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QTL architecture of vine growth habit and gibberellin oxidase gene diversity in wild soybean (Glycine soja).

ABSTRACT: Vine growth habit (VGH) is a beneficial phenotype in many wild plants, and is considered an important domesticated-related trait in soybean. However, its genetic basis remains largely unclear. Hence, in the present study we used an integrated strategy combining linkage mapping and population genome diversity analyses to reveal the genetics of VGH in soybean. In this regard, two recombinant inbred line (RIL) populations derived by crossing a common wild soybean genotype (PI342618B) with two cultivated lines viz., NN 86-4 and NN 493-1 were used to map quantitative trait loci (QTL) for VGH. Here, we identified seven and five QTLs at flowering stage (R1) and maturity stage (R8), respectively, and among them qVGH-18-1, qVGH-18-2, qVGH-19-3, qVGH-19-4 were identified as major loci (R² > 10% and detection time ≥2). However, qVGH-18-2 was considered as a main QTL for VGH being consistently identified in both RIL populations as well as all growth stages and cropping years. Out of all the annotated genes within qVGH-18-2, Glyma18g06870 was identified as the candidate gene and named as VGH1, which was a gibberellin oxidase (GAox) belongs to 2-oxoglutarate-dependent dioxygenase (2- ODD). Interestingly, there was one member of 2-ODD/GAox in qVGH-18-1 and qVGH-19-4 named as VGH2 and VGH3, respectively. Moreover, from sequencing data analysis VGH1 and three other GAox genes were found significantly divergent between vine and erect soybean with F_ST value larger than 0.25. Hence, GAox was assumed to play a major role in governing inheritance of VGH in soybean. Therefore, elucidating the genetic mechanism of GAox is very useful for exploring VGH and other stem traits, as well as genetic improvement of plant type in soybean.

SUBMITTER: Wang R

PROVIDER: S-EPMC6517428 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Background and aimsWild soybean (Glycine soja), a native species of East Asia, is the closest wild relative of the cultivated soybean (G. max) and supplies valuable genetic resources for cultivar breeding. Analyses of the genetic variation and population structure of wild soybean are fundamental for effective conservation studies and utilization of this valuable genetic resource.MethodsIn this study, 40 wild soybean populations from China were genotyped with 20 microsatellites to investigate the natural population structure and genetic diversity. These results were integrated with previous microsatellite analyses for 231 representative individuals from East Asia to investigate the genetic relationships of wild soybeans from China.Key resultsAnalysis of molecular variance (AMOVA) revealed that 43·92 % of the molecular variance occurred within populations, although relatively low genetic diversity was detected for natural wild soybean populations. Most of the populations exhibited significant effects of a genetic bottleneck. Principal co-ordinate analysis, construction of a Neighbor-Joining tree and Bayesian clustering indicated two main genotypic clusters of wild soybean from China. The wild soybean populations, which are distributed in north-east and south China, separated by the Huang-Huai Valley, displayed similar genotypes, whereas those populations from the Huang-Huai Valley were different.ConclusionsThe previously unknown population structure of the natural populations of wild soybean distributed throughout China was determined. Two evolutionarily significant units were defined and further analysed by combining genetic diversity and structure analyses from Chinese populations with representative samples from Eastern Asia. The study suggests that during the glacial period there may have been an expansion route between south-east and north-east China, via the temperate forests in the East China Sea Land Bridge, which resulted in similar genotypes of wild soybean populations from these regions. Genetic diversity and bottleneck analysis supports that both extensive collection of germplasm resources and habitat management strategies should be undertaken for effective conservation studies of these important wild soybean resources.

Dataset Information

QTL architecture of vine growth habit and gibberellin oxidase gene diversity in wild soybean (Glycine soja).

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