Deyue Yu

Detection of quantitative trait loci for phosphorus deficiency tolerance at soybean seedling stage

Phosphorus deficiency is a primary constraint to soybean productivity in acid and calcareous soils. Our aim was to map quantitative trait loci (QTL) controlling phosphorus deficiency tolerance using 152 recombinant inbred lines derived from a cross between the P stress tolerant variety Nannong94-156 and the P stress sensitive variety Bogao. Five traits were used as parameters to evaluate phosphorus deficiency tolerance at seedling stage under different phosphorus levels in experiments 2005 and 2006. As a result, thirty-four additive QTLs were detected on nine linkage groups, with corresponding contribution ratios of 6.6–19.3%. There were three clusters of QTL found in genomic regions S506-Satt534 (on linkage group B2-1), Sat_183-Satt274 (on linkage group D1bxa0+xa0W), and Sat_185-Satt012 (on linkage group G). The locus flanked by Sat_183-Satt274 on linkage group D1bxa0+xa0W was coincident with four previously discovered QTLs with phosphorus efficiency. Another interesting locus flanked by Sat_185-Satt012 on linkage group G was detected across years. The identified QTL will be useful to improve the stress resistance of soybean against a complex nutritional disorder caused by phosphorus deficiency. In addition, more QTLs were detected under low phosphorus condition and some QTLs were detected that specifically expressed under different phosphorus levels. These particular QTLs could help provide greater understanding of the genetic basis of phosphorus efficiency in soybean.

Mapping of SMV resistance gene Rsc-7 by SSR markers in soybean

Soybean mosaic virus (SMV) is one of the most prevalent pathogens that limit soybean production. In this study, segregation ratios of resistant plants to susceptible plants in P1, P2, F1, F2 populations of Kefeng No. 1 (P1)×Nannong 1138-2 (P2) and derived RIL populations, were used to study the inheritance of resistance to the SMV strain SC-7. Populations Kefeng No. 1 and F1 were found to be completely resistant to this SMV strain while Nannong 1138-2 was susceptible to it. The F2 and RIL populations segregated to fit a ratio of 3:1 and 1:1for resistant plants to susceptible ones, respectively. These results indicated that a single dominant gene, designated as Rsc-7, controlled resistance to the SMV strain SC-7 in Kefeng No.1. SSR markers were used to analyze the RIL population and MAPMAKER/EXP 3.0b was employed to establish linkage between markers and this resistance gene. Combining the data of SSRs and resistance identification, a soybean genetic map was constructed. This map, covering 2625.9xa0cM of the genome, converged into 24 linkage groups, consisted of 221 SSR markers and the resistance gene Rsc-7. The Rsc-7 gene was mapped to the molecular linkage group G8-D1b+W. SSR markers Satt266, Satt634, Satt558, Satt157, and Satt698 were found linked to Rsc-7 with distances of 43.7, 18.1, 26.6, 36.4 and 37.9xa0cM, respectively.

Genome-wide association analysis detecting significant single nucleotide polymorphisms for chlorophyll and chlorophyll fluorescence parameters in soybean (Glycine max) landraces

Chlorophyll fluorescence parameters are generally used to characterize the intrinsic action of photosystem II (PSII), which is interrelated with the photosynthetic capacity. Mapping of quantitative trait loci for chlorophyll fluorescence parameters and associated traits is important for genetic improvement in soybean. In this study, a genome-wide association analysis was conducted to detect key single-nucleotide polymorphisms (SNPs) associated with chlorophyll content (chl) and chlorophyll fluorescence using 1,536 SNPs in a soybean landraces panel. The analysis revealed significant correlations among chl and five chlorophyll fluorescence parameters, including maximum quantum yield of PSII primary photochemistry in the dark-adapted state (Fv/Fm), light energy absorbed per reaction center (ABS/RC), quantum yield for electron transport (ETo/ABS), probability that a trapped exciton moves an electron into the electron transport chain beyond QA− (ETo/TRo), and performance index on absorption basis (PIABS). Genome-wide association analysis using a mixed linear model detected 51 SNPs associated with chl and chlorophyll fluorescence parameters. Among these identified SNPs, 14 SNPs were co-associated with two or more different traits in this study, and 8 SNPs were co-associated with soybean yield and yield components in our previous study. These significant SNPs will help to better understand the genetic basis of photosynthesis-related physiological traits, and facilitate the pyramiding of favorable alleles for photosynthetic traits in soybean marker assisted selection schemes for high photosynthetic efficiency.

Identification of quantitative trait loci associated with salt tolerance during seedling growth in soybean (Glycine max L.)

Salt stress is an important factor affecting the growth and development of soybean. The inheritance and expressionoftraitsassociatedwithsalttoleranceduringtheseedlingstagearecomplex.Thepresentstudywasconductedto identifyquantitativetraitloci(QTLs)associatedwithsalttoleranceduringseedlinggrowthinsoybean.Fieldandgreenhouse experimentswereconductedtoevaluate184recombinantinbredlines(RILs)derivedfromacrossbetweenKefengNo.1and Nannong1138-2forsalttoleranceandQTLsthatareassociatedwithsalttolerance.ThemolecularmapofthisRILpopulation, covering 2625.9cM of the genome, converged into 24 linkage groups and consisted of 221 SSR markers and 1 disease- resistant gene(Rsc-7).QTLmappingwas conductedusingWinQTLCart. Eight putativeQTLssignificantlyassociated with salt tolerance were identified. One QTL was identified both in field and greenhouse experiments. In the field, salt tolerance wasassessed(tolerancerating,TR)visuallyona0(death)to5(unaffectedbysaltstress)scale.ThreeQTLsweredetectedon two linkage groups explaining 7.1-19.7% of the total phenotypic variance for salt tolerance. In the greenhouse, plant survival days (PSD) and percentage of plant survival (PPS) under salt stress were measured. Six QTLs were detected on six linkage groups, and explained 7.8-19.2% of total phenotypic variation for salt tolerance. A major QTL was identified betweenmarkersSat_164andSat_358onlinkagegroupGinboththe fieldandgreenhouse.ThisQTLqppsN.1wasidentified in the same location as a salt tolerance QTL previously reported in soybean. The detection of new QTLs will provide important information for marker-assisted selection (MAS) and further genetic studies on salt tolerance in soybean.

Proteomics-based analysis of novel genes involved in response toward soybean mosaic virus infection.

Soybean mosaic virus (SMV) is one of the most serious virus diseases of soybean. However, little is known about the molecular basis of the soybean defense mechanism against this pathogen. We identified differentially expressed proteins in soybean leaves infected with SMV by proteomic approaches. Twenty-eight protein spots that showed ≥2-fold difference in intensity were identified between mock-inoculated and SMV-infected samples. Among them, 16 spots were upregulated and 12 spots were downregulated in the SMV-infected samples. We recovered 25 of the 28 differentially expressed proteins from two-dimensional electrophoresis (2-DE) gels. These spots were identified as 16 different proteins by Matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and tandem TOF/TOF MS, and were potentially involved in protein degradation, defense signal transfer, reactive oxygen, cell wall reinforcement, and energy and metabolism regulation. Gene expression analysis of 13 genes by quantitative real time polymerase chain reaction (qRT–PCR) showed that metabolism genes and photosynthesis genes were downregulated at all time points. One energy gene was downregulated, whereas another energy gene was upregulated at five of the six time points. The other interesting genes that were altered by SMV infection showed changes in transcription over time. This is the first extensive application of proteomics to the SMV-soybean interaction. These results contribute to a better understanding of the molecular basis of soybean’s responses to SMV.

Genetic structure composed of additive QTL, epistatic QTL pairs and collective unmapped minor QTL conferring oil content and fatty acid components of soybeans

The relative importance of various types of quantitative trait locus (QTL) conferring oil content and its fatty acid components in soybean seeds was assessed through testing a recombinant inbred line (RIL) population (derived from KF1xa0×xa0NN1138-2) in randomized blocks experiments in 2004–2006. The contents of oil and oleic, linoleic, linolenic, palmitic and stearic acids were determined with automatic Soxhlet extraction system and gas chromatography, respectively. Based on the established genetic linkage map with 834 markers, QTLNetwork2.0 was used to detect QTL under the genetic model composed of additive, additivexa0×xa0additive (epistasis), additivexa0×xa0year and epistasisxa0×xa0year effects. The contributions to the phenotypic variances of additive QTL and epistatic QTL pairs were 15.7% (3 QTL) and 10.8% (2 pairs) for oil content, 10.4% (3 QTL) and 10.3% (3 pairs) for oleic acid, 11.6% (3 QTL) and 8.5% (2 pairs) for linoleic acid, 28.5% (7 QTL) and 7.6% (3 pairs) for linolenic acid, 27.0% (6 QTL) and 16.6% (7 pairs) for palmitic acid and 29.7% (5 QTL) and 4.3% (1 pair) for stearic acid, respectively. Those of additive QTL by year interaction were small and no epistatic QTL pair by year interaction was found. Among the 27 additive QTL and 36 epistatic QTL (18 pairs), three are duplicated between the two QTL types. A large difference was found between the genotypic variance among RILs and the total variance of mapped QTL, which accounted for 52.9–74.8% of the genotypic variation, much larger than those of additive QTL and epistatic QTL pairs. This part of variance was recognized as that due to a collection of unmapped minor QTL, like polygenes in biometrical genetics, and was designated as collective unmapped minor QTL. The results challenge the breeders for how to pyramid different types of QTL. In addition, the present study supports the mapping strategy of a full model scanning followed by verification with other procedures corresponding to the first results.

Isolation and Functional Characterization of a SERK Gene from Soybean (Glycine max (L.) Merr.)

It is well accepted that somatic embryogenesis serves a primary role in plant regeneration. However, it is also a model system to explore the regulatory and morphogenetic events in the life of a plant. To date, a suite of genes that serve important roles in somatic embryogenesis have been isolated and identified. In the present study, a novel gene designated as GmSERK1 was isolated from soybean (Glycine max (L.) Merr). Sequence and structural analysis determined that the GmSERK1 protein, which encodes 624 amino acids, belongs to the somatic embryogenesis receptor-like kinase (SERK) gene family. GmSERK1 shared all the characteristic domains of the SERK family, including five leucine-rich repeats, one proline-rich region motif, transmembrane domain, and kinase domains. DNA gel blot analysis indicated that a single copy of the GmSERK1 gene resides in the soybean genome. The GmSERK1 tissue-specific and induced expression patterns were explored using quantitative real-time PCR. Dissimilar expression levels in various tissues under different treatments were found. In addition, transient expression experiments in onion epidermal cells indicated that the GmSERK1 protein was located on the plasma membrane. The results from this study suggested that GmSERK1, a member of the SERK gene family, exhibits a broader role in various aspects of plant development and function, in addition to its basic functions in somatic embryogenesis.

Genetic dissection of the relationship of apparent biological yield and apparent harvest index with seed yield and yield related traitsin soybean

Improving seed yield is an important goal of soybean breeding programs. In this investigation, two sets of recombinant inbred line (RIL) populations with 184 and 151 RI lines derived from Kefeng No. 1 × Nannong 1138-2 (F7:11, NJRIKY) and Bogao × Nannong 94-156 (F7:10, NJ(SP)BN) were used to map QTLs for five agronomic and physiological traits including plant height (PH), days to maturity (MD), seed yield (SY), apparent biological yield (ABY) and apparent harvest index (AHI), and correlation analysis among the five traits were also conducted. 221 SSR markers and 248 markers were used to construct genetic maps in NJRIKY and NJ(SP)BN population, respectively. The QTL mapping was done with the program WinQTLCart. The results indicated there were 14 putative QTL significantly associated with five agronomic and physiological traits in two sets of RIL populations and several coincident QTLs associated to SY and it related traits were observed. For SY, two QTLs, qsyC2.1 mapped on LG-C2 in NJRIKY and qsyL.1 on LG-L in NJ(SP)BN coincided or neared with QTLs detected in previous reports, and one major SY QTLs were detected on LG-O in which none of QTLs for yield were identified before. QTLs for SY co-located with QTLs for ABY and/or AHI and these co-located QTLs in each of genomic regions all showed their additive effects in the same direction except for SY/AHI QTLs on LG-C2 in NJ(SP)BN. These revealed that SY increase could be genetically explained by either biological yield enhancement and/or harvest index improvement. It was also found that some QTLs for PH in both sets of RIL population co-located with some QTLs for yield and/or ABY, and all of the coincident showed the additive effects in the same direction, but none of the QTLs was found to co-locate to any of the AHI QTLs.

Polymorphisms of soybean isoflavone synthase and flavanone 3-hydroxylase genes are associated with soybean mosaic virus resistance

Soybean mosaic disease, caused by soybean mosaic virus (SMV), is one of the most devastating diseases that limit soybean production throughout the world. Soybean isoflavone synthase (IFS) and flavanone 3-hydroxylase (F3H) genes catalyze the production of isoflavones and flavonoids, the increase of which is correlated with increased disease resistance. We have cloned, sequenced, and analyzed the IFS1, IFS2 and F3H genomic regions from 33 Chinese soybean accessions including 16 Glycine soja and 17 Glycine max. High nucleotide diversity and low extent of linkage disequilibrium (LD) in these three genes provided sufficient genetic resolution for association mapping. As a result, a set of single nucleotide polymorphisms (SNPs) with significant (Pxa0<xa00.05) association to SMV strain SC-3 and SC-7 resistance were discovered in these genes. Among them, the SNP haplotype ‘TCACAACGA-TACA’ in IFS1 gene was found to be extremely significantly (Pxa0<xa00.01) associated with SMV SC-3 resistance. After 7xa0days of SC-3 inoculation, the expression level of IFS1 gene in the two SC-3 resistance accessions that have this significant site continued to increased and reach to 30–160 folds high, while in the SC-3 susceptible accession which does not carry the significant site the expression level decreased to near zero. These polymorphisms were corresponding to the trait variance and thus can be considered as the candidate sites for functional molecular markers for future SMV resistance breeding.