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 ( R 2 > 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.

Increased copy number of gibberellin 2‐oxidase 8 genes reduced trailing growth and shoot length during soybean domestication

“…A mutation in the soybean gene GmLHY led to lower expression of GA pathway genes and reduced plant heights in young soybean plants (Cheng et al, 2019). A major quantitative trait locus (QTL) associating with the vine growth habit was found on chromosome 18 and a GA oxidase gene (VGH1) was proposed to be a candidate causal gene, although functional tests have yet to be conducted (Wang et al, 2019). A dwarf phenotype was also found in other legume crops (Hughes et al, 2020;Massawe et al, 2005;Saxena, 2008), although the genetic basis for this transition during domestication was largely unknown.…”

“…A major quantitative trait locus (QTL) associating with the vine growth habit was found on chromosome 18 and a GA oxidase gene ( VGH1 ) was proposed to be a candidate causal gene, although functional tests have yet to be conducted (Wang et al. , 2019). A dwarf phenotype was also found in other legume crops (Hughes et al.…”

Identification of a Locus Controlling Compound Raceme Inflorescence in Mungbean [Vigna radiata (L.) R. Wilczek]

“…Several traits have been selected from wild and exotic species to produce modern cultivated varieties with a suitable plant architecture and high crop productivity. Such traits include vine to erect growth habit (Wang et al, 2019 ), stem termination (Tian et al, 2010 ), and pod shattering (Dong et al, 2014 ). In this study, we identified IT208075, a simple raceme genotype having a single primary inflorescence.…”

Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean

“…However, mutants of GA2ox responses opposite of GA20ox and GA3ox , resulting long and slender stem in pea ( Martin et al, 1999 ) and switchgrass ( Wuddineh et al, 2015 ). In soybean, Glyma18g06870 ( GAox ), 2-oxoglutarate-dependent dioxygenase is identified as a candidate gene responsible for vine growth habit (VGH) ( Wang et al, 2019 ).…”