Genome-wide association study for flowering time,maturity dates and plant height in early maturing soybean (Glycine max) germplasm

Background

Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean adaptability and yield. To dissect the genetic architecture of these agronomically important traits, a population consisting of 309 early maturity soybean germplasm accessions was genotyped with the Illumina Infinium SoySNP50K BeadChip and phenotyped in multiple environments. A genome-wide association study (GWAS) was conducted using a mixed linear model that involves both relative kinship and population structure.

Results

The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly.

Conclusions

This study identified multiple new loci and refined chromosomal regions of known loci associated with DTF, DTM, DFTM and/or PH in soybean. It demonstrates that GWAS is powerful in dissecting complex traits and identifying candidate genes although LD decayed slowly in soybean. The loci and trait-associated SNPs identified in this study can be used for soybean genetic improvement, especially the major-effect loci associated with PH could be used to improve soybean yield potential. The candidate genes may serve as promising targets for studies of molecular mechanisms underlying the related traits in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1441-4) contains supplementary material, which is available to authorized users.     

Susceptibility of Soybean Introductions to Races 1, 2, 3, and 4 of Heterodera glycines

Thirteen soybean plant introduction (PI) lines, selected for their apparent susceptibility to Heterodera glycines, were compared with cultivar Lee 74 as hosts of H. glycines races 1, 2, 3, and 4. Race 3 produced the highest average number of females of the four races. Compared to Lee 74, more (P = 0.05) females of H. glycines race 1 were extracted from eI 274420, PI 274423, and PI 317333; PI 86457 had more females of H. glycines race 2; and PI 86443, PI 86457, PI 261467, PI 274420, PI 274421, and PI 274423 had more females of H. glycines race 3. Similar numbers of females of H. glycines race 4 developed on all of the soybean lines and Lee 74. PI 274421, PI 274420, or PI 196159 could provide a more or equally susceptible host for H. glycines races 1, 2, 3, and 4 than Lee 74. One of these three lines could be substituted for Lee as the standard susceptible cultivar in the race determination test.     

A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences

Background and Aims

It is essential to illuminate the evolutionary history of crop domestication in order to understand further the origin and development of modern cultivation and agronomy; however, despite being one of the most important crops, the domestication origin and bottleneck of soybean (Glycine max) are poorly understood. In the present study, microsatellites and nucleotide sequences were employed to elucidate the domestication genetics of soybean.

Methods

The genomes of 79 landrace soybeans (endemic cultivated soybeans) and 231 wild soybeans (G. soja) that represented the species-wide distribution of wild soybean in East Asia were scanned with 56 microsatellites to identify the genetic structure and domestication origin of soybean. To understand better the domestication bottleneck, four nucleotide sequences were selected to simulate the domestication bottleneck.

Key Results

Model-based analysis revealed that most of the landrace genotypes were assigned to the inferred wild soybean cluster of south China, South Korea and Japan. Phylogeny for wild and landrace soybeans showed that all landrace soybeans formed a single cluster supporting a monophyletic origin of all the cultivars. The populations of the nearest branches which were basal to the cultivar lineage were wild soybeans from south China. The coalescent simulation detected a bottleneck severity of K′ = 2 during soybean domestication, which could be explained by a foundation population of 6000 individuals if domestication duration lasted 3000 years.

Conclusions

As a result of integrating geographic distribution with microsatellite genotype assignment and phylogeny between landrace and wild soybeans, a single origin of soybean in south China is proposed. The coalescent simulation revealed a moderate genetic bottleneck with an effective wild soybean population used for domestication estimated to be ≈2 % of the total number of ancestral wild soybeans. Wild soybeans in Asia, especially in south China contain tremendous genetic resources for cultivar improvement.     

Identification of quantitative trait loci for plant height, lodging, and maturity in a soybean population segregating for growth habit

The use of molecular markers to identify quantitative trait loci (QTLs) has the potential to enhance the efficiency of trait selection in plant breeding. The purpose of the present study was to identify additional QTLs for plant height, lodging, and maturity in a soybean, Glycine max (L.) Merr., population segregating for growth habit. In this study, 153 restriction fragment length polymorphisms (RFLP) and one morphological marker (Dt1) were used to identify QTLs associated with plant height, lodging, and maturity in 111 F₂-derived lines from a cross of PI 97100 and Coker 237. The F₂-derived lines and two parents were grown at Athens, Ga., and Blackville, S.C., in 1994 and evaluated for phenotypic traits. The genetic linkage map of these 143 loci covered about 1600 cM and converged into 23 linkage groups. Eleven markers remained unlinked. Using interval-mapping analysis for linked markers and single-factor analysis of variance (ANOVA), loci were tested for association with phenotypic data taken at each location as well as mean values over the two locations. In the combined analysis over locations, the major locus associated with plant height was identified as Dt1 on linkage group (LG) L. The Dt1 locus was also associated with lodging. This locus explained 67.7% of the total variation for plant height, and 56.4% for lodging. In addition, two QTLs for plant height (K007 on LG H and A516b on LG N) and one QTL for lodging (cr517 on LG J) were identified. For maturity, two independent QTLs were identified in intervals between R051 and N100, and between B032 and CpTI, on LG K. These QTLs explained 31.2% and 26.2% of the total variation for maturity, respectively. The same QTLs were identified for all traits at each location. This consistency of QTLs may be related to a few QTLs with large effects conditioning plant height, lodging, and maturity in this population.     

Relationships between initial population densities of Meloidogyne incognita race 2 and nematode population development in terms of variable soybean resistance

The effect of increasing initial population density levels (Pi) of Meloidogyne incognita race 2 on nematode population development and yield of a susceptible (Prima2000) and resistant (LS5995) soybean cultivar was investigated. Two experiments, one in a hail net cage and one in microplots, were conducted one each during two consecutive growing seasons at Potchefstroom in the North West Province of South Africa. Nematode reproduction was assessed by determining the number of eggs and second-stage juveniles (J2) in the rhizosphere and roots, egg masses, egg-laying females (ELF) and reproduction factor (Rf) values per root system at harvesting 110 days after planting. Percentage yield reduction in the two cultivars was also calculated. Strong non-linear relationships existed between all nematode variables as well as between Pi and percentage yield loss in both cultivars for both experiments in this study. Significantly higher numbers of eggs and J2, egg masses and ELF were maintained in the roots of the nematode-susceptible Prima2000 than in the resistant LS5995 from Pi = 100 and higher in both experiments. Rf values were inversely related to Pi for both cultivars and were lowest on LS5995, with Prima2000 maintaining significantly higher Rf values in both experiments. Yield loss in LS5995 was at least six times higher than that of Prima2000. The difference in monetary terms is demonstrated, although it is suggested that host plant resistance to plant-parasitic nematodes may not be sufficient as the only management tool in highly infested soils or in rotation systems including nematode susceptible crops.     

Hourglass cell development in the soybean seed coat

Background and Aims

Hourglass cells (HGCs) are prominent cells in the soybean seed coat, and have potential use as ‘phytofactories’ to produce specific proteins of interest. Previous studies have shown that HGCs initiate differentiation at about 9 d post-anthesis (dpa), assuming their characteristic morphology by 18 dpa. This study aims to document the structural changes in HGCs during this critical period, and to relate these changes to the concurrent development of a specific soybean peroxidase (SBP) encoded by the Ep gene.

Methods

Pods were collected from plants at specific growth stages. Fresh material was processed for analysis of Ep peroxidase activity. Tissues were processed for scanning and transmission electron microscopy, as well as extracted for western blotting. A null variety lacking expression of Ep peroxidase was grown as a control.

Key Results and Conclusions

At 9 dpa, HGCs are typical undifferentiated plant cells, but from 12–18 dpa they undergo rapid changes in their internal and external structure. By 18 dpa, they have assumed the characteristic hourglass shape with thick cell walls, intercellular air spaces and large central vacuoles. By 45 dpa, all organelles in HGCs have been degraded. Additional observations indicate that plasmodesmata connect all cell types. SBP activity and SBP protein are detectable in the HGC before they are fully differentiated (approx. 18 dpa). In very early stages, SBP activity appears localized in a vacuole as previously predicted. These results increase our understanding of the structure and development of the HGC and will be valuable for future studies aimed at protein targeting to components of the HGC endomembrane systems.     

Identification of the soybean HyPRP family and specific gene response to Asian soybean rust disease

Soybean [Glycine max (L.) Merril], one of the most important crop species in the world, is very susceptible to abiotic and biotic stress. Soybean plants have developed a variety of molecular mechanisms that help them survive stressful conditions. Hybrid proline-rich proteins (HyPRPs) constitute a family of cell-wall proteins with a variable N-terminal domain and conserved C-terminal domain that is phylogenetically related to non-specific lipid transfer proteins. Members of the HyPRP family are involved in basic cellular processes and their expression and activity are modulated by environmental factors. In this study, microarray analysis and real time RT-qPCR were used to identify putative HyPRP genes in the soybean genome and to assess their expression in different plant tissues. Some of the genes were also analyzed by time-course real time RT-qPCR in response to infection by Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease. Our findings indicate that the time of induction of a defense pathway is crucial in triggering the soybean resistance response to P. pachyrhizi. This is the first study to identify the soybean HyPRP group B family and to analyze disease-responsive GmHyPRP during infection by P. pachyrhizi.     

显性E1基因背景下大豆开花和成熟期的全基因组关联分析

【目的】深入解析大豆开花期和成熟期的遗传基础,发掘控制性状的重要基因组区间,为分子标记辅助选择育种和新基因克隆提供依据。【方法】以224份携带显性E1基因的大豆种质为试验材料,在4个种植环境下调查表型数据,采用R-mrMLM软件包中的6种多位点关联分析模型对大豆开花和成熟期进行全基因组关联分析。【结果】共检测到91个开花期和83个成熟期QTNs（quantitative trait nucleotides）,其中6个开花期和10个成熟期QTNs能在多环境中检测到。这些环境稳定QTNs分布于15个区间大小在90~490 Kb的单倍型（基因组）内,并有6个基因组区间为本研究新检测到。【结论】研究表明显性E1基因背景下大豆开花和成熟期的QTN构成复杂,位于5号染色体39.52~40.01Mb等15个基因组区间是该群体中控制大豆开花期或成熟期的重要位点。     

Response of Soybean to Heterodera glycines Races 1 and 2 in Different Soil Types

Experiments were conducted for 3 years at four locations and 1 year with six soil types at a common location in North Carolina to determine damage and control-cost functions for Heterodera glycines races 1 and 2 on soybean. In the experiments on native loamy sand and sandy soils, tolerance limits for initial population densities were 0 or very low, whereas in a muck, the tolerance limit was 315 eggs/500 cm³ soil. The aggressive race 2 was more damaging than race 1 in Lakeland sand and Norfolk loamy sand. The crop response was not different between races in the Appling sandy clay loam and Belhaven muck. Soybean yield responses to H. glycines were linear in six soil types in microplots at a common site. The amount of damage varied among these soil types, with lowest yields in the muck because of severe drought stress in this soil. An exponential function adequately described soybean yield response relative to nematode control with increasing rates of aldicarb in Norfolk loamy sand. Treatment with aldicarb in the Lakeland sand decreased the effective egg population of H. glycines but had only a minor effect in the muck.     

An Alternative Method for Evaluating Soybean Tolerance to Heterodera glycines in Field Plots

Alternate planting dates and periodic destruction of the previous year''s soybean crop as well as 1-year bare fallow were used to establish a range of population densities ofHeterodera glycines for the subsequent year. Soybean cultivar Coker 156 (susceptible, moderately tolerant) was compared to cultivars Essex (susceptible, intolerant) and Bedford (resistant) to evaluate tolerance at different H. glycines population densities established through the previous year''s treatments. Yield of Coker 156 was consistently intermediate between yields of Bedford and Essex in 1986 and 1987. Yield of Essex was negatively correlated (P = 0.05) with preplant egg numbers of H. glycines in 1987, whereas yield of Bedford and Coker 156 were not related to nematode density. Reproduction of H. glycines was greater (P = 0.05) on the moderately tolerant Coker 156 than on either of the other cultivars.     

Effect of the rhg1 Gene on Population Development of Heterodera glycines

The effect of the rhg1 gene on equilibrium population densities (E) and reproduction factors (Rf) of Heterodera glycines was studied by comparing the nematode population development on two near-isogenic soybean lines (NIL), differing at the rhg1 locus. The NIL were inoculated with a series of initial egg densities (Pi) in the greenhouse. The relationships between final population densities (Pf = females per plant or eggs per plant) or Rf (final egg density/Pi) on both NIL and Pi were adequately described by quadratic models. The rhg1 gene suppressed Pf and Rf at all Pi of a population of H. glycines race 3 (HG Type 0-); E and maximum Rf were higher on the NIL-S line than on the NIL-R line. After two generations of culture of the race 3 population on the NIL-R line, the population selected by the rhg1 gene (R-eggs) had higher Pf and Rf on the NIL-R line than the population cultured on the NIL-S line (S-eggs) at all Pi. Both R-eggs and S-eggs produced similar egg numbers on the NIL-S line, which was higher than the egg number of either population on the NIL-R line at all Pi. The ratio of E in female numbers on the NIL-R line to E on the NIL-S line increased from 29% for the original race 3 population (S-eggs) to 46% for the rhg1-selected population (R-eggs). Regardless of different egg sources, a trend of increase in the number of eggs per female with the rise of Pi was observed on the NIL-S line. In contrast, female fecundity of both populations declined with the increase of Pi on the NIL-R line. At most inoculum densities, the highest number of eggs per female was observed on the NIL-S line inoculated with the R-eggs, whereas the lowest number of eggs per female was detected on the NIL-R line inoculated with the S-eggs. This study demonstrated that the E and maximum Rf determined by the quadratic models are useful measurements of plant resistance to nematodes.     

Penetration and Post-infectional Development and Reproduction of Meloidogyne arenaria Races 1 and 2 on Susceptible and Resistant Soybean Genotypes

Penetration, post-infectional development, reproduction, and fecundity of Meloidogyne arenaria races 1 and 2 were studied on susceptible (CNS), partially resistant (Jackson), and highly resistant (PI 200538 and PI 230977) soybean genotypes in the greenhouse. The ability to locate and invade roots was similar between races, but more juveniles penetrated roots of susceptible CNS than the resistant genotypes. At 10 days after inoculation, 56% and 99% to 100% of race 1 second-stage juveniles were vermiform or sexually undifferentiated in CNS and the resistant genotypes, respectively. In contrast, only 2%, 42%, 44%, and 62% of race 2 juveniles had not initiated development in CNS, Jackson, PI 200538, and PI 230977, respectively. By 20 days after inoculation, 88% to 100% of race 2 nematodes in roots of all genotypes were females, whereas only 25% and 1% of race 1 were females in CNS and the resistant genotypes, respectively. For all four genotypes, race 1 produce 85% to 96% fewer eggs per root system 45 days after inoculation than race 2. At 45 days after inoculation race 2 produced more eggs on CNS than the other genotypes.     

Impact of Planting 'Bell', a Soybean Cultivar Resistant to Heterodera glycines, in Wisconsin

Although the soybean cyst nematode (SCN), Heterodera glycines, has been known to exist in Wisconsin for at least 14 years, relatively few growers sample for SCN or use host resistance as a means to manage this nematode. The benefit of planting the SCN-resistant cultivar Bell on a sandy soil in Wisconsin was evaluated in 1992 and 1993. A range of SCN population densities was achieved by planting 11 crops with varying degrees of susceptibility for 1 or 2 years before the evaluation. Averaged over nematode population densities, yield of ''Bell'' was 30 to 43% greater than that of the susceptible cultivars, ''Corsoy 79'' and ''BSR 101''. Counts of cysts collected the fall preceding soybean were more predictive of yield than counts taken at planting. Yields of all three cultivars were negatively related (P < 0.001) to cyst populations. Fewer (P < 0.01) eggs were produced on ''Bell'' than on the susceptible cultivars. The annual (fall to fall) change in cyst population densities was dependent on initial nematode density for all cultivars in 1992 and for the susceptible cultivars in 1993. Yield reductions induced by the SCN under the conditions of this study indicate that planting a SCN-resistant cultivar in Wisconsin can be beneficial if any cysts are detected.     

Genetic parameters and selection strategies for soybean genotypes resistant to the stink bug-complex

Soybean genotypes resistant to stink bugs are derived from complex breeding processes obtained through indirect selection. The aim of the present work was to estimate genetic parameters for guiding selection strategies towards resistant genotypes, based on those traits associated with responses to pod-attacking stink bugs, such as the grain filling period (GFP), leaf retention (LR), percentage index of pod damage (PIPD) and percentage of spotted seeds (PSS). We assessed the parental lines IAC-100 (resistant) and FT-Estrela (susceptible), the progenies F(2) and F (4) , 30 progenies F (2:3) , 30 progenies BC (1) F (2:3) and 30 progenies BC (2) F (2:3) , besides the cultivars BRS Celeste and MGBR-46 (Conquista). Three field experiments, using randomized complete block design with three replications, were installed in Goiania-GO, in the 2002/03 season. Each experiment consisted of 36 treatments (6 common and 30 regular). Heritability estimates were: 74.6 and 36.1 (GFP); 51.9 and 19.9 (LR); 49.6 and 49.6 (PIPD) and 55.8 and 20.3 (PSS), in both the broad and narrow senses, respectively. Based on these results, we concluded that the best strategy for obtaining stink bug-resistant genotypes consists of selecting the PIPD trait in early generations (F (3) or F (4) ), followed by selection for the GFP, LR and PSS traits in generations with higher endogamy levels.     

Effect of Planting Date,Alachlor, and Fenamiphos on Heterodera glycines Development

The effects of alachlor (2.25 kg a.i./ha) and fenamiphos (2.25 kg a.i./ha) on the penetration and development of Heterodera glycines were examined on Glycine max cultivars Deltapine 105 planted 29 April, 29 May, and 29 June 1986 and Deltapine 105 and Centennial planted 15 May, 15 June, and 15 July 1987. Penetration was lowest on the third planting of soybeans and on fenamiphos-treated plants. Development from second-stage juveniles to adult females required 270 (1986) and 260 (1987) DD20/32 on roots from the first planting control and alachlor treatments. Fenamiphos, alone or with alachlor, retarded development in Deltapine 105 (1986) and in Centennial (1987). Males matured in roots from the second planting in 190 (1986) and 180 (1987) DD20/32 regardless of treatment or cultivar. No development occurred in roots from the third planting until 400 DD20/32 in 1986, but in 1987 development was similar to that in roots from the second planting. Nematode development was similar in alachlor-treated and control roots regardless of planting date. Fenamiphos restricted nematode penetration on most planting dates and slowed development. Simultaneous applications of alachlor and fenamiphos usually also inhibited development.     

Galling and Yields of Soybean Cultivars Grown in Meloidogyne arenana-Infested Soil

Field trials with 39 soybean cultivars and five breeding lines from public and private sources were conducted from 1982 through 1985 at sites infested with Meloidogyne arenaria. Nematode population densities and root-knot galling were measured for each soybean entry. All were efficient hosts for the nematode, and average juvenile numbers in the soil increased 5-50 × from planting to harvest. Differences (P < 0.05) in galling were found among entries in each year. Centennial, Cobb, Coker 368, Hutton, and Jeff cultivars, recognized for their resistance to M. incognita, were severely galled and yielded poorly. Bedford, Forrest, A7372, Bragg, Braxton, Gordon, and Kirby, also recognized for their resistance to M. incognita, were among the least galled cultivars. Yields of all entries, however, were too low to justify their planting in sites heavily infested with M. arenaria.     

Population Density and Spatial Pattern of Heterodera glycines in Relation to Soybean Phenology

Population dynamics of Heterodera glycines (SCN) were influenced by initial nematode population density in soil, soybean root growth pattern, soil type, and environmental conditions in two field experiments. Low initial populations (Pi) of SCN increased more rapidly during the growing season than high Pi and resulted in greater numbers of nematodes at harvest. Egg and juvenile (J2) populations increased within 2-6 weeks after planting when early-season soil temperatures were 20 C and above and were delayed by soil temperatures of 17 C or below in May and early June. Frequencies of occurrence and number of nematodes decreased with increasing depth and distance from center of the soybean row. Spatial pattern of SCN paralleled that of soybean roots. Higher clay content in the subsoil 30-45 cm deep in one field restricted soil penetration by roots, indirectly influencing vertical distribution of SCN. Shoot dry weight was a good indicator of the effect of SCN on seed yield. Root dry weight was poorly correlated with soybean growth and yield. The relationship of yield (seed weight) to Pi was best described by a quadratic equation at one site, but did not fit any regression model tested at the second site.     

Evaluation of Pea and Soybean as Trap Crops for Managing Heterodera glycines

Trap crops that stimulate nematode egg hatching but not reproduction have been reported as an effective means for managing certain nematodes. Studies were carried out at two field sites each year in 1998 and 1999 to evaluate the potential of trapping the soybean cyst nematode (Heterodera glycines) with soybean and pea in the corn year to manage the nematode in Minnesota. The trap crops were planted on the same day as corn at each site and later killed with the herbicide glyphosate. Nematode egg densities were determined at planting, 1 and 2 months after planting, and at harvest. Treatments included four seeding rates (0, 124,000, 247,000, and 494,000 seeds/ha) of resistant soybean as a trap crop and four kill dates (3, 4, 5, and 6 weeks after planting). No effects of the trap-crop and kill-date treatments on H. glycines population density, corn yield, and the followingyear soybean yield were observed at the two locations. In a second study, the experiment included four trap-crop comparisons (resistant soybean at 494,000 seeds/ha, susceptible soybean at 494,000 seeds/ha, pea at 1,482,000 seeds/ha, and no trap crop) and five kill dates (3, 4, 5, 6 weeks after planting, and no-kill). At the Waseca site, egg density at harvest was lower where resistant soybean was grown for 6 weeks and where pea was grown for 5 and 6 weeks compared with where no trap crop was grown. Maintaining pea plants for more than 5 weeks, however, reduced corn yield by 20% at the Waseca site. At the Lamberton site, egg density at harvest was lower where the susceptible soybean was grown for 5 weeks compared with where no trap crop was grown. Even with significant reduction of eggs in some treatments, use of soybean and pea as trap crops in the corn year was not an effective means for managing H. glycines.     

Evolutionary history of mitogen-activated protein kinase (MAPK) genes in Lotus,Medicago, and Phaseolus

Mitogen-Activated Protein Kinase (MAPK) genes encode proteins that mediate various signaling pathways associated with biotic and abiotic stress responses in eukaryotes. The MAPK genes form a 3-tier signal transduction cascade between cellular stimuli and physiological responses. Recent identification of soybean MAPKs and availability of genome sequences from other legume species allowed us to identify their MAPK genes. The main objectives of this study were to identify MAPKs in 3 legume species, Lotus japonicus, Medicago truncatula, and Phaseolus vulgaris, and to assess their phylogenetic relationships. We used approaches in comparative genomics for MAPK gene identification and named the newly identified genes following Arabidopsis MAPK nomenclature model. We identified 19, 18, and 15 MAPKs and 7, 4, and 9 MAPKKs in the genome of Lotus japonicus, Medicago truncatula, and Phaseolus vulgaris, respectively. Within clade placement of MAPKs and MAPKKs in the 3 legume species were consistent with those in soybean and Arabidopsis. Among 5 clades of MAPKs, 4 founder clades were consistent to MAPKs of other plant species and orthologs of MAPK genes in the fifth clade-"Clade E" were consistent with those in soybean. Our results also indicated that some gene duplication events might have occurred prior to eudicot-monocot divergence. Highly diversified MAPKs in soybean relative to those in 3 other legume species are attributable to the polyploidization events in soybean. The identification of the MAPK genes in the legume species is important for the legume crop improvement; and evolutionary relationships and functional divergence of these gene members provide insights into plant genome evolution.