Soybean Time Research Articles

Deciphering of Genomic Loci Associated with Alkaline Tolerance in Soybean [Glycine max (L.) Merr.] by Genome-Wide Association Study

Alkaline stress is one of the major abiotic constraints that limits plant growth and development. However, the genetic basis underlying alkaline tolerance in soybean [Glycine max (L.) Merr.] remains largely unexplored. In this study, an integrated genomic analysis approach was employed to elucidate the genetic architecture of alkaline tolerance in a diverse panel of 326 soybean cultivars. Through association mapping, we detected 28 single nucleotide polymorphisms (SNPs) significantly associated with alkaline tolerance. By examining the genomic distances around these significant SNPs, five genomic regions were characterized as stable quantitative trait loci (QTLs), which were designated as qAT1, qAT4, qAT14, qAT18, and qAT20. These QTLs are reported here for the first time in soybean. Seventeen putative candidate genes were identified within the physical intervals of these QTLs. Haplotype analysis indicated that four of these candidate genes exhibited significant allele variation associated with alkaline tolerance-related traits, and the haplotype alleles for these four genes varied in number from two to four. The findings of this study may have important implications for soybean breeding programs aimed at enhancing alkaline tolerance.

AP1c and SOC1 Form a Regulatory Feedback Loop to Regulate Flowering Time in Soybean.

Flowering time is a key agronomic trait that directly affects soybean yield. Both APETALA1 (AP1) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) regulate flowering time in soybean, but their genetic and regulatory relationships have not been clarified. Here, we report that AP1c physically interacted with two SOC1 proteins, SOC1a and SOC1b, and that these SOC1s upregulated the expression of AP1c, promoting flowering. Moreover, AP1c repressed the expression of the SOC1s by directly binding to their promoters, thus preventing plants from flowering too early. These findings indicate that AP1c and SOC1s form a regulatory feedback loop that regulates flowering time. Importantly, we identified an exceptional allele, AP1cG, that was selected for during soybean domestication and promotes the early-flowering phenotype in cultivated soybean. Collectively, our work identifies a previously unknown allelic combination potentially useful for both classical and molecular soybean breeding.

GmAP1d regulates flowering time under long-day photoperiods in soybean

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 qFT02-2 locus (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 AP1 homolog as the candidate gene for the qFT02-2 locus, 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 GmAP1d in the ‘Williams 82’ background by gene editing promoted flowering under long-day conditions, confirming that GmAP1d is the causal gene for qFT02-2. An analysis of the region surrounding GmAP1d revealed that GmAP1d was 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.

Genome-wide association study for temperature response and photo-thermal interaction of flowering time in soybean using a panel of cultivars with diverse maturity groups.

A total of 101 QTNs were found to be associated with soybean flowering time responses to photo-thermal conditions; three candidate genes with non-synonymous substitutions were identified: Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). The flowering transition is a crucial component of soybean (Glycine max L. Merr.) development. The transition process is regulated by photoperiod, temperature, and their interaction. To examine the genetic architecture associated with temperature- and photo-thermal-mediated regulation of soybean flowering, we here performed a genome-wide association study using a panel of 201 soybean cultivars with maturity groups ranging from MG 000 to VIII. Each cultivar was grown in artificially controlled photoperiod and different seasons in 2017 and 2018 to assess the thermal response (TR) and the interactive photo-thermal response (IPT) of soybean flowering time. The panel contained 96,299SNPs with minor allele frequencies > 5%; 33, 19, and 49 of these SNPs were significantly associated with only TR, only IPT, and both TR and IPT, respectively. Twenty-one SNPs were located in or near previously reported quantitative trait loci for first-flowering; 16 SNPs were located within 200kb of the main-effect flowering genes GmFT2a, GmFT2b, GmFT3a, GmFT3b, GmFT5a, GmFT5b, GmCOL2b, GmPIF4b, and GmPIF4c, or near homologs of the known Arabidopsis thaliana flowering genes BBX19, VRN1, TFL1, FUL, AGL19, SPA1, HY5, PFT1, and EDF1. Natural non-synonymous allelic variations were identified in the candidate genes Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). Cultivars with different haplotypes showed significant variations in TR, IPT, and flowering time in multiple environments. The favorable alleles, candidate genes, and diagnostic SNP markers identified here provide valuable information for future improvement of soybean photo-thermal adaptability, enabling expansion of soybean production regions and improving plant resilience to global climate change.

Two soybean homologues of TERMINAL FLOWER 1 control flowering time under long day conditions

Flowering time is a key agronomic trait that directly affect the adaptation and yield of soybean. After whole genome duplications, about 75% of genes being represented by multiple copies in soybean. There are four TERMINAL FLOWER 1 (TFL1) genes in soybean, and the TFL1b (Dt1) has been characterized as the determinant of stem growth habit. The function of other TFL1 homologs in soybean is still unclear. Here, we generated knockout mutants by CRISPR/Cas9 genome editing technology and found that the tfl1c/tfl1d double mutants flowered significantly earlier than wild-type plants. We investigated that TFL1c and TFL1d could physically interact with the bZIP transcription factor FDc1 and bind to the promoter of APETALA1a (AP1a). RNA-seq and qRT-PCR analyses indicated that TFL1c and TFL1d repressed the expressions of the four AP1 homologs and delayed the flowering time in soybean. The two genes play important roles in the regulation of flowering time in soybean and mainly act as the flowering inhibitors under long-day conditions. Our results identify novel components in the flowering-time regulation network of soybean and will be invaluable for molecular breeding of improved soybean yield.

Soil bacterial community dynamics in plots managed with cover crops and no-till farming in the Lower Mississippi Alluvial Valley, USA.

Assess bacterial community changes over time in soybean (Glycine max) crop fields following cover crop (CC) and no-till (NT) implementation under natural abiotic stressors. Soil bacterial community composition was obtained by amplifying, sequencing, and analysing the V4 region of the 16S rRNA gene. Generalized linear mixed models were used to assess the effects of tillage, CC, and time on bacterial community response. The most abundant phyla present were Acidobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Bacterial diversity increased in periods with abundant water. Reduced tillage (RT) increased overall bacterial diversity, but NT with a CC was not significantly different than RT treatments under drought conditions. CCs shifted abundances of Firmicutes and Bacteroidetes depending on abiotic conditions. In the Lower Mississippi Alluvial Valley (LMAV), USA, NT practices lower diversity and influence long-term community changes while cover crops enact a seasonal response to environmental conditions. NT and RT management affect soil bacterial communities differently than found in other regions of the country.

Genetic and molecular control of the flowering time in soybean (Glycine max (L.) Merrill)

Photoperiod response to flowering is one of the most vital factors that affect in regional adaptation and yield in soybean. Soybean adaption at high latitude areas (long-day) requires early flowering and low photoperiod sensitive cultivars; adaptation to low latitudes (short-day) areas needs delayed flowering cultivars, which maximize vegetative growth and seed yield. This paper represents a genetic and molecular regulation of flowering time in soybean, which will help broad adaptability across latitudes. It is revealed that one to eleven main genes control the flowering time in soybean. The FT family of flowering integrators plays a central role in controlling the flowering time. The juvenile growth phase (JGP) determines the development rate for flowering; a long JGP results in the lengthening of the vegetative period and increases the soybean production in low latitude areas. This review outlines the JGP-related gene in soybean. We emphasize the interaction between major genes and QTLs for flowering in soybean. Several major genes and quantitative trait loci (QTLs) for flowering interact with one another including the environment to greatly influence flowering time. The molecular ground information of the flowering in Arabidopsis will help to understand the molecular dissection of flowering in soybean. This information could be used for breeding of high‐yielding soybean cultivars in different latitudinal areas.
 Res. Agric., Livest. Fish.9(1): 1-10, April 2022

Salmonella enterica in soybean production chain: Occurrence, characterization, and survival during soybean storage

This study aimed to determine Salmonella enterica occurrence along the soybean meal production chain (raw material, in-processing samples, final products, and in the environment of five processing plants), characterize the isolates, and assess the survival of Salmonella Senftenberg 775W in soybeans stored under different temperature conditions. Among 713 samples analyzed, 12.9% (n = 92) were positive for Salmonella enterica. Dust collected inside and outside processing plants (n = 148) comprised the samples with the highest positivity for Salmonella enterica, 47.3%. The occurrence of Salmonella enterica varied among the different processing plants. Twenty-nine (n = 29) Salmonella serotypes were isolated, with S. Mbandaka as the most frequent serotype, whereas S. Typhimurium was mainly linked to final product samples (soybean meal). S. Senftenberg 775W did not survive for a long time in soybean stored at 20-37 °C, but at 20 °C, cells were viable for more than 60 days. This study suggests that soybean meal may harbor Salmonella serotypes related to foodborne disease outbreaks in humans and can be responsible for Salmonella introduction into livestock and, consequently, in foods of animal origin. This study provides crucial data on contamination pathways of Salmonella in the soybean production chain, contributing to the understanding of Salmonella epidemiology which is strategic for the development of preventive and control measures to reduce the burden of salmonellosis linked to products of animal origin.

CRISPR/Cas9-engineered mutation to identify the roles of phytochromes in regulating photomorphogenesis and flowering time in soybean

Soybean (Glycine max) responds to ambient light variation by undergoing multiform morphological alterations, influencing its yield potential and stability in the field. Phytochromes (PHYs) are plant-specific red (R) and far-red (FR) light photoreceptors mediating photomorphogenesis and photoperiodic flowering. As an ancient tetraploid, soybean harbors four PHYA, two PHYB, and two PHYE paralogs. Except for GmPHYA2/E4 and GmPHYA3/E3, which have been identified as photoperiod-dependent flowering repressors, the functions of GmPHYs are still largely unclear. We generated a series of individual or combined mutations targeting the GmPHYA or GmPHYB genes using CRISPR/Cas9 technology. Phenotypic analysis revealed that GmPHYB1 mediates predominantly R-light induced photomorphogenesis, whereas GmPHYA2/E4 and GmPHYA3/E3, followed by GmPHYA1 and GmPHYB2, function redundantly and additively in mediating FR light responses in seedling stage. GmPHYA2/E4 and GmPHYA3/E3, with weak influence from GmPHYA1 and GmPHYA4, delay flowering time under natural long-day conditions. This study has demonstrated the diversified functions of GmPHYAs and GmPHYBs in regulating light response, and provides a core set of phytochrome mutant alleles for characterization of their functional mechanisms in regulating agronomic traits of soybean.

Function analysis of GmELF3s in regulating soybean flowering time and circadian rhythm

<p id="C3">Soybean is a typical short-day crop. Photoperiod sensitivity seriously affects flowering time, yield, and planting range of soybean, but the mechanism underlying photoperiod and circadian rhythm regulation is still unclear. In <italic>Arabidopsis thaliana</italic>, ELF3, together with ELF4 and LUX, forms the ELF4-ELF3-LUX complex (Evening Complex, EC), which plays an important role in circadian rhythm and flowering time regulation. In this study, soybean mutants of <italic>Gmelf3a/j</italic>, <italic>Gmelf3b-1</italic>, and <italic>Gmelf3b-2 </italic>were obtained by CRISPR/Cas9 gene editing system. We found that GmELF3b-1 regulated the flowering time in soybean under long-day conditions by observing flowering phenotypes in these mutants. The phenotypes of heterozygous double mutants revealed that there was functional redundancy among GmELF3a/J, GmELF3b-1<italic>, </italic>and GmELF3b-2 in regulating flowering time of soybean. Through detecting the expression of circadian related genes in soybean by using qRT-PCR, it was found that the relative expression patterns of <italic>GmCAB</italic>, <italic>GmPRR9a</italic>, and <italic>GmPRR7a</italic> were changed in soybean. In summary, these results suggested that GmELF3a/J, GmELF3b-1, and GmELF3b-2 may regulate the circadian rhythm and flowering time through GmPRR9a and GmPRR7a in soybean.

Co-silencing E1 and its homologs in an extremely late-maturing soybean cultivar confers super-early maturity and adaptation to high-latitude short-season regions

Soybean (Glycine max (L.) Merr.), a typical short-day plant, is sensitive to photoperiod, which limits the geographical range for its cultivation. In the flowering pathway regulated by photoperiod, E1, a flowering inhibitor in soybean, plays the dominant role in flowering time regulation. Two E1 homologs, E1-like-a (E1La) and E1-like-b (E1Lb), play overlapping or redundant roles in conjunction with E1. In the present study, E1 and E1La/b were simultaneously silenced via RNA interference (RNAi) in Zigongdongdou (ZGDD), an extremely late-flowering soybean landrace from southern China. As a result, RNAi lines showed a much earlier-flowering phenotype and obvious photoperiod insensitivity compared with wild-type (WT) plants. In RNAi transgenic plants, the expression levels of flowering inhibitor GmFT4 and flowering promoters GmFT2a/GmFT5a were significantly down- and up-regulated, respectively. Further, the maturity group (MG) of the RNAi lines was reduced from WT ZGDD's MG VIII (extremely late-maturity) to MG 000 (super-early maturity), which can even grow in the northernmost village of China located at a latitude of 53.5°N. Our study confirms that E1 and E1La/b can negatively regulate flowering time in soybean. The RNAi lines generated in this study, with early flowering and maturity traits, can serve as valuable materials and a technical foundation for breeding soybeans that are adapted to high-latitude short-season regions.

Pengaruh Lama Perendaman Biji Kedelai (Glycine max L.Merr) terhadap Karakateristik Organoleptik Susu Kedelai

&#x0D; &#x0D; &#x0D; &#x0D; Soybeans (Glycine max (L) Merr.) are legumes that contain high vegetable protein, fat source, vitamins, and minerals. One of the products is soy milk. Soy milk has a strong beany flavour and a chalky mouthfeel. The flavour of soybeans in soy milk can be reduced by applying the appropriate processing techniques. One of the important steps in processing soybeans into soy milk is to soak soybeans. Studies related to soaking soybeans to soy milk are rarely found. This research was intended to find out the long-lasting influence of soybean to the organoleptic characteristics of soy milk so that the soy milk is produced by its acceptance (good acceptance). A completely randomized design was used with three treatments of soybean soaking long as follows, 6 hours, 12 hours, and 24 hours. The organoleptic data was carried out with ANOVA method at α=5% and followed by DMRT. The results showed that long soaking the soybean only affected the level of taste and overall acceptance of soy milk. In addition, the best soaking time of soybean was 12 hours because it was able to influence the taste level of flavor with the highest acceptance and the most distinct acceptance compared to other treatment with a preferred assessment score and gave the highest value of the favorite level on all parameters.&#x0D; &#x0D; &#x0D; &#x0D;

FT5a interferes with the Dt1-AP1 feedback loop to control flowering time and shoot determinacy in soybean.

Flowering time and stem growth habit determine inflorescence architecture in soybean, which in turn influences seed yield. Dt1, a homolog of Arabidopsis TERMINAL FLOWER 1 (TFL1), is a major controller of stem growth habit, but its underlying molecular mechanisms remain unclear. Here, we demonstrate that Dt1 affects node number and plant height, as well as flowering time, in soybean under long-day conditions. The bZIP transcription factor FDc1 physically interacts with Dt1, and the FDc1-Dt1 complex directly represses the expression of APETALA1 (AP1). We propose that FT5a inhibits Dt1 activity via a competitive interaction with FDc1 and directly upregulates AP1. Moreover, AP1 represses Dt1 expression by directly binding to the Dt1 promoter, suggesting that AP1 and Dt1 form a suppressive regulatory feedback loop to determine the fate of the shoot apical meristem. These findings provide novel insights into the roles of Dt1 and FT5a in controlling the stem growth habit and flowering time in soybean, which determine the adaptability and grain yield of this important crop.

Multiplex CRISPR/Cas9-mediated knockout of soybean LNK2 advances flowering time

Flowering time is an important agronomic trait for soybean yield and adaptation. However, the genetic basis of soybean adaptation to diverse latitudes is still not clear. Four NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED 2 (LNK2) homeologs of Arabidopsis thaliana LNK2 were identified in soybean. Three single-guide RNAs were designed for editing the four LNK2 genes. A transgene-free homozygous quadruple mutant of the LNK2 genes was developed using the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9). Under long-day (LD) conditions, the quadruple mutant flowered significantly earlier than the wild-type (WT). Quantitative real-time PCR (qRT-PCR) revealed that transcript levels of LNK2 were significantly lower in the quadruple mutant than in the WT under LD conditions. LNK2 promoted the expression of the legume-specific E1 gene and repressed the expression of FT2a. Genetic markers were developed to identify LNK2 mutants for soybean breeding. These results indicate that CRISPR/Cas9-mediated targeted mutagenesis of four LNK2 genes shortens flowering time in soybean. Our findings identify novel components in flowering-time control in soybean and may be beneficial for further soybean breeding in high-latitude environments.

Overexpression of GmUBC9 Gene Enhances Plant Drought Resistance and Affects Flowering Time via Histone H2B Monoubiquitination.

Ubiquitylation is a form of post-translational modification of proteins that can alter localization, functionality, degradation, or transcriptional activity within a cell. E2 ubiquitin-conjugating enzyme (UBC) and E3 ubiquitin ligases are the primary determinants of substrate specificity in the context of ubiquitin conjugation. Multiubiquitination modifies target proteins for 26S proteasome degradation, while monoubiquitination controls protein activation and localization. At present, research on the monoubiquitination, especially histone monoubiquitination, has mostly focused on model plants with relatively few on crop species. In this study, we identified 91 UBC-like genes in soybean. The chromosomal localization, phylogenetic relationships, gene structures, and putative cis-acting elements were evaluated. Furthermore, the tissue-specific expression patterns of UBC Class I genes under drought stress were also investigated. Among Class I genes, GmUBC9 induction in response to drought stress was evident, and so this gene was selected for further analysis. GmUBC9 localized to the nucleus and endoplasmic reticulum. The overexpression of GmUBC9 in Arabidopsis led to enhanced tolerance for drought conditions across a range of stages of development, while overexpression in soybean hairy roots similarly led to improvements in tolerance for drought conditions, increased proline content, and reduced MDA content in soybean seedlings compared to wild type plants. HISTONE MONOUBIQUITINATION 2 (HUB2), an E3-like protein involved in histone H2B ubiquitylation (H2Bub1), was found to interact with GmUBC9 through Y2H analysis and BiFC assays in Arabidopsis and soybean. Under drought conditions, the level of H2Bub1 increased, and transcription of drought response genes was activated in GmUBC9 transgenic Arabidopsis and soybean. In addition, GmUBC9 transgenic Arabidopsis and soybean showed a late-flowering phenotype and had increased expression levels of the flowering related genes FLC and MAF4. These findings indicate that GmUBC9 is important for drought stress response and regulation of flowering time in soybean.

DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm.

DNA 6mA modification, an important newly discovered epigenetic mark, plays a crucial role in organisms and has been attracting more and more attention in recent years. The soybean is economically the most important bean in the world, providing vegetable protein for millions of people. However, the distribution pattern and function of 6mA in soybean are still unknown. In this study, we decoded 6mA modification to single-nucleotide resolution in wild and cultivated soybeans, and compared the 6mA differences between cytoplasmic and nuclear genomes and between wild and cultivated soybeans. The motif of 6mA in the nuclear genome was conserved across the two kinds of soybeans, and ANHGA was the most dominant motif in wild and cultivated soybeans. Genes with 6mA modification in the nucleus had higher expression than those without modification. Interestingly, 6mA distribution patterns in cytoplasm for each soybean were significantly different from those in nucleus, which was reported for the first time in soybean. Our research provides a new insight in the deep analysis of cytoplasmic genomic DNA modification in plants.

A Domestication-Associated Gene GmPRR3b Regulates the Circadian Clock and Flowering Time in Soybean

Improved soybean cultivars have been adapted to grow at a wide range of latitudes, enabling expansion of cultivation worldwide. However, the genetic basis of this broad adaptation is still not clear. Here, we report the identification of GmPRR3b as a major flowering time regulatory gene that has been selected during domestication and genetic improvement for geographic expansion. Through a genome-wide association study of a diverse soybean landrace panel consisting of 279 accessions, we identified 16 candidate quantitative loci associated with flowering time and maturity time. The strongest signal resides in the known flowering gene E2, verifying the effectiveness of our approach. We detected strong signals associated with both flowering and maturity time in a genomic region containing GmPRR3b. Haplotype analysis revealed that GmPRR3bH6 is the major form of GmPRR3b that has been utilized during recent breeding of modern cultivars. mRNA profiling analysis showed that GmPRR3bH6 displays rhythmic and photoperiod-dependent expression and is preferentially induced under long-day conditions. Overexpression of GmPRR3bH6 increased main stem node number and yield, while knockout of GmPRR3bH6 using CRISPR/Cas9 technology delayed growth and the floral transition. GmPRR3bH6 appears to act as a transcriptional repressor of multiple predicted circadian clock genes, including GmCCA1a, which directly upregulates J/GmELF3a to modulate flowering time. The causal SNP (Chr12:5520945) likely endows GmPRR3bH6 a moderate but appropriate level of activity, leading to early flowering and vigorous growth traits preferentially selected during broad adaptation of landraces and improvement of cultivars.

Genome-wide association and epistatic interactions of flowering time in soybean cultivar.

Genome-wide association studies (GWAS) have enabled the discovery of candidate markers that play significant roles in various complex traits in plants. Recently, with increased interest in the search for candidate markers, studies on epistatic interactions between single nucleotide polymorphism (SNP) markers have also increased, thus enabling the identification of more candidate markers along with GWAS on single-variant-additive-effect. Here, we focused on the identification of candidate markers associated with flowering time in soybean (Glycine max). A large population of 2,662 cultivated soybean accessions was genotyped using the 180k Axiom® SoyaSNP array, and the genomic architecture of these accessions was investigated to confirm the population structure. Then, GWAS was conducted to evaluate the association between SNP markers and flowering time. A total of 93 significant SNP markers were detected within 59 significant genes, including E1 and E3, which are the main determinants of flowering time. Based on the GWAS results, multilocus epistatic interactions were examined between the significant and non-significant SNP markers. Two significant and 16 non-significant SNP markers were discovered as candidate markers affecting flowering time via interactions with each other. These 18 candidate SNP markers mapped to 18 candidate genes including E1 and E3, and the 18 candidate genes were involved in six major flowering pathways. Although further biological validation is needed, our results provide additional information on the existing flowering time markers and present another option to marker-assisted breeding programs for regulating flowering time of soybean.

Development and validation of InDel markers for identification of QTL underlying flowering time in soybean

Soybean [Glycine max (L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding for many useful agronomic traits. Next-generation sequence data available in public databases provides valuable information and offers new insights for rapid and efficient development of molecular markers. In this study, we attempted to show the feasibility and facility of using genomic resequencing data as raw material for identifying putative InDel markers. First, we identified 17,613 InDel sites among 56 soybean accessions and obtained 12,619 primer pairs. Second, we constructed a genetic map with a random subset of 2841 primer pairs and aligned 300 polymorphic markers with the 20 consensus linkage groups (LG). The total genetic distance was 2347.3cM and the number of mapped markers per LG ranged from 10 to 23 with an average of 15 markers. The largest and smallest genetic distances between adjacent markers were 52.3cM and 0.1cM, respectively. Finally, we validated the genetic map constructed by newly developed InDel markers by QTL analysis of days to flowering (DTF) under different environments. One major QTL (qDTF4) and four minor QTL (qDTF20, qDTF13, qDTF12, and qDTF11) on 5 LGs were detected. These results demonstrate the utility of the InDel markers developed in this work for map-based cloning and molecular breeding in soybean.

Genetic variation of maturity groups and four E genes in the Chinese soybean mini core collection.

The mini core collection (MCC) has been established by streamlining core collection (CC) chosen from China National Genebank including 23,587 soybean (Glycine max) accessions by morphological traits and simple sequence repeat (SSR) markers. Few studies have been focused on the maturity that has been considered as one of the most critical traits for the determination of the adaptation-growing region of the soybean. In the current study, two hundred and ninty-nine accessions of MCC planted for two years at four locations namely in Heihe, Harbin, Jining and Wuhan cities in China were used to assess the variation of maturity in MCC and identify the integrated effect of 4 E loci on flowering and maturity time in soybean. Forty-two North American varieties served as references of maturity groups (MG). Each accession in MCC was classified by comparing with the MG references in the days from VE (emergence) and physiological maturity (R7). The results showed that MCC covered a large range of MGs from MG000 to MGIX/X. Original locations and sowing types were revealed as the major affecting factors for maturity groups of the MCC accessions. The ratio of the reproductive period to the vegetative period (R/V) varied among MCC accessions. Genotyping of 4 maturity genes (i.e. E1, E2, E3 and E4) in 228 accessions indicated that recessive alleles e1, e2, e3 and e4 promoted earlier flowering and shortened the maturity time with different effects, while the dominate alleles were always detected in accessions with longer maturity. The allelic combinations determined the diversification of soybean maturity groups and adaptation to different regions. Our results indicated that the maturity of Chinese soybean MCC showed genetic diversities in phenotype and genotype, which provided information for further MG classification, geographic adaptation analysis of Chinese soybean cultivars, as well as developing new soybean varieties with adaptation to specific regions.