Zongbiao Duan, Min Zhang, Zhifang Zhang, Shan Liang, Lei Fan, Xia Yang, Yaqin Yuan, Yi Pan, Guoan Zhou, Shulin Liu, Zhixi Tian

Plant Biotechnol J.; 2022 Sep; 20(9):1807-1818. doi: 10.1111/pbi.13865. Epub 2022 Jul 4.

Abstract

Seed size is one of the most important agronomic traits determining the yield of crops. Cloning the key genes controlling seed size and pyramiding their elite alleles will facilitate yield improvement. To date, few genes controlling seed size have been identified in soybean, a major crop that provides half of the plant oil and one quarter of the plant protein globally. Here, through a genome-wide association study of over 1800 soybean accessions, we determined that natural allelic variation at GmST05 (Seed Thickness 05) predominantly controlled seed thickness and size in soybean germplasm. Further analyses suggested that the two major haplotypes of GmST05 differed significantly at the transcriptional level. Transgenic experiments demonstrated that GmST05 positively regulated seed size and influenced oil and protein contents, possibly by regulating the transcription of GmSWEET10a. Population genetic diversity analysis suggested that allelic variations of GmST05 were selected during geographical differentiation but have not been fixed. In summary, natural variation in GmST05 determines transcription levels and influences seed size and quality in soybean, making it an important gene resource for soybean molecular breeding.

See https://pubmed.ncbi.nlm.nih.gov/35642379/

Figure 1

GWAS of seed thickness in the soybean germplasm. (a) Manhattan plot of GWAS results for seed thickness from 2016 and 2017 best linear unbiased prediction (BLUP) data. (b) Quantile–quantile plot of the GWAS results under a mixed linear model (MLM). (c) Local Manhattan plot (top) and linkage disequilibrium plot (bottom) for SNPs surrounding the peak on chromosome 5. The red dashed lines indicate the candidate region for the peak. The red plot indicates the nucleotide variation of GmST05. The solid lines above the plot represent the genomic locations of quantitative trait loci (QTLs) retrieved from SoyBase (https://soybase.org/). The red, green and orange lines are QTLs for seed size (yield), seed oil content and protein content, respectively. (d) A heat map for candidate genes located in the candidate region. The colour key (blue to red) represents gene expression (fragments per kilobase per million mapped reads, FPKM).