed genotypes. - In our study, most of the genotypes had weak Table 7 Genetic differentiation among sub-populations. - Sub-population pairwise Fst. - Sub-populations SSx a SSy b SPxy Rxy c P value. - Most of the economically important traits are quanti- tative in nature. - We found that the overall LD of the entire collection was 0.03 and LD decay was not observed within short distance for the entire collection as well as each sub-population. - This is because of the autogamous (self-pollination) mating mode of flax [65] and LD declines more slowly in self- pollinated crops where recombination is less effective than in cross-pollinating species [24, 66]. - The identified SNPs provide a clear picture of genetic structure, diversity, relatedness and linkage disequilib- rium of the studied population which leads to higher precision in parent selection for a need-based future breeding program. - Sequencing of the library was done at Table 9 Linkage disequilibrium in the studied collection. - Sub-populations Mean linked LD Mean unlinked LD Mean LD Loci pairs in linked LD. - a Graphical representation of Delta K for different number of sub-population determined by Evanno ’ s method. - Colors represent sub-populations identified at K = 7 in Fig. - 4 Within sub-population pairwise mean relatedness ( r ) for flax collections. - The average pair- wise between sub-population Fst and relatedness (r) values. - GenAlex v6.5 was also used to estimate percentage of polymorphic loci, number of effective alleles, Shannon’s information index, expected heterozygosity and unbiased expected heterozy- gosity of each marker and sub-population. - 5 Linkage disequilibrium (LD) differences and decay pattern among sub-populations. - We performed a mantel test [85] within each sub- population based on genetic distance and geographic dis- tance in GenAlex v6.5 as each sub-population was com- posed of genotypes, collected from different locations.. - List of the genotypes analyzed in this study.. - Sub-population wise marker diversity parameters.. - Chromosomewise LD decay rate (Kb) within each sub-population.. - Mantel test output for whole collection and each sub-populations.. - All authors participated in revising and editing the manuscript and approved the final version of the manuscript.. - Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus. - Preliminary study of genetic diversity in Swedish flax (Linum usitatissimum). - Genetic diversity among north American spring wheat cultivars: III. - Inter simple sequence repeat analysis of genetic diversity and relationship in four egyptian flaxseed genotypes. - Agro- morphological traits and microsatellite markers based genetic diversity in Indian genotypes of linseed ( Linum usitatissimum L. - Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs. - Genetic diversity and population structure of a Camelina sativa spring panel. - De novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways. - Genetic diversity and population structure of F3: 6 Nebraska winter wheat genotypes using genotyping-by-sequencing. - Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. - Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers. - Assessment of genetic diversity among low-nitrogen-tolerant early generation maize inbred lines using SNP markers. - Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. - Assessment of genetic diversity in Salvadora persica L. - Genetic diversity analysis reveals genetic differentiation and strong population structure in calotropis plants.. - Genetic diversity of cultivated flax (Linum usitatissimum L.) and its wild progenitor pale flax (Linum bienne mill.) as revealed by ISSR markers. - Genetic diversity and genome size variability in Linum austriacum (Lineaceae) populations. - Application of association mapping to understanding the genetic diversity of plant germplasm resources. - GenAlEx 6.5: genetic analysis in excel. - A retrospective assessment of the accuracy of the paternity inference program CERVUS
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt