Transgressive Potential Prediction and Optimal Cross Design of Seed Protein Content in the Northeast China Soybean Population Based on Full Exploration of the QTL-Allele System

Abstract

Northeast China is a major soybean production region in China. A representative sample of the Northeast China soybean germplasm population (NECSGP) composed of 361 accessions was evaluated for their seed protein content (SPC) in Tieling, Northeast China. This SPC varied greatly, with a mean SPC of 40.77%, ranging from 36.60 to 46.07%, but it was lower than that of the Chinese soybean landrace population (43.10%, ranging from 37.51 to 50.46%). The SPC increased slightly from 40.32-40.97% in the old maturity groups (MG, MGIII + II + I) to 40.93-41.58% in the new MGs (MG0 + 00 + 000). The restricted two-stage multi-locus genome-wide association study (RTM-GWAS) with 15,501 SNP linkage-disequilibrium block (SNPLDB) markers identified 73 SPC quantitative trait loci (QTLs) with 273 alleles, explaining 71.70% of the phenotypic variation, wherein 28 QTLs were new ones. The evolutionary changes of QTL-allele structures from old MGs to new MGs were analyzed, and 97.79% of the alleles in new MGs were inherited from the old MGs and 2.21% were new. The small amount of new positive allele emergence and possible recombination between alleles might explain the slight SPC increase in the new MGs. The prediction of recombination potentials in the SPC of all the possible crosses indicated that the mean of SPC overall crosses was 43.29% (+2.52%) and the maximum was 50.00% (+9.23%) in the SPC, and the maximum transgressive potential was 3.93%, suggesting that SPC breeding potentials do exist in the NECSGP. A total of 120 candidate genes were annotated and functionally classified into 13 categories, indicating that SPC is a complex trait conferred by a gene network.

Keywords: Northeast China soybean germplasm population (NECSGP); QTL-allele matrix; optimal cross prediction; restricted two stage multi-locus model GWAS (RTM-GWAS); seed protein content (SPC); transgressive potential.

Figure 1

The SPC QTL-allele information of the Northeast China soybean germplasm population obtained from RTM-GWAS. (A) Manhattan plot; (B) Quantile - quantile plot; (C) The phenotypic contribution of the 61 main-effect QTLs, blue bars denote small-contribution QTL (R² < 1%), red bars represent large-contribution QTL (R² ≥ 1%); (D) The frequency distribution of allele number per locus for the 61 main-effect QTLs; (E) SPC allele effects of the 61 main-effect QTLs; (F) QTL-matrix of SPC in the NECSGP; (G) Predicted SPC of progenies in possible crosses; (H) Gene Ontology (GO) biological process annotations of the candidate genes for SPC QTLs in the NECSGP. “other” GO biological processes include snoRNA localization, localization, anatomical structure development, post-embryonic development, multicellular organism development, activation of protein kinase activity, Golgi organization, chloroplast organization, macromolecule methylation, and methylation.