QTL mapping and whole-genome sequencing analysis for novel genetic resources associated with sucrose content in soybean [Glycine max (L.) Merr.]

Dongho Lee, Tri D. Vuong, James G. Shannon, Qijian Song, Feng Lin & Henry T. Nguyen

Theoretical and Applied Genetics; February 3 2025; vol.138; article 43

Key message

A major QTL for sucrose content was mapped on chromosome 8 in PI 506593. The novel genetic variants and candidate genes were further identified within the major QTL.

Abstract

Sucrose in soybean [Glycine max (L.) Merr.] contribute to animal feed efficiency and natural sweetness of soy products. Thus, identifying novel genetic resources, such as quantitative trait loci (QTL), associated with sucrose content in soybean is essential for enhancing seed values. In this study, two recombinant inbred line populations derived from the same high sucrose donor parent, PI 506593, were used to identify significant QTLs. A total of 11 sucrose-related regions on chromosomes (Chrs.) 4, 5, 6, 8, 10, and 13 were identified using QTL analysis. Among them, four QTLs (qSUC_08.1, qSUC_08.2, qSUC_08.3, and qSUC_08.4) were clustered in the interval of 40,597,410–42,861,364 bp on Chr. 8, which was considered major QTL region. A desirable marker at 41,834,095 bp was tested in two populations, showing that two phenotypically extreme groups were efficiently differentiated. We further identified 44 and 54 candidate genes with non-synonymous mutations in the major QTL region based on the annotations of Wm82.a2.v1 and Wm82.a5.v1 assemblies, respectively. Among 54 candidate genes from Wm82.a5.v1, Protein Variation Effect Analyzer (PROVEAN) revealed that 18 genes contained 34 variants that had deleterious impacts on biological functions. RNA-seq analysis highlighted five candidate genes that were highly expressed in pod and seed tissues during reproductive stages and other plant parts. A gene, Gm_Wm82_23219 (Glyma.08G293800, Wm82.a2.v1) encoding proline-rich protein 4-like, was highlighted in both PROVEAN and RNA-seq analyses. Novel findings in this study will be valuable genetic resources in soybean breeding programs that aim to improve efficiency in animal feed and human food.

See https://link.springer.com/article/10.1007/s00122-024-04808-5

Figure 3: The candidate gene expression levels within the major QTL region on Chr. 8 using publicly available gene expression datasets from a Severin et al. (2010) and b Almeida-Silva et al. (2023), respectively. The read counts for a and b were normalized using Reads Per Kilobase of transcript per Million mapped reads (RPKM) and Transcripts Per Million (TPM) method, respectively.