E1 Loci Research Articles

Molecular characterization of E1 and E3 maturity loci of soybean [Glycine Max (L.) merrill] genotypes with contrasting maturity

Molecular characterization of E1 and E3 maturity loci of soybean [Glycine Max (L.) merrill] genotypes with contrasting maturity

Allelic Variation of Soybean Maturity Genes E1–E4 in the Huang-Huai-Hai River Valley and the Northwest China

Soybean is planted in a wide span of the world, and flowering and maturity time is an important trait determining soybean yield formation and adaptation. Maturity loci E1, E2, E3 and E4 were frequently reported as the most influential genetic loci for soybean flowering and maturity. To understand the allelic variation and assess the phenological traits of cultivars with different E allelic combinations in natural environments, 251 cultivars of maturity group (MG) I–V were field tested in 42 locations across four sub-regions in the Huang-Huai-Hai and Northwest region of China and genotyped with KASP markers for E1–E4 loci. The results indicated that mutant alleles were only found in the E1 and E2 locus, all of the cultivars carried functional alleles in the E3 and E4 loci in this area, with the frequency of mutant allele to be higher in early maturity groups (MGs) than late MGs. Among nine E allelic combinations in this area, one photoperiodic insensitive mutation in E2 loci (E1/e2-ns/E3-Ha/E4 and E1/e2-ns/E3-Mi/E4) made up the largest proportion (25.10 and 18.33%), while two photoperiodic insensitive mutations in both E1 and E2 loci (e1-as/e2-ns/E3-Ha/E4) (1.20%) occupied the lowest proportion in this panel. The major combinations of E locus for MGI, MGII and MG III in this area were E1/E2-dl/E3-Mi/E4, E1/e2-ns/E3-Mi/E4 and E1/e2-ns/E3-Ha/E4, respectively. Cultivars carrying e1-as/e2-ns/E3-Ha/E4 genotype flowered earliest (34 days) on average, 7.6 days earlier than the latest-flowering E haplotype (E1/e2-ns/E3-Ha/E4). This study provided an opportunity to detect the E allelic combinations in the Huang-Huai-Hai River Valley and the Northwest China, which would facilitate the improvement of soybean adaptation in the future.

The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity.

The general concept of photoperiodism, i.e., the photoperiodic induction of flowering, was established by Garner and Allard (1920). The genetic factor controlling flowering time, maturity, or photoperiodic responses was observed in soybean soon after the discovery of the photoperiodism. E1, E2, and E3 were named in 1971 and, thereafter, genetically characterized. At the centennial celebration of the discovery of photoperiodism in soybean, we recount our endeavors to successfully decipher the molecular bases for the major maturity loci E1, E2, and E3 in soybean. Through systematic efforts, we successfully cloned the E3 gene in 2009, the E2 gene in 2011, and the E1 gene in 2012. Recently, successful identification of several circadian-related genes such as PRR3a, LUX, and J has enriched the known major E1-FTs pathway. Further research progresses on the identification of new flowering and maturity-related genes as well as coordinated regulation between flowering genes will enable us to understand profoundly flowering gene network and determinants of latitudinal adaptation in soybean.

Can a reference ‘match’ an evidence profile if these have no loci in common?

Cold case reinvestigations are a common occurrence. Occasionally some of the original work was conducted up to 30 years ago using profiling systems of the early 1990s, which targeted HLA-DQA1, ApoB, D1S80 and D17S5. When contemporary work is carried out, if a suspect is identified they will be profiled in contemporary profiling kits such as GlobalFiler. It would be common to then also attempt to profile the evidence profiles in the same contemporary profiling kit. Imagine a scenario where two evidence samples, E1 and E2, had previously produced single-source profiles, but only E2 had any DNA extract left to re-profile with GlobalFiler. At the old loci E1 matched E2, and at the new loci E2 matched the suspect reference. Of interest to the investigation was whether anything could be said about the suspect being a donor of DNA to E1 even though the reference of the suspect and the profile from E1 had no loci in common, by using the information from the profile of E2. This paper explores that possibility.

Novel role of photoinsensitive alleles in adaptation of soybean [Glycine max (L.) Merr.] to rainfed short growing seasons of lower latitudes

Soybean is a temperate photosensitive crop but has adapted to sub-tropical and tropical countries of lower latitudes also. Photoperiodic and maturity genes confer latitudinal adaptation in this crop. Genotyping of accessions of higher latitudes have shown the role of photoinsensitivity, conferred by recessive photoperiodic alleles (e1/e2/e3/e4), in adaptation of the crop to high latitudes but information is not available for lower latitudinal countries like India. We genotyped and calculated the photosensitivity of 101 cultivated Indian soybean varieties and found that majority of the varieties (86) were photosensitive and had the dominant alleles at these loci. Four genotypic classes (e1-as/E2/E3/E4, E1/e2/e3/E4, E1/e2/E3/E4 and E1/E2/e3/E4) were observed for varieties with recessive alleles. Photoinsensitive alleles at E1 and E2 loci significantly reduced the days to flower, maturity and photosensitivity percentage. Adaptive role of photoperiodic alleles was inferred from breeder seed requirement of these varieties for 35 years. Although the photosensitive class contributed 81% to the total seed requirement the weighted mean contribution of this class (380 Q/year) was far less than that of photoinsensitive class (648 Q/year). Photoinsensitivity is essential for perpetuation of crop in higher latitudes. Present report highlights the novel role of photoinsensitive alleles in adaptation of soybean to rainfed, short growing and sub-tropical conditions of lower latitudes by conferring earliness.

Positional Cloning of the Flowering Time QTL qFT12-1 Reveals the Link Between the Clock Related PRR Homolog With Photoperiodic Response in Soybeans.

Flowering time and maturity are important agronomic traits for soybean cultivars to adapt to different latitudes and achieve maximal yield. Genetic studies on genes and quantitative trait loci (QTL) that control flowering time and maturity are extensive. In particular, the molecular bases of E1-E4, E6, E9, E10, and J have been deciphered. For a better understanding of regulation of flowering time gene networks, we need to understand if more molecular factors carrying different biological functions are also involved in the regulation of flowering time in soybeans. We developed a population derived from a cross between a landrace Jilincailihua (male) and a Chinese cultivar Chongnong16 (female). Both parents carry the same genotypes of E1e2E3HaE4 at E1, E2, E3, and E4 loci. Nighty-six individuals of the F2 population were genotyped with Illumina SoySNP8k iSelect BeadChip. A total of 2,407 polymorphic single nucleotide polymorphism (SNP) markers were used to construct a genetic linkage map. One major QTL, qFT12-1, was mapped to an approximately 567-kB region on chromosome 12. Genotyping and phenotyping of recombinant plant whose recombination events were occurring within the QTL region allowed us to narrow down the QTL region to 56.4 kB, in which four genes were annotated. Allelism and association analysis indicated Glyma.12G073900, a PRR7 homolog, is the strongest candidate gene for qFT12-1. The findings of this study disclosed the possible involvement of circadian clock gene in flowering time regulation of soybeans.

Highly multiplexed AmpliSeq technology identifies novel variation of flowering time-related genes in soybean (Glycine max).

Whole-genome re-sequencing is a powerful approach to detect gene variants, but it is expensive to analyse only the target genes. To circumvent this problem, we attempted to detect novel variants of flowering time-related genes and their homologues in soybean mini-core collection by target re-sequencing using AmpliSeq technology. The average depth of 382 amplicons targeting 29 genes was 1,237 with 99.85% of the sequence data mapped to the reference genome. Totally, 461 variants were detected, of which 150 sites were novel and not registered in dbSNP. Known and novel variants were detected in the classical maturity loci—E1, E2, E3, and E4. Additionally, large indel alleles, E1-nl and E3-tr, were successfully identified. Novel loss-of-function and missense variants were found in FT2a, MADS-box, WDR61, phytochromes, and two-component response regulators. The multiple regression analysis showed that four genes—E2, E3, Dt1, and two-component response regulator—can explain 51.1–52.3% of the variation in flowering time of the mini-core collection. Among them, the two-component response regulator with a premature stop codon is a novel gene that has not been reported as a soybean flowering time-related gene. These data suggest that the AmpliSeq technology is a powerful tool to identify novel alleles.

Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean

BackgroundSoybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both correlations among different traits and genetic interactions among genes that affect a single trait pose a challenge to soybean breeding.ResultsTo understand the genetic networks underlying phenotypic correlations, we collected 809 soybean accessions worldwide and phenotyped them for two years at three locations for 84 agronomic traits. Genome-wide association studies identified 245 significant genetic loci, among which 95 genetically interacted with other loci. We determined that 14 oil synthesis-related genes are responsible for fatty acid accumulation in soybean and function in line with an additive model. Network analyses demonstrated that 51 traits could be linked through the linkage disequilibrium of 115 associated loci and these links reflect phenotypic correlations. We revealed that 23 loci, including the known Dt1, E2, E1, Ln, Dt2, Fan, and Fap loci, as well as 16 undefined associated loci, have pleiotropic effects on different traits.ConclusionsThis study provides insights into the genetic correlation among complex traits and will facilitate future soybean functional studies and breeding through molecular design.

The transition time from the juvenile phase to the adult phase differs in soybean cultivars ‘Enrei’ and ‘Peking’

AbstractPlants develop juvenile phase to adult phase in vegetative stage. Although soybean is a very important crop worldwide, there has been only one study of the juvenile–adult phase change. In this study, we determined that the juvenile–adult phase change occurred at different stages in two soybean cultivars that differ in their photosensitivity. Cultivar ‘Enrei’ (E1e2e3E4) is weakly photosensitive and cultivar ‘Peking’ (E1E2E3E4) is strongly photosensitive. In ‘Enrei’, the leaf size gradually increased at a constant leaf position regardless of the difference in day length. In ‘Peking’ plants transferred to short‐day conditions at several leaf development stages, leaf size gradually increased at different leaf positions. Expression of miR156 by ‘Enrei’ transferred to short‐day conditions had nearly the same pattern as that of ‘Enrei’ grown under long‐day conditions. In ‘Peking’, the expression of miR156 had different patterns in younger leaves of plants subjected to either a short‐day treatment or long‐day conditions. These results indicate that the E2 and E3 loci that regulate photosensitivity also regulate the expression of miR156 and the juvenile–adult phase change in soybean.

Identification of environmentally stable QTLs controlling Saponin content in Glycine max.

Saponins are secondary metabolites that are widely distributed in plants. There are two major saponin precursors in soybean: soyasapogenol A, contributing to the undesirable taste, and soyasapogenol B, some of which have health benefits. It is important to control the ratio and content of the two major saponin groups to enhance the appeal of soybean as a health food. The structural diversity of saponin in the sugar chain composition makes it hard to quantify the saponin content. We measured the saponin content in soybean by removing the sugar chain from the saponin using acidic hydrolysis and detected novel quantitative trait loci (QTLs) for saponin content. Major QTLs in the hypocotyl were identified on chromosome 5 near the SSR marker, Satt 384, while those in the cotyledon were on chromosome 6 near Sat_312, which is linked to the T and E1 loci. Our results suggest that saponin contents in the hypocotyl and cotyledon are controlled by different genes and that it is difficult to increase the beneficial group B saponin and to decrease the undesirable group A saponin at the same time.

A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog.

FLOWERING LOCUS T (FT) is an important floral integrator whose functions are conserved across plant species. In soybean, two orthologs, FT2a and FT5a, play a major role in initiating flowering. Their expression in response to different photoperiods is controlled by allelic combinations at the maturity loci E1 to E4, generating variation in flowering time among cultivars. We determined the molecular basis of a quantitative trait locus (QTL) for flowering time in linkage group J (Chromosome 16). Fine-mapping delimited the QTL to a genomic region of 107kb that harbors FT5a We detected 15 DNA polymorphisms between parents with the early-flowering (ef) and late-flowering (lf) alleles in the promoter region, an intron, and the 3' untranslated region of FT5a, although the FT5a coding regions were identical. Transcript abundance of FT5a was higher in near-isogenic lines for ef than in those for lf, suggesting that different transcriptional activities or mRNA stability caused the flowering time difference. Single-nucleotide polymorphism (SNP) calling from re-sequencing data for 439 cultivated and wild soybean accessions indicated that ef is a rare haplotype that is distinct from common haplotypes including lf The ef allele at FT5a may play an adaptive role at latitudes where early flowering is desirable.

Quantitative trait locus mapping of soybean maturity gene E5.

Time to flowering and maturity in soybean is controlled by loci E1 to E5, and E7 to E9. These loci were assigned to molecular linkage groups (MLGs) except for E5. This study was conducted to map the E5 locus using F2 populations expected to segregate for E5. F2 populations were subjected to quantitative trait locus (QTL) analysis for days to flowering (DF) and maturity (DM). In Harosoy-E5 × Clark-e2 population, QTLs for DF and DM were found at a similar position with E2. In Harosoy × Clark-e2E5 population, QTLs for DF and DM were found in MLG D1a and B1, respectively. In Harosoy-E5Dt2 × Clark-e2 population, a QTL for DF was found in MLG B1. Thus, results from these populations were not fully consistent, and no candidate QTL for E5 was found. In Harosoy × PI 80837 population, from which E5 was originally identified, QTLs corresponding to E1 and E3 were found, but none for E5 existed. Harosoy and PI 80837 had the e2-ns allele whereas Harosoy-E5 had the E2-dl allele. The E2-dl allele of Harosoy-E5 may have been generated by outcrossing and may be responsible for the lateness of Harosoy-E5. We conclude that a unique E5 gene may not exist.

QTL mapping for flowering time in different latitude in soybean

Flowering represents the transition from the vegetative to reproductive phase and plays an important role in many agronomic traits. For soybean, a short day (SD) induced and photoperiod-sensitive plant, delaying flowering time under SD environments is very important and has been used by breeders to increase yields and enhance plant adaptabilities at lower latitudes. The purpose of this study was to identify quantitative trait loci (QTLs) associated with flowering time, especially QTLs underlying the long juvenile (LJ) trait which delays flowering time under SD environments. A population of 91 recombinant inbred lines derived from a cross between AGS292 and K3 was used for map construction and QTL analysis. The map covered 2546.7 cM and included 52 new promoter-specific indel and 9 new exon-specific indel markers. The phenotypic days-to-flowering data were examined in nine environments, including four short-day (SD, low latitude) and five long-day photoperiod (LD, high latitude) environments. For the SD environments, six QTLs were detected. Five of them were associated with the LJ trait. Among the five LJ QTLs, four QTLs may be attributed to the known flowering time genes, including qFT-J-1 for FT5a locus, qFT-J-2 for the FT2a locus, qFT-O for the E2 locus and qFT-L for the E3 locus. This is the first report that the E2, E3, FT2a and FT5a loci may be associated with the LJ trait. Under the five LD environments, as expected, qFT-O for the E2 locus and qFT-L for the E3 locus were identified, suggesting that E2 and E3 loci are very important for soybean adaptation in LD photoperiod. Conjoint analysis of multiple environments identified nine additive QTLs and nine pairs of epistatic QTLs, among which most were involved in interactions with the environments. In total, five QTLs (qFT-B2-1, qFT-C1-1, qFT-K, qFT-D2 and qFT-F) were identified that may represent novel flowering time genes. This provides a fundamental foundation for future studies of flowering time in soybean using fine mapping, map-based cloning, and molecular-assisted breeding.

Allelic Combinations of Soybean Maturity Loci E1, E2, E3 and E4 Result in Diversity of Maturity and Adaptation to Different Latitudes

Soybean cultivars are extremely diverse in time to flowering and maturation as a result of various photoperiod sensitivities. The underlying molecular genetic mechanism is not fully clear, however, four maturity loci E1, E2, E3 and E4 have been molecularly identified. In this report, cultivars were selected with various photoperiod sensitivities from different ecological zones, which covered almost all maturity groups (MG) from MG 000 to MG VIII and MG X adapted from latitude N 18° to N 53°. They were planted in the field under natural daylength condition (ND) in Beijing, China or in pots under different photoperiod treatments. Maturity-related traits were then investigated. The four E maturity loci were genotyped at the molecular level. Our results suggested that these four E genes have different impacts on maturity and their allelic variations and combinations determine the diversification of soybean maturity and adaptation to different latitudes. The genetic mechanisms underlying photoperiod sensitivity and adaptation in wild soybean seemed unique from those in cultivated soybean. The allelic combinations and functional molecular markers for the four E loci will significantly assist molecular breeding towards high productivity.

Allelic variations at four major maturity E genes and transcriptional abundance of the E1 gene are associated with flowering time and maturity of soybean cultivars.

The time to flowering and maturity are ecologically and agronomically important traits for soybean landrace and cultivar adaptation. As a typical short-day crop, long day conditions in the high-latitude regions require soybean cultivars with photoperiod insensitivity that can mature before frost. Although the molecular basis of four major E loci (E1 to E4) have been deciphered, it is not quite clear whether, or to what degree, genetic variation and the expression level of the four E genes are associated with the time to flowering and maturity of soybean cultivars. In this study, we genotyped 180 cultivars at E1 to E4 genes, meanwhile, the time to flowering and maturity of those cultivars were investigated at six geographic locations in China from 2011 to 2012 and further confirmed in 2013. The percentages of recessive alleles at E1, E2, E3 and E4 loci were 38.34%, 84.45%, 36.33%, and 7.20%, respectively. Statistical analysis showed that allelic variations at each of four loci had a significant effect on flowering time as well as maturity. We classified the 180 cultivars into eight genotypic groups based on allelic variations of the four major E loci. The genetic group of e1-nf representing dysfunctional alleles at the E1 locus flowered earliest in all the geographic locations. In contrast, cultivars in the E1E2E3E4 group originated from the southern areas flowered very late or did not flower before frost at high latitude locations. The transcriptional abundance of functional E1 gene was significantly associated with flowering time. However, the ranges of time to flowering and maturity were quite large within some genotypic groups, implying the presence of some other unknown genetic factors that are involved in control of flowering time or maturity. Known genes (e.g. E3 and E4) and other unknown factors may function, at least partially, through regulation of the expression of the E1 gene.

Maturity group classification and maturity locus genotyping of early-maturing soybean varieties from high-latitude cold regions.

BackgroundWith the migration of human beings, advances of agricultural sciences, evolution of planting patterns and global warming, soybeans have expanded to both tropical and high-latitude cold regions (HCRs). Unlike other regions, HCRs have much more significant and diverse photoperiods and temperature conditions over seasons or across latitudes, and HCR soybeans released there show rich diversity in maturity traits. However, HCR soybeans have not been as well classified into maturity groups (MGs) as other places. Therefore, it is necessary to identify MGs in HCRs and to genotype the maturity loci.MethodsLocal varieties were collected from the northern part of Northeast China and the far-eastern region of Russia. Maturity group reference (MGR) soybeans of MGs MG000, MG00, and MG0 were used as references during field experiments. Both local varieties and MGR soybeans were planted for two years (2010-2011) in Heihe (N 50°15′, E 127°27′, H 168.5 m), China. The days to VE (emergence), R1 (beginning bloom) and R7 (beginning maturity) were recorded and statistically analyzed. Furthermore, some varieties were further genotyped at four molecularly-identified maturity loci E1, E2, E3 and E4.ResultsThe HCR varieties were classified into MG0 or even more early-maturing. In Heihe, some varieties matured much earlier than MG000, which is the most early-maturing known MG, and clustered into a separate group. We designated the group as MG0000, following the convention of MGs. HCR soybeans had relatively stable days to beginning bloom from emergence. The HCR varieties diversified into genotypes of E1, E2, E3 and E4. These loci had different effects on maturity.ConclusionHCRs diversify early-maturing MGs of soybean. MG0000, a new MG that matures much earlier than known MGs, was developed. HCR soybean breeding should focus more on shortening post-flowering reproductive growth. E1, E2, E3, and E4 function differentially.

Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean

The timing of flowering has a direct impact on successful seed production in plants. Flowering of soybean (Glycine max) is controlled by several E loci, and previous studies identified the genes responsible for the flowering loci E1, E2, E3 and E4. However, natural variation in these genes has not been fully elucidated. The aims of this study were the identification of new alleles, establishment of allele diagnoses, examination of allelic combinations for adaptability, and analysis of the integrated effect of these loci on flowering. The sequences of these genes and their flanking regions were determined for 39 accessions by primer walking. Systematic discrimination among alleles was performed using DNA markers. Genotypes at the E1-E4 loci were determined for 63 accessions covering several ecological types using DNA markers and sequencing, and flowering times of these accessions at three sowing times were recorded. A new allele with an insertion of a long interspersed nuclear element (LINE) at the promoter of the E1 locus (e1-re) was identified. Insertion and deletion of 36 bases in the eighth intron (E2-in and E2-dl) were observed at the E2 locus. Systematic discrimination among the alleles at the E1-E3 loci was achieved using PCR-based markers. Allelic combinations at the E1-E4 loci were found to be associated with ecological types, and about 62-66 % of variation of flowering time could be attributed to these loci. The study advances understanding of the combined roles of the E1-E4 loci in flowering and geographic adaptation, and suggests the existence of unidentified genes for flowering in soybean.

Integration Sites and Genotype Distributions of Human Papillomavirus in Cervical Intraepithelial Neoplasia

To analyse HPV integration prevalence and genotype distributions in cervical intraepithelial neoplasia (CIN) in east part of China, furthermore to assess preferential sites for common HPV integrations and provide baseline information for cervical abnormality screening and prevention. Integration of HPV in 113 paraffin-embedded cervical intraepithelial neoplasia samples was assessed using Gencap technology in Key Laboratory of Biotechnologies in BGI-Shenzhen. 64 samples were HPV-integrated and as the cervical lesions increased, the integration rate became higher significantly (P=0.002). Fifteen different HPV genotypes were detected, 14 high-risk (16, 18, 31, 33, 51, 52, 56, 58, 66, 68) and 1 low-risk (11). The most common genotypes were HPV-16, 58, 33, 52, 66, and 56. Thirteen patients had co-integration involving mainly HPV-16 and 58. The frequency of HPV gene disruption was higher in L1 and E1 genes than in other regions of the viral genomes. Some 56.6% of CIN lesions in Qingdao had HPV integrations, and 67.2% of HPV-integrated patients were HPV-16 and 58, more prone to be integrated in younger patients below 45 years old. There exist preferential sites for HPV-16 and HPV-58 integration, and they are more likely to be disrupted in the L1 and E1 loci.

Molecular markers for the E2 and E3 genes controlling flowering and maturity in soybean

Natural variation in flowering time may play a role in the adaptation of plants to various environments, and understanding the genetic basis of flowering and maturity would facilitate the development of early maturing cultivars. Molecular markers for the E2 and E3 loci, which control the time of flowering and maturity in soybean (Glycinemax), were developed in this study. Single nucleotide-amplified polymorphism (SNAP) markers were developed from the nonsense mutation in E2 (GmGIa), which is a circadian clock-controlled gene. The E2- and e2-specific SNAP markers were validated using six E2 isolines. The soybean E3 gene is a photoreceptor phytochrome A (GmPhyA3) gene, and a co-dominant marker was designed based on sequence deletions within the E3 allele. A multiplex PCR assay using three primers for the E3 gene allowed allelic discrimination based on the sizes of PCR products. Furthermore, this E3 marker successfully detected two alleles in a single reaction when two types of DNA were pooled. These markers determined the genotypes of our mapping population previously reported to detect flowering quantitative trait loci close to the E2 and E3 loci, confirming that the mutations are responsible for the early flowering phenotype. The use of SNAP markers for E2 and a co-dominant marker for E3 is a simple, fast, and reproducible method, requiring only PCR and agarose gel electrophoresis. The molecular resources developed in this study could accelerate marker-assisted selection and cultivar development for short-season areas in a soybean breeding program.

Identification of population-specific QTLs for flowering in soybean

Flowering is an important stage in plant development and crucial for adaptation of plant species to different environments. Two soybean mapping populations were used to identify quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) by genotyping simple sequence repeat (SSR) markers. Single-factor analysis of variance detected association of phenotypic data with SSR markers in each population. DF QTLs were identified on four chromosomes (chrs.); two QTLs located on chrs. 2 and 13 with Satt041 and Satt206 in the Jinpumkong 2 × SS2-2 population and other two DF QTLs were detected on chrs. 6 and 19 with Satt100 and Satt373 in the Iksannamulkong × SS2-2 population. The major QTLs associated with Satt100 explained 30.3% of maximum phenotypic variation. Especially, all DF QTLs included QTLs for DM, except Satt206 on chr. 13. Moreover, two additional DM QTLs were mapped on chrs. 10 and 11 with Satt243 and Satt359, respectively. DF QTL on chr. 2 with Satt041 was the newly identified QTL only in the Jinpumkong 2 × SS2-2 population and explained 10.3% of the phenotypic variation. The single locus of Satt100 on chr. 6 and Satt373 on chr. 19 were located on soybean genomic regions of the known flowering gene loci E1 and E3, respectively. These population-specific QTLs (Satt100 and Satt373) are the major QTLs for flowering time, putatively, they may be related to maturity QTLs with large effect. Additionally, these QTLs are valuable for marker-assisted approaches and could be widely adopted by soybean breeders.