Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Abstract

Key message The major soy protein QTL, cqProt-003, was analysed for haplotype diversity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Abstract Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait-associated region within a 173 kb linkage block was identified, and variants in the region were characterized, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the second exon of gene Glyma.20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304 bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximize protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterization and modification.

Natural allelic variation of GmST05 controlling seed size and quality in soybean

“…To pyramid elite alleles in molecular breeding, the identification of functional genes with natural allelic variations is essential (Tian et al., 2021). Several seed size and quality regulatory genes with natural allelic variations in the soybean germplasm were cloned, such as GmPP2C‐1 (Lu et al., 2017), GmOLEO1 (Zhang et al., 2019), GmSWEET10a and GmSWEET10b (Miao et al., 2020; Wang et al., 2020; Zhang et al., 2020a, 2020b), GmST1 (Li et al., 2022) and cqSeed protein ‐ 003 (Fliege et al., 2022; Marsh et al., 2022). Moreover, GmSWEET10a and GmSWEET10b were also found to have an effect on oil content and protein content simultaneously (Wang et al., 2020).…”

Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization

“…High-throughput SNP markers were identified and validated for semi-dwarf gene sd1 ( Angira et al, 2019 ), Cercospora disease locus CRSP2.1 ( Addison et al, 2021 ), and an aroma gene BADH2 ( Addison et al, 2020 ) of rice using haplotype characterization approach in the recent studies. Similar haplotype analysis approaches were reported in other crops ( Maldonado et al, 2019 ; Brinton et al, 2020 ; Bruce et al, 2020 ; Marsh et al, 2022 ) and proven to be vital in understanding the trait genetic architecture in a particular germplasm. We developed KASP (Kompetitive allele specific polymerase) SNP markers using the haplotype characterization approach.…”

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

“…A comprehensive association and linkage analysis surveyed 985 soybean accessions, including wild species, landraces, and old and modern cultivars, to capture haplotypic variation in the high SPC locus cqProt-003 on chromosome 20 [ 200 ]. The study uncovered significant trait-associated genomic regions within a 173 kb linkage block containing three causal candidate genes: Glyma.20G084500 , Glyma.20G085250 , and Glyma.20G085100 [ 200 ]. Of these, Glyma.20G085100 (containing a 304 bp deletion and trinucleotide insertions) was tightly linked with the high protein content phenotype [ 200 ].…”

“…The study uncovered significant trait-associated genomic regions within a 173 kb linkage block containing three causal candidate genes: Glyma.20G084500 , Glyma.20G085250 , and Glyma.20G085100 [ 200 ]. Of these, Glyma.20G085100 (containing a 304 bp deletion and trinucleotide insertions) was tightly linked with the high protein content phenotype [ 200 ].…”