MOTHER-OF-FT-AND-TFL1 regulates the seed oil and protein content in soybean.

Soybean is a major crop that produces valuable seed oil and protein for global consumption. Seed oil and protein are regulated by complex quantitative trait loci (QTLs) and have undergone intensive selections during the domestication of soybean. It is essential to identify the major genetic components and understand their mechanism behind seed oil and protein in soybean. We report that MOTHER-OF-FT-AND-TFL1 (GmMFT) is the gene of a classical QTL that has been reported to regulate seed oil and protein content in many studies. Mutation of MFT decreased seeds oil content and weight in both Arabidopsis and soybean, whereas increased expression of GmMFT enhanced seeds oil content and weight. Haplotype analysis showed that GmMFT has undergone selection, which resulted in the extended haplotype homozygosity in the cultivated soybean and the enriching of the oil-favorable allele in modern soybean cultivars. This work unraveled the GmMFT-mediated mechanism regulating seed oil and protein content and seed weight, and revealed a previously unknown function of MFT that provides new insights into targeted soybean improvement and breeding.

GmGSTU23 Encoding a Tau Class Glutathione S-Transferase Protein Enhances the Salt Tolerance of Soybean (Glycine max L.).

Salt stress has a detrimental impact on crop yield, quality, and profitability. The tau-like glutathione transferases (GSTs) represent a significant group of enzymes that play a crucial role in plant stress responses, including salt stress. In this study, we identified a tau-like glutathione transferase family gene from soybean named GmGSTU23. Expression pattern analysis revealed that GmGSTU23 was predominantly expressed in the roots and flowers and exhibited a concentration-time-specific pattern in response to salt stress. Transgenic lines were generated and subjected to phenotypic characterization under salt stress. The transgenic lines exhibited increased salt tolerance, root length, and fresh weight compared to the wild type. Antioxidant enzyme activity and malondialdehyde content were subsequently measured, and the data revealed no significant differences between the transgenic and wild-type plants in the absence of salt stress. However, under salt stress, the wild-type plants exhibited significantly lower activities of SOD, POD, and CAT than the three transgenic lines, whereas the activity of APX and the content of MDA showed the opposite trend. We identified changes in glutathione pools and associated enzyme activity to gain insights into the underlying mechanisms of the observed phenotypic differences. Notably, under salt stress, the transgenic Arabidopsis's GST activity, GR activity, and GSH content were significantly higher than those of the wild type. In summary, our findings suggest that GmGSTU23 mediates the scavenging of reactive oxygen species and glutathione by enhancing the activity of glutathione transferase, thereby conferring enhanced tolerance to salt stress in plants.

Natural variation of GmFATA1B regulates seed oil content and composition in soybean.

Soybean (Glycine max) produces seeds that are rich in unsaturated fatty acids and is an important oilseed crop worldwide. Seed oil content and composition largely determine the economic value of soybean. Due to natural genetic variation, seed oil content varies substantially across soybean cultivars. Although much progress has been made in elucidating the genetic trajectory underlying fatty acid metabolism and oil biosynthesis in plants, the causal genes for many quantitative trait loci (QTLs) regulating seed oil content in soybean remain to be revealed. In this study, we identified GmFATA1B as the gene underlying a QTL that regulates seed oil content and composition, as well as seed size in soybean. Nine extra amino acids in the conserved region of GmFATA1B impair its function as a fatty acyl-acyl carrier protein thioesterase, thereby affecting seed oil content and composition. Heterogeneously overexpressing the functional GmFATA1B allele in Arabidopsis thaliana increased both the total oil content and the oleic acid and linoleic acid contents of seeds. Our findings uncover a previously unknown locus underlying variation in seed oil content in soybean and lay the foundation for improving seed oil content and composition in soybean.

GsMYB7 encoding a R2R3-type MYB transcription factor enhances the tolerance to aluminum stress in soybean (Glycine max L.).

BACKGROUND: MYB transcription factor (TF) is one of the largest families of TFs in plants and play essential roles in plant growth and development, and is involved in responses to biological and abiotic stress. However, there are few reports on GsMYB7 gene in soybean under aluminum acid stress, and its regulatory mechanism remains unclear. RESULTS: The GsMYB7 protein is localized in the nucleus and has transcriptional activation ability. Quantitative real-time PCR (qRT-PCR) results showed that GsMYB7 held a constitutive expression pattern rich in roots. When AlCl3 concentration was 25 µM, the total root surface area (SA) of GsMYB7 transgenic lines were 34.97% higher than that of wild-type Huachun 6 (HC6). While the accumulation of Al3+ in root tip of transgenic plants after aluminum treatment was 17.39% lower than that of wild-type. RNA-sequencing analysis indicated that over 1181 genes were regulated by GsMYB7 and aluminum stress. Among all the regulated genes, the expression levels of glutathione peroxidase, protein kinase, cytochrome and other genes in the transgenic lines were significantly higher than those in wild type by acidic aluminum stress. The bioinformatics and qRT-PCR results showed that 9 candidate genes were induced under the treatments of acidic aluminum stress which were indirectly and/or directly regulated by GsMYB7. After AlCl3 treatments, the transcripts of these genes in GsMYB7 transgenic seedlings were significantly higher than those of wide-type HC6. CONCLUSIONS: The results suggested that GsMYB7 may enhance soybean tolerance to acidic aluminum stress by regulating the downstream genes.

Identification of quantitative trait loci (QTLs) and candidate genes of seed Iron and zinc content in soybean [Glycine max (L.) Merr.].

BACKGROUND: Deciphering the hereditary mechanism of seed iron (Fe) and zinc (Zn) content in soybean is important and sustainable to address the "hidden hunger" that presently affects approximately 2 billion people worldwide. Therefore, in order to detect genomic regions related to soybean seed Fe and Zn content, a recombinant inbred line (RIL) population with 248 lines was assessed in four environments to detect Quantitative Trait Loci (QTLs) related to soybean seed Fe and Zn content. RESULT: Wide variation was found in seed Fe and Zn content in four environments, and genotype, environment, and genotype × environment interactions had significant influences on both the seed Fe and Zn content. A positive correlation was observed between seed Fe content and seed Zn content, and broad-sense heritability (H2) of seed Fe and Zn content were 0.73 and 0.75, respectively. In this study, five QTLs for seed Fe content were detected with 4.57 - 32.71% of phenotypic variation explained (PVE) and logarithm of odds (LOD) scores ranging from 3.60 to 33.79. Five QTLs controlling the seed Zn content were detected, and they individually explained 3.35 to 26.48% of the phenotypic variation, with LOD scores ranging from 3.64 to 20.4. Meanwhile, 409,541 high-quality single-nucleotide variants (SNVs) and 85,102 InDels (except intergenic regions) between two bi-parental lines were identified by whole genome resequencing. A total of 12 candidate genes were reported in one major QTL for seed Fe content and two major QTLs for seed Zn content, with the help of RNA-Seq analysis, gene ontology (GO) enrichment, gene annotation, and bi-parental whole genome sequencing (WGS) data. CONCLUSIONS: Limited studies were performed about microelement of soybean, so these results may play an important role in the biofortification of Fe and Zn and accelerate the development of marker-assisted selection (MAS) for breeding soybeans fortified with iron and zinc.

GsERF1 enhances Arabidopsis thaliana aluminum tolerance through an ethylene-mediated pathway.

Ethylene response factor (ERF) transcription factors constitute a subfamily of the AP2/ERF superfamily in plants and play multiple roles in plant growth and development as well as in stress responses. In this study, the GsERF1 gene from the wild soybean BW69 line (an Al-resistant Glycine soja line) was rapidly induced in response to aluminum stress. Quantitative real-time PCR (qRT-PCR) analysis showed that the GsERF1 gene maintained a constitutive expression pattern and was induced in soybean in response to aluminum stress, with increased amounts of transcripts detected in the roots. The putative GsERF1 protein, which contains an AP2 domain, was located in the nucleus and maintained transactivation activity. In addition, under AlCl3 treatment, GsERF1 overexpression increased the relative growth rate of the roots of Arabidopsis and weakened the hematoxylin staining of hairy roots. Ethylene synthesis-related genes such as ACS4, ACS5 and ACS6 were upregulated in GsERF1 transgenic lines compared with the wild type under AlCl3 treatment. Furthermore, the expression levels of stress/ABA-responsive marker genes, including ABI1, ABI2, ABI4, ABI5 and RD29B, in the GsERF1 transgenic lines were affected by AlCl3 treatment, unlike those in the wild type. Taken together, the results indicated that overexpression of GsERF1 may enhance aluminum tolerance of Arabidopsis through an ethylene-mediated pathway and/or ABA signaling pathway, the findings of which lay a foundation for breeding soybean plants tolerant to aluminum stress.

Silicon-enhanced tolerance to cadmium toxicity in soybean by enhancing antioxidant defense capacity and changing cadmium distribution and transport.

Cadmium (Cd) is a widely distributed heavy metal that is toxic to plants and humans. Although silicon (Si) has been reported to reduce Cd accumulation and toxicity in plants, evidence on the functions of Si and its mechanisms in the possible alleviation of soybean are limited. Therefore, a controlled experiment was conducted to investigate the impacts and mechanisms of Si on Cd retention in soybean. Here, we determined the growth index, Cd distribution, and antioxidant activity systems of Si, as well as expression levels of differentially expressed genes (DEGs) in Si under Cd stress, and conducted RNA-seq analysis. We not only found that Si can significantly promote soybean plant growth, increase plant antioxidant activities, and reduce the Cd translocation factor, but also revealed that a total of 636 DEGs were shared between CK and Cd, CK and Cd + Si, and Cd and Cd + Si. Moreover, several genes were significantly enriched in antioxidant systems and Cd distribution and transport systems. Therefore, the expression status of Si-mediated Cd stress response genes is likely involved in improving oxidative stress and changing Cd uptake and transport, as well as improving plant growth that contributes to Si alleviating Cd toxicity in plants. Moreover, numerous potential target genes were identified for the engineering of Cd-tolerant cultivars in soybean breeding programs.

GmWRKY81 Encoding a WRKY Transcription Factor Enhances Aluminum Tolerance in Soybean.

Aluminum (Al) toxicity is an essential factor that adversely limits soybean (Glycine max (L.) Merr.) growth in acid soils. WRKY transcription factors play important roles in soybean responses to abiotic stresses. Here, GmWRKY81 was screened from genes that were differentially expressed under Al treatment in Al-tolerant soybean Baxi10 and Al-sensitive soybean Bendi2. We found that GmWRKY81 was significantly induced by 20 µM AlCl3 and upregulated by AlCl3 treatment for 2 h. In different tissues, the expression of GmWRKY81 was differentially induced. In 0-1 cm root tips, the expression of GmWRKY81 was induced to the highest level. The overexpression of GmWRKY81 in soybean resulted in higher relative root elongation, root weight, depth, root length, volume, number of root tips and peroxidase activity but lower root average diameter, malonaldehyde and H2O2 contents, indicating enhanced Al tolerance. Moreover, RNA-seq identified 205 upregulated and 108 downregulated genes in GmWRKY81 transgenic lines. Fifteen of these genes that were differentially expressed in both AlCl3-treated and GmWRKY81-overexpressing soybean had the W-box element, which can bind to the upstream-conserved WRKY domain. Overall, the combined functional analysis indicates that GmWRKY81 may improve soybean Al tolerance by regulating downstream genes participating in Al3+ transport, organic acid secretion and antioxidant reactions.

Identification of an ATP-Binding Cassette Transporter Implicated in Aluminum Tolerance in Wild Soybean (Glycine soja).

The toxicity of aluminum (Al) in acidic soil limits global crop yield. The ATP-binding cassette (ABC) transporter-like gene superfamily has functions and structures related to transportation, so it responds to aluminum stress in plants. In this study, one half-size ABC transporter gene was isolated from wild soybeans (Glycine soja) and designated GsABCI1. By real-time qPCR, GsABCI1 was identified as not specifically expressed in tissues. Phenotype identification of the overexpressed transgenic lines showed increased tolerance to aluminum. Furthermore, GsABCI1 transgenic plants exhibited some resistance to aluminum treatment by ion translocation or changing root components. This work on the GsABCI1 identified the molecular function, which provided useful information for understanding the gene function of the ABC family and the development of new aluminum-tolerant soybean germplasm.

Wild Soybean Oxalyl-CoA Synthetase Degrades Oxalate and Affects the Tolerance to Cadmium and Aluminum Stresses.

Acyl activating enzyme 3 (AAE3) was identified as being involved in the acetylation pathway of oxalate degradation, which regulates the responses to biotic and abiotic stresses in various higher plants. Here, we investigated the role of Glycine sojaAAE3 (GsAAE3) in Cadmium (Cd) and Aluminum (Al) tolerances. The recombinant GsAAE3 protein showed high activity toward oxalate, with a Km of 105.10 ± 12.30 µM and Vmax of 12.64 ± 0.34 µmol min-1 mg-1 protein, suggesting that it functions as an oxalyl-CoA synthetase. The expression of a GsAAE3-green fluorescent protein (GFP) fusion protein in tobacco leaves did not reveal a specific subcellular localization pattern of GsAAE3. An analysis of the GsAAE3 expression pattern revealed an increase in GsAAE3 expression in response to Cd and Al stresses, and it is mainly expressed in root tips. Furthermore, oxalate accumulation induced by Cd and Al contributes to the inhibition of root growth in wild soybean. Importantly, GsAAE3 overexpression increases Cd and Al tolerances in A. thaliana and soybean hairy roots, which is associated with a decrease in oxalate accumulation. Taken together, our data provide evidence that the GsAAE3-encoded protein plays an important role in coping with Cd and Al stresses.

GsMAS1 Encoding a MADS-box Transcription Factor Enhances the Tolerance to Aluminum Stress in Arabidopsis thaliana.

The MADS-box transcription factors (TFs) are essential in regulating plant growth and development, and conferring abiotic and metal stress resistance. This study aims to investigate GsMAS1 function in conferring tolerance to aluminum stress in Arabidopsis. The GsMAS1 from the wild soybean BW69 line encodes a MADS-box transcription factor in Glycine soja by bioinformatics analysis. The putative GsMAS1 protein was localized in the nucleus. The GsMAS1 gene was rich in soybean roots presenting a constitutive expression pattern and induced by aluminum stress with a concentration-time specific pattern. The analysis of phenotypic observation demonstrated that overexpression of GsMAS1 enhanced the tolerance of Arabidopsis plants to aluminum (Al) stress with larger values of relative root length and higher proline accumulation compared to those of wild type at the AlCl3 treatments. The genes and/or pathways regulated by GsMAS1 were further investigated under Al stress by qRT-PCR. The results indicated that six genes resistant to Al stress were upregulated, whereas AtALMT1 and STOP2 were significantly activated by Al stress and GsMAS1 overexpression. After treatment of 50 µM AlCl3, the RNA abundance of AtALMT1 and STOP2 went up to 17-fold and 37-fold than those in wild type, respectively. Whereas the RNA transcripts of AtALMT1 and STOP2 were much higher than those in wild type with over 82% and 67% of relative expression in GsMAS1 transgenic plants, respectively. In short, the results suggest that GsMAS1 may increase resistance to Al toxicity through certain pathways related to Al stress in Arabidopsis.

Characterization of the Soybean GmIREG Family Genes and the Function of GmIREG3 in Conferring Tolerance to Aluminum Stress.

The IREG (IRON REGULATED/ferroportin) family of genes plays vital roles in regulating the homeostasis of iron and conferring metal stress. This study aims to identify soybean IREG family genes and characterize the function of GmIREG3 in conferring tolerance to aluminum stress. Bioinformatics and expression analyses were conducted to identify six soybean IREG family genes. One GmIREG, whose expression was significantly enhanced by aluminum stress, GmIREG3, was studied in more detail to determine its possible role in conferring tolerance to such stress. In total, six potential IREG-encoding genes with the domain of Ferroportin1 (PF06963) were characterized in the soybean genome. Analysis of the GmIREG3 root tissue expression patterns, subcellular localizations, and root relative elongation and aluminum content of transgenic Arabidopsis overexpressing GmIREG3 demonstrated that GmIREG3 is a tonoplast localization protein that increases transgenic Arabidopsis aluminum resistance but does not alter tolerance to Co and Ni. The systematic analysis of the GmIREG gene family reported herein provides valuable information for further studies on the biological roles of GmIREGs in conferring tolerance to metal stress. GmIREG3 contributes to aluminum resistance and plays a role similar to that of FeIREG3. The functions of other GmIREG genes need to be further clarified in terms of whether they confer tolerance to metal stress or other biological functions.

Heterologous Expression of a Glycine soja C2H2 Zinc Finger Gene Improves Aluminum Tolerance in Arabidopsis.

Aluminum (Al) toxicity limits plant growth and has a major impact on the agricultural productivity in acidic soils. The zinc-finger protein (ZFP) family plays multiple roles in plant development and abiotic stresses. Although previous reports have confirmed the function of these genes, their transcriptional mechanisms in wild soybean (Glycine soja) are unclear. In this study, GsGIS3 was isolated from Al-tolerant wild soybean gene expression profiles to be functionally characterized in Arabidopsis. Laser confocal microscopic observations demonstrated that GsGIS3 is a nuclear protein, containing one C2H2 zinc-finger structure. Our results show that the expression of GsGIS3 was of a much higher level in the stem than in the leaf and root and was upregulated under AlCl3, NaCl or GA3 treatment. Compared to the control, overexpression of GsGIS3 in Arabidopsis improved Al tolerance in transgenic lines with more root growth, higher proline and lower Malondialdehyde (MDA) accumulation under concentrations of AlCl3. Analysis of hematoxylin staining indicated that GsGIS3 enhanced the resistance of transgenic plants to Al toxicity by reducing Al accumulation in Arabidopsis roots. Moreover, GsGIS3 expression in Arabidopsis enhanced the expression of Al-tolerance-related genes. Taken together, our findings indicate that GsGIS3, as a C2H2 ZFP, may enhance tolerance to Al toxicity through positive regulation of Al-tolerance-related genes.

QTL fine-mapping of soybean (Glycine max L.) leaf type associated traits in two RILs populations.

BACKGROUND: The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to identify quantitative trait loci (QTLs) affecting leaf type traits, two advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3; GB, Guizao 1 × Brazil 13) populations were introduced to score phenotypic values in plants across nine different environments (years, seasons, locations and soybean growth stages). Two restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage maps with an average distance of 1.00 centimorgan (cM) between adjacent bin markers were utilized for QTL fine mapping. RESULTS: Correlation analysis showed that most of the traits were correlated with each other and regulated both by hereditary and environmental factors. A total of 190 QTLs were identified for leaf type associated traits in the two populations, of which 14 loci were found to be environmentally stable. Moreover, these detected QTLs were categorized into 34 QTL hotspots, and four important QTL hotspots with phenotypic variance ranging from 3.89-23.13% were highlighted. Furthermore, Glyma04g05840, Glyma19g37820, Glyma14g07140 and Glyma19g39340 were predicted in the intervals of the stable loci and important QTL hotspots for leaf type traits by adopting Gene Ontology (GO) enrichment analysis. CONCLUSIONS: Our findings of the QTLs and the putative genes will be beneficial to gain new insights into the genetic basis for soybean leaf type traits and may further accelerate the breeding process for reasonable leaf type soybean.

Genetic mapping of powdery mildew resistance genes in soybean by high-throughput genome-wide sequencing.

KEY MESSAGE: The Mendelian locus conferring resistance to powdery mildew in soybean was precisely mapped using a combination of phenotypic screening, genetic analyses, and high-throughput genome-wide sequencing. Powdery mildew (PMD), caused by the fungus Microsphaera diffusa Cooke & Peck, leads to considerable yield losses in soybean [Glycine max (L.) Merr.] under favourable environmental conditions and can be controlled by identifying germplasm resources with resistance genes. In this study, resistance to M. diffusa among resistant varieties B3, Fudou234, and B13 is mapped as a single Mendelian locus using three mapping populations derived from crossing susceptible with resistant cultivars. The position of the PMD resistance locus in B3 is located between simple sequence repeat (SSR) markers GMES6959 and Satt_393 on chromosome 16, at genetic distances of 7.1 cM and 4.6 cM, respectively. To more finely map the PMD resistance gene, a high-density genetic map was constructed using 248 F8 recombinant inbred lines derived from a cross of Guizao1 × B13. The final map includes 3748 bins and is 3031.9 cM in length, with an average distance of 0.81 cM between adjacent markers. This genotypic analysis resulted in the precise delineation of the B13 PMD resistance locus to a 188.06-kb genomic region on chromosome 16 that harbours 28 genes, including 17 disease resistance (R)-like genes in the reference Williams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed differences in the expression levels of 9 R-like genes between the resistant and susceptible parents. These results provide useful information for marker-assisted breeding and gene cloning for PMD resistance.

GsMATE encoding a multidrug and toxic compound extrusion transporter enhances aluminum tolerance in Arabidopsis thaliana.

BACKGROUND: Multidrug and toxic compound extrusion (MATE) transporters, which exist widely in plants, function as crucial regulators in plant resistance to aluminum (Al) toxicity by inducing citrate efflux. However, the functions of most MATE family members in soybean (Glycine soja) remain to be elucidated. RESULTS: Expression pattern analysis showed that GsMATE was constitutively expressed in different soybean organs, with the highest level in root compared with those in stem, leaf and cotyledon. In addition, Al stress induced expression of GsMATE in soybean. Temporal analysis indicated that GsMATE expression was greatly enhanced by increasing concentrations of aluminum [Al3+] after short exposure, reaching the high levels detected in the BW69 (Al-resistant) and the JW81 (Al-sensitive) lines of Glycine soja of wild soybean at 6 h and 8 h, respectively. Furthermore, transient GsMATE expression in Arabidopsis protoplasts showed that GsMATE protein localized to the plasma membrane. Overexpression of GsMATE on an Arabidopsis columbia-0 (Col-0) background resulted in increased Al tolerance in transgenic plants. Analysis of hematoxylin staining showed that the roots of GsMATE transgenic lines were stained less intensely than those of the wild-type exposured to the same AlCl3 concentrations. Therefore, GsMATE enhanced the resistance of transgenic plants to Al toxicity by reducing Al accumulation in Arabidopsis roots. CONCLUSIONS: In summary, our results indicate that GsMATE is responsive to aluminum stress and may participate in the regulation of sensitivity to Al toxicity in Arabidopsis. In addition, the GsMATE protein is an Al-induced citrate transporter of the MATE family and exerts an essential role in Al tolerance in Glycine soja.

Fine-mapping of QTLs for individual and total isoflavone content in soybean (Glycine max L.) using a high-density genetic map.

KEY MESSAGE: Fifteen stable QTLs were identified using a high-density soybean genetic map across multiple environments. One major QTL, qIF5-1, contributing to total isoflavone content explained phenotypic variance 49.38, 43.27, 46.59, 45.15 and 52.50%, respectively. Soybeans (Glycine max L.) are a major source of dietary isoflavones. To identify novel quantitative trait loci (QTL) underlying isoflavone content, and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population comprised of 196 F7:8-10 recombinant inbred lines (RILs, Huachun 2 × Wayao) was utilized to evaluate individual and total isoflavone content in plants grown in four different environments in Guangdong. A high-density genetic linkage map containing 3469 recombination bin markers based on 0.2 × restriction site-associated DNA tag sequencing (RAD-seq) technology was used to finely map QTLs for both individual and total isoflavone contents. Correlation analyses showed that total isoflavone content, and that of five individual isoflavone, was significantly correlated across the four environments. Based on the high-density genetic linkage map, a total of 15 stable quantitative trait loci (QTLs) associated with isoflavone content across multiple environments were mapped onto chromosomes 02, 05, 07, 09, 10, 11, 13, 16, 17, and 19. Further, one of them, qIF5-1, localized to chromosomes 05 (38,434,171-39,045,620 bp) contributed to almost all isoflavone components across all environments, and explained 6.37-59.95% of the phenotypic variance, especially explained 49.38, 43.27, 46.59, 45.15 and 52.50% for total isoflavone. The results obtained in the present study will pave the way for a better understanding of the genetics of isoflavone accumulation and reveals the scope available for improvement of isoflavone content through marker-assisted selection.

Acid phosphatase gene GmHAD1 linked to low phosphorus tolerance in soybean, through fine mapping.

KEY MESSAGE: Map-based cloning identified GmHAD1, a gene which encodes a HAD-like acid phosphatase, associated with soybean tolerance to low phosphorus stress. Phosphorus (P) deficiency in soils is a major limiting factor for crop growth worldwide. Plants may adapt to low phosphorus (LP) conditions via changes to root morphology, including the number, length, orientation, and branching of the principal root classes. To elucidate the genetic mechanisms for LP tolerance in soybean, quantitative trait loci (QTL) related to root morphology responses to LP were identified via hydroponic experiments. In total, we identified 14 major loci associated with these traits in a RIL population. The log-likelihood scores ranged from 2.81 to 7.43, explaining 4.23-13.98% of phenotypic variance. A major locus on chromosome 08, named qP8-2, was co-localized with an important P efficiency QTL (qPE8), containing phosphatase genes GmACP1 and GmACP2. Another major locus on chromosome 10 named qP10-2 explained 4.80-13.98% of the total phenotypic variance in root morphology. The qP10-2 contains GmHAD1, a gene which encodes an acid phosphatase. In the transgenic soybean hairy roots, GmHAD1 overexpression increased P efficiency by 8.4-16.5% relative to the control. Transgenic Arabidopsis plants had higher biomass than wild-type plants across both short- and long-term P reduction. These results suggest that GmHAD1, an acid phosphatase gene, improved the utilization of organic phosphate by soybean and Arabidopsis plants.

Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing.

BACKGROUND: One of the overarching goals of soybean breeding is to develop lines that combine increased yield with improved quality characteristics. High-density-marker QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped a recombinant inbred line (RIL) population (Zhonghuang 24 × Huaxia 3) using a restriction-site associated DNA sequencing (RAD-seq) approach. A high-density soybean genetic map was constructed and used to identify several QTLs that were shown to influence six yield-related and two quality traits. RESULTS: A total of 47,472 single-nucleotide polymorphisms (SNPs) were detected for the RILs that were integrated into 2639 recombination bin units, with an average distance of 1.00 cM between adjacent markers. Forty seven QTLs for yield-related traits and 13 QTLs for grain quality traits were found to be distributed on 16 chromosomes in the 2 year studies. Among them, 18 QTLs were stable, and were identified in both analyses. Twenty six QTLs were identified for the first time, with a single QTL (qNN19a) in a 56 kb region explaining 32.56% of phenotypic variation, and an additional 10 of these were novel, stable QTLs. Moreover, 8 QTL hotpots on four different chromosomes were identified for the correlated traits. CONCLUSIONS: With RAD-sequencing, some novel QTLs and important QTL clusters for both yield-related and quality traits were identified based on a new, high-density bin linkage map. Three predicted genes were selected as candidates that likely have a direct or indirect influence on both yield and quality in soybean. Our findings will be helpful for understanding common genetic control mechanisms of co-localized traits and to select cultivars for further analysis to predictably modulate soybean yield and quality simultaneously.

Fine mapping of a Phytophthora-resistance gene RpsWY in soybean (Glycine max L.) by high-throughput genome-wide sequencing.

KEY MESSAGE: Using a combination of phenotypic screening, genetic and statistical analyses, and high-throughput genome-wide sequencing, we have finely mapped a dominant Phytophthora resistance gene in soybean cultivar Wayao. Phytophthora root rot (PRR) caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. Two soybean populations of 191 F2 individuals and 196 F7:8 recombinant inbred lines (RILs) were developed to map Rps gene by crossing a susceptible cultivar Huachun 2 with the resistant cultivar Wayao. Genetic analysis of the F2 population indicated that PRR resistance in Wayao was controlled by a single dominant gene, temporarily named RpsWY, which was mapped on chromosome 3. A high-density genetic linkage bin map was constructed using 3469 recombination bins of the RILs to explore the candidate genes by the high-throughput genome-wide sequencing. The results of genotypic analysis showed that the RpsWY gene was located in bin 401 between 4466230 and 4502773 bp on chromosome 3 through line 71 and 100 of the RILs. Four predicted genes (Glyma03g04350, Glyma03g04360, Glyma03g04370, and Glyma03g04380) were found at the narrowed region of 36.5 kb in bin 401. These results suggest that the high-throughput genome-wide resequencing is an effective method to fine map PRR candidate genes.