Construction of Soybean Mutant Diversity Pool (MDP) Lines and an Analysis of Their Genetic Relationships and Associations Using TRAP Markers

Abstract

Mutation breeding is useful for improving agronomic characteristics of various crops. In this study, we conducted a genetic diversity and association analysis of soybean mutants to assess elite mutant lines. On the basis of phenotypic traits, we chose 208 soybean mutants as a mutant diversity pool (MDP). We then investigated the genetic diversity and inter-relationships of these MDP lines using target region amplification polymorphism (TRAP) markers. Among the different TRAP primer combinations, polymorphism levels and polymorphism information content (PIC) values averaged 59.71% and 0.15, respectively. Dendrogram and population structure analyses divided the MDP lines into four major groups. According to an analysis of molecular variance (AMOVA), the percentage of inter-population variation among mutants was 11.320 (20.6%), whereas mutant intra-population variation ranged from 0.231 (0.4%) to 14.324 (26.1%). Overall, intra-population genetic similarity was higher than that of inter-populations. In an analysis of the association between TRAP markers and agronomic traits using three different statistical approaches based on the single factor analysis (SFA), the Q general linear model (GLM), and the mixed linear model (Q+K MLM), we detected six significant marker–trait associations involving five phenotypic traits. Our results suggest that the MDP has great potential for soybean genetic resources and that TRAP markers are useful for the selection of soybean mutants for soybean mutation breeding.

Detecting Genetic Mobility Using a Transposon-Based Marker System in Gamma-Ray Irradiated Soybean Mutants

“…The AMOVA revealed that the major proportion of the genetic diversity was from within-population variation using the three different markers ( Table 3). This indicates that molecular variation induced by TEs in irradiated mutant populations is attributed to differences within individual populations and corresponds with results of the AMOVA analysis using the TRAP marker system on MDP lines [39]. The percentage of estimated among-population variation as assessed by the PONG marker (29%) was greater than those assessed by M-t (20%) and M-s (18%), indicating that genetic diversity was induced in the loci amplified by the PONG primers.…”

“…The PIC value of the TE-TRAP in sorghum is 0.172. When comparing the results of the TE-TRAP with the conventional TRAP marker system, using MDP mutant lines, which were constructed by Kim et al [ 39 ], the latter obtained an average 59% polymorphism level and an average of 34.44 fragments. In the present study, we observed a 58% polymorphism level and an average of 33.92 fragments.…”

“…Overall, only the clustering pattern of the PONG marker separated the lines into three major groups, whereas those of the M-t and M-s markers did not show clear distinctions between mutants and original cultivars. In a previous genetic diversity analysis of an MDP mutant population using the TRAP marker system, MDP lines clustered into four major groups that largely corresponded to their wild-type cultivars and pedigree data [ 39 ]. These different patterns revealed by TRAP and TE-TRAP, markers indicate that the TE-TRAP technique using TIR consensus sequences of M-t and M-s could detect a great variability in the irradiated soybean mutant population.…”

“…In the previous study by Kim et al 2020, seeds of eight soybean cultivars (as mentioned in the material and methods section) were irradiated and mutant populations were constructed through 12 generations to reach 208 genetically fixed mutant lines (201 mutant associated with their original cultivars). Their usefulness for mutation breeding was determined by the TRAP marker.…”

Differences in Seed Weight, Amino Acid, Fatty Acid, Oil, and Squalene Content in γ-Irradiation-Developed and Commercial Amaranth Varieties (Amaranthus spp.)

“…One of the tools for improving seed traits of important crops is mutation breeding, which has been successfully utilized for variety development and generating polygenic variability [ 22 , 23 ]. Our previous research focused on the improvement of quality and quantity traits in amaranth through γ-radiation [ 24 , 25 , 26 , 27 , 28 , 29 ].…”