Fine mapping and cloning of the major seed protein quantitative trait loci on soybean chromosome 20

Abstract

Soybean [Glycine max (L.) Merr.] is a unique crop species because it has high levels of both protein and oil in its seed. Of the many quantitative trait loci (QTL) controlling soybean seed protein content, alleles of the cqSeed protein-003 QTL on chromosome 20 exert the greatest additive effect. The high-protein allele exists in both cultivated and wild soybean (Glycine soja Siebold & Zucc.) germplasm. Our objective was to fine map this QTL to enable positional-based cloning of its underlying causative gene(s). Fine mapping was achieved by developing and testing a series of populations in which the chromosomal region surrounding the segregating high-versus low-protein alleles was gradually narrowed, using marker-based detection of recombinant events. The resultant 77.8 kb interval was directly sequenced from a G. soja source and compared with the reference genome to identify structural and sequence polymorphisms. An insertion/deletion variant detected in Glyma.20G85100 was found to have near-perfect +/À concordance with high/low-protein allele genotypes inferred for this QTL in parents of published mapping populations. The indel structure was concordant with an evolutionarily recent insertion of a TIR transposon into the gene in the low-protein lineage. Seed protein was significantly greater in soybean expressing an RNAi hairpin downregulation element in two independent events relative to control null segregant lineages. We conclude that a transposon insertion within the CCT domain protein encoded by the Glyma.20G85100 gene accounts for the high/low seed protein alleles of the cqSeed protein-003 QTL.

Identification of Candidate Genes and Genomic Selection for Seed Protein in Soybean Breeding Pipeline

“…In addition, the QTL qtl-chr15_prot (3.30–4.71 Mb) overlapped with the qPro15-1 ( Zhang et al, 2019 ) and qtl-chr17_prot (12.80–13.81 Mb) with the protein 26-2 ( Reinprecht et al, 2006 ). The position of QTL qtl-chr20_prot (26.57–33.51 Mb) was consistent with that of the confirmed QTL cqPro-20 ( Diers et al, 1992 ; Pandurangan et al, 2012 ; Vaughn et al, 2014 ; Sonah et al, 2015 ; Warrington et al, 2015 ; Zhang Y. et al, 2018 ; Fliege et al, 2022 ). Fliege et al (2022) concluded that a transposon insertion within the CONSTANS, CO-like, and TOC1 (CCT) domain protein encoded by the Glyma.20G85100 gene accounted for the high/low seed protein alleles of the cqSeed protein-003 QTL (31.74–31.84 Mb).…”

Ensuring Global Food Security by Improving Protein Content in Major Grain Legumes Using Breeding and ‘Omics’ Tools

“…High-protein soybean lines include Danbaegkong (48.9%) [ 133 ] and Kwangankong (44.7%) [ 134 ], and TN11-5102 selected from 5601T cultivar (421 g kg −1 protein on a dry weight basis) [ 108 ]. Apart from cultivated species, soybean CWRs (e.g., Glycine soja ) are an important source of high-protein QTLs [ 135 , 136 , 137 ]. A population developed by incorporating exotic soybean germplasm exhibited significant genetic variability for SPC [ 138 ].…”

“…Of the identified QTLs, qPro-7-1 was highly stable across all tested environments. Recently, Fliege et al [ 137 ] cloned a major SPC governing QTL ( cqSeed protein-003 ) and elucidated the underlying causative candidate gene Glyma.20G85100 , encoding a CCT domain protein. Thus, efforts are needed to fine map or clone major QTLs controlling SPC in other grain legumes to delineate the underlying candidate gene(s) and their function for genomic-assisted breeding to improve SPC in grain legumes.…”

“…Of the nine candidate genes underlying these QTL regions, Glyma.20G088000 , Glyma.20G111100 , and Glyma.20 g087600 were functionally validated and identified as the most potential candidate genes controlling SPC [ 197 ]. RNAi technology—a robust functional genomic tool—offered novel insight into the regulatory role of Glyma.20g085100 harboring transposon insertion in the SPC-controlling genomic region of soybean [ 137 ]. Reduced expression of Glyma.20g085100 using RNAi enhanced the protein level in the low-protein Thorne soybean genotype [ 137 ].…”

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

“…Teng et al ( 2017 ) identified 8 SPC QTLs in 12 environments using the RIL population derived from Dongnong46 × L-100 , in which qPR-2, qPR-3, qPR-5, qPR-7 , and qPR-8 were detected simultaneously in 6, 8, 7, 6, 7 environments, respectively. The candidate gene Glyma.20g085100 underlying the major SPC QTL on chromosome 20 was mapped and cloned (Fliege et al, 2022 ). The haplotype variation at this major QTL in wild and domesticated soybean was also explored using a germplasm population consisting of 985 accessions (Marsh et al, 2022 ).…”