Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. 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. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers. 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). The pairwise F st comparison revealed a great degree of divergence ( F st > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest ( F st > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.
Estimation of genetic diversity in rapeseed is important for sustainable breeding program to provide an option for the development of new breeding lines. The objective of this study was to elucidate the patterns of genetic diversity within and among different structural groups, and measure the extent of linkage disequilibrium (LD) of 383 globally distributed rapeseed germplasm using 8,502 single nucleotide polymorphism (SNP) markers. We divided the germplasm collection into five subpopulations (P1 to P5) according to geographic and growth habit-related patterns. All subpopulations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.24) between most of the combinations. The rutabaga type showed highest divergence with spring and winter types. Higher divergence was also found between winter and spring types. Admixture model based structure analysis, principal component and neighbor-joining tree analysis placed all subpopulations into three distinct clusters. Admixed genotype constituted 29.24% of total genotypes, while remaining 70.76% belongs to identified clusters. Overall, mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 45 kb distance for whole genome. The LD decay was slower in C genome (< 93 kb); relative to the A genome (< 21 kb) which was confirmed by availability of larger haplotype blocks in C genome than A genome. The findings regarding LD pattern and population structure will help to utilize the collection as an important resource for association mapping efforts to identify genes useful in crop improvement as well as for selection of parents for hybrid breeding.
An experiment was conducted at the experimental farm of the Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh with fifteen maize (Zea mays L.) genotypes to assess the genetic variability, characters association and divergence among the genotypes for yield and yield attributing traits. The experiment was conducted during November 2015 to May 2016, following Randomized Complete Block Design (RCBD) with three replicates in two adjacent environments to discern the performance of the genotypes in interacting environments. No significant variation was observed for environments, which was perhaps due to their close proximity. The genotypes differed significantly for most of the studied traits. The phenotypic co-efficient of variation (PCV) was higher than genotypic co-efficient of variation (GCV) for all the evaluated traits. High heritability along with high genetic advance was observed for 1000 seed weight, seed numbers ear-1 and yield plant-1. Yield plant-1 was significantly associated with plant height, ear length, ear girth, husk girth, kernel length, 1000 seed weight, kernel numbers row-1, seed numbers ear-1 in positive direction and negatively associated with days to anthesis and moisture loss (%). Path co-efficient analysis revealed that the maximum positive direct contribution towards yield was through 1000 seed weight, seed number ear-1 and kernel length whereas plant height, ear girth, ear length, kernel numbers row-1 showed negative direct contribution towards yield due to negative indirect effects of several parameters. Cluster analysis exhibited five distinct groups. Considering mean values Cluster II provided the best result in terms of yield and earliness, followed by Cluster IV and V. The results of principal component analysis (PCA) revealed that first five components accounted for 82.7% of total variation. The findings indicate the presence of ample genetic diversity among maize genotypes which can be exploited in future breeding program for better utilization of maize germplasm.The Agriculturists 2017; 15(2) 101-114
An experiment was carried out to assess the genetic diversity of advanced rice (Oryza sativa L.) breeding lines using three SSR markers viz., RM147, RM167 and RM215. Thirty T-aman advanced breeding lines at F 9 generation along with 4 check varieties were assessed. All three primers showed polymorphism. A total of 29 alleles were detected among the rice genotypes with an average of 9.67 alleles per locus. Polymorphism information content (PIC) ranged from 0.47 to 0.88 with an average of 0.71. A dendrogram was constructed based on total microsatellite polymorphism and 34 genotypes were grouped into four major clusters at 0.36 similarity co-efficient differentiating the early maturing genotypes from the late maturing types. The information about the genetic diversity might be utilized in future breeding programs for developing rice varieties with much shorter growth duration. The results also suggested that microsatellite markers which are linked to genes or QTLs responsible for growth duration properties are suitable tools for marker assisted selection (MAS) to select the rice genotypes of shorter growth duration.
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