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Soybean (Glycine maxL.) is a protein and oil crop grown worldwide. Its fitness may be reduced by deleterious mutations, whose identification and purging is desirable for crop breeding. In the published whole-genome re-sequenced data of 2214 soybean accessions, including 221 wild soybean, 1132 landrace cultivars and 861 improved soybean lines, we identified 115,275 deleterious single-nucleotide polymorphisms (SNPs). Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved lines. Genes in selective-sweep regions showed fewer deleterious mutations than the remaining genes. Deleterious mutations explained 4.3%–48% more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2 (SCN2), soybean cyst nematode race 3 (SCN3) and soybean mosaic virus race 3 (SMV3). These findings illustrate how mutation load has shifted during soybean domestication, expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.

Branch number (BN) is an important agronomic attribute related to the plant architecture, adaptability, and yield of soybean. To date, few studies of BN have been conducted to elucidate its genetic background. We aimed to localize genetic factors affecting BN using segregating populations derived from the high-branching cultivar ‘Kennong24’ (KN24) and the low-branching cultivar ‘Kenfeng19’ (KF19). Composite interval mapping analysis detected a QTL (qBN-1) on chromosome 6 between the SSR markers BARCSOYSSR_06_0993 and BARCSOYSSR_06_1070 using an F2population. To fine-map qBN-1, a RIL population was developed and genotyped with 14 SSR markers located in the QTL region. qBN-1was localized to a 115.67-kb interval flanked by markers BARCSOYSSR_06_1048 and BARCSOYSSR_06_1053. The QTL was further confirmed using backcross populations of size 1305 (BC2F2with KN24 as a recurrent parent) and 1712 (BC3F2with KF19 as a recurrent parent).The fine-mapping region of qBN-1contained only two candidate genes, Glyma.06G208800and Glyma.06G208900, whose expression patterns were investigated by qRT-PCR. Compared to Glyma.06G208800gene expression, Glyma.06G208900showed the highest expression of the two genes and showed a significant difference in expression between high- and low-branching genotypes in either axillary meristem or shoot apical meristem, and showed opposite expression patterns in the two tissues at V4 and R1 stages. These results identify Glyma.06G208900as a novel candidate gene controlling BN. Taken together, the results of this study provide a foundation for cloning and functional analysis of the qBN-1gene and for the improvement of BN by marker-assisted selection in soybean breeding.

Flowering time is important for adaptation of soybean (Glycine max) to different environments. Here, we conducted a genome-wide association study of flowering time using a panel of 1490 cultivated soybean accessions. We identified three strong signals at the qFT02-2locus (Chr02: 12037319–12238569), which were associated with flowering time in three environments: Gongzhuling, Mengcheng, and Nanchang. By analyzing linkage disequilibrium, gene expression patterns, gene annotation, and the diversity of variants, we identified an AP1homolog as the candidate gene for the qFT02-2locus, which we named GmAP1d. Only one nonsynonymous polymorphism existed among 1490 soybean accessions at position Chr02:12087053. Accessions carrying the Chr02:12087053-T allele flowered significantly earlier than those carrying the Chr02:12087053-A allele. Thus, we developed a cleaved amplified polymorphic sequence (CAPS) marker for the SNP at Chr02:12087053, which is suitable for marker-assisted breeding of flowering time. Knockout of GmAP1din the ‘Williams 82’ background by gene editing promoted flowering under long-day conditions, confirming that GmAP1dis the causal gene for qFT02-2. An analysis of the region surrounding GmAP1drevealed that GmAP1dwas artificially selected during the genetic improvement of soybean. Through stepwise selection, the proportion of modern cultivars carrying the Chr02:12087053-T allele has increased, and this allele has become nearly fixed (95%) in northern China. These findings provide a theoretical basis for better understanding the molecular regulatory mechanism of flowering time in soybean and a target gene that can be used for breeding modern soybean cultivars adapted to different latitudes.

Soybean cyst nematode (SCN) is a highly destructive pathogen. The soybean host genome harbors at least two major genes for resistance (rhg1and Rhg4), as well as a minor locus (SCN3-11). In the present study, a splicing site in GmSNAP11, the potential causal gene of SCN3-11, was identified by comparison of the GmSNAP11cDNA sequences generated from resistant and susceptible soybean accessions. The sequence information was used to design a codominant CAPS marker, GmSNAP11-2565, which was used to genotype a panel of 209 soybean accessions varying with respect to SCN resistance. Analyses of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect (nonsynonymous) locus, GmSNAP11-2307, previously identified in GmSNAP11, revealed linkage disequilibrium (P < 0.0001) between the two loci, suggesting that GmSNAP11-2565 could be used as a marker for GmSNAP11. GmSNAP11-2565 was accordingly used, along with established markers for GmSNAP18(rhg1) and GmSHMT(Rhg4), to characterize the panel accessions. The mean SCN female index of accessions carrying only the GmSNAP11allele associated with resistance (20.3%) was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11and GmSNAP18(12.4%), while the index for accessions carrying alleles for resistance at all of GmSNAP11, GmSNAP18, and GmSHMTwas very low (1.9%). Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3.