Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean

- Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean.
- This study reports the results of a genome-wide association study and evaluation of epistatic interactions for four agronomic and seed-related traits in soybean..
- For SW, candidate genes include an ortholog of the AP2 gene, which in other species is involved in maintaining seed size, embryo size, seed weight and seed yield.
- Improvement of seed yield is a major objective in soybean breeding.
- including seed weight (SW), internode number (IN) and plant height (PH).
- Internode number and plant height affect seed yield via their impact on important traits including lodging and adaptability in soybean [2]..
- Many linkage mapping studies in soybean have been curated and compiled at SoyBase (https://www.soybase..
- Plant height and internode number have significant correlations with flowering and maturity traits, which are important agronomic traits associated with adapt- ability and productivity in soybean [8].
- Chang et al.
- Similarly, Fang et al.
- A linkage mapping study by Sun et al.
- Similarly, Chang et al.
- [3] reported that several loci of IN and PH were captured at different growth stages in soybean.
- Several other studies that associated develop- mental quantitative traits with genetic markers have been reported in soybean .
- “genome wide epistatic study” (GWES) approach to comple- ment the more widely-used GWAS analysis and provide a fuller understanding of the genetic architecture of complex traits.
- In particular, GWES helps reveal the genetic basis of IN, PH, SW and SYP in soybean..
- Internode number (count Plant height (cm seed weight (gm Seed yield per plant (gm SEM = Standard Error of the Mean.
- A candidate gene Glyma.01 g022500 on.
- (NAM) protein and is homologous to AT3G49530, which is involved in formation of the SAM [24–26]..
- flowering time and development of the inflorescence meristem (Fig.
- Genome wide epistatic interaction.
- Previous studies have showed the Dt1 gene to regulate many agronomic traits including plant height and flowering in soybean [8, 42–44].
- The presence of the dominant alleles (Dt1/Dt1) sup- presses the transition to a reproductive inflorescence [45]..
- Through numerous studies, more than 200 QTLs have been identified for SW in soybean (https://soybase.org.
- Glyma.19 g151900 is annotated as a member of the AHP (Arabidopsis histidine phospho- transfer) protein family (Additional file 3).
- Simi- larly, the ahp1,2,3,4,5 “penta” histidine phosphotransfer protein mutation in Arabidopsis resulted in larger seeds and embryos [50], suggesting that the homologous AHP Glyma.19 g151900 could also be involved in a cytokinin- mediated seed weight regulating pathway in soybean [6]..
- Further studies will be needed to test the functions and effects of these genes in soybean..
- For plant height, Gly- ma.02G245600, encodes a gibberellin-regulated family protein, with homologs known to have key function in plant development, while Glyma.19 g194300 encodes a phosphatidylethanolamine binding protein, and has been shown to play key role in regulating of flowering time in soybean and other plants [4, 8, 44].
- The internode number of the main stem was taken as the average of three such measurements.
- The “SoySNP50k” SNP dataset for the panel was de- scribed by Song et al.
- The average LD decay graph was plotted using an R script, which was computed according to Remington et al.
- Genome-wide association (GWA) and genome wide epistatic (GWE) interaction analysis.
- 0.001, determined by 1000 permutations, was used as the significance threshold of SNPs-trait associations as described in Zhang et al.
- Frequency distribution of observation of internode number, plant height, seed weight, and seed yield per plant in soybean.
- GWA: genome-wide association;.
- GWAS: genome-wide association study.
- GWE: genome-wide epistatis;.
- GWES: genome-wide epistatic study.
- SW: seed weight;.
- All authors contributed to the preparation and development of the manuscript.
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