Quantitative Trait Locus Mapping of Soybean Maturity Gene E6

Soybean [ Glycine max (L.) Merr.] sensitivity to photoperiod determines adaptation to a specific range of latitudes for soybean cultivars. When temperate-adapted soybean cultivars are grown in low latitude under short day conditions, they flower early, resulting in low grain yield, and consequently limiting their utility in tropical areas. Most cultivars adapted to low-latitude environments have the trait of delayed flowering under short day conditions, and this trait is commonly called long juvenile (LJ). In this study, the E6 locus, the classical locus conditioning the LJ trait, was molecularly mapped on Gm04 near single-nucleotide polymorphism marker HRM101. Testcross, genetic mapping, and sequencing suggest that the E6 and J loci might be tightly linked. Genetic interaction evaluation between E6 and E1 suggests that E6 has a suppressive effect on E1 and that the function of E6 is dependent on E1. The tagging markers for E6 are very useful for molecular breeding for wide adaptation and stable productivity of soybean under lowlatitude environments. Molecular identification and functional characterization of the E6 gene will greatly facilitate the understanding of the genetic and molecular mechanisms underlying the LJ trait

Genetic Analysis of High Protein Content in ‘AC Proteus’ Related Soybean Populations Using SSR, SNP, DArT and DArTseq Markers

Key message: Several AC Proteus derived genomic regions (QTLs, SNPs) have been identified which may prove useful for further development of high yielding high protein cultivars and allele-specific marker developments. High seed protein content is a trait which is typically difficult to introgress into soybean without an accompanying reduction in seed yield. In a previous study, ‘AC Proteus’ was used as a high protein source and was found to produce populations that did not exhibit the typical association between high protein and low yield. Five high x low protein RIL populations and a high x high protein RIL population were evaluated by either quantitative trait locus (QTL) analysis or bulk segregant analyses (BSA) following phenotyping in the field. QTL analysis in one population using SSR, DArT and DArTseq markers found two QTLs for seed protein content on chromosomes 15 and 20. The BSA analyses suggested multiple genomic regions are involved with high protein content across the five populations, including the two previously mentioned QTLs. In an alternative approach to identify high protein genes, pedigree analysis identified SNPs for which the allele associated with high protein was retained in seven high protein descendants of AC Proteus on chromosomes 2, 17 and 18. Aside from the two identified QTLs (five genomic regions in total considering the two with highly elevated test statistic, but below the statistical threshold and the one with epistatic interactions) which were some distance from Meta-QTL regions and which were also supported by our BSA analysis within five populations. These high protein regions may prove useful for further development of high yielding high protein cultivars

Differential gene expression provides leads to environmentally regulated soybean seed protein content

Soybean is an important global source of plant-based protein. A persistent trend has been observed over the past two decades that soybeans grown in western Canada have lower seed protein content than soybeans grown in eastern Canada. In this study, 10 soybean genotypes ranging in average seed protein content were grown in an eastern location (control) and three western locations (experimental) in Canada. Seed protein and oil contents were measured for all lines in each location. RNA-sequencing and differential gene expression analysis were used to identify differentially expressed genes that may account for relatively low protein content in western-grown soybeans. Differentially expressed genes were enriched for ontologies and pathways that included amino acid biosynthesis, circadian rhythm, starch metabolism, and lipid biosynthesis. Gene ontology, pathway mapping, and quantitative trait locus (QTL) mapping collectively provide a close inspection of mechanisms influencing nitrogen assimilation and amino acid biosynthesis between soybeans grown in the East and West. It was found that western-grown soybeans had persistent upregulation of asparaginase (an asparagine hydrolase) and persistent downregulation of asparagine synthetase across 30 individual differential expression datasets. This specific difference in asparagine metabolism between growing environments is almost certainly related to the observed differences in seed protein content because of the positive correlation between seed protein content at maturity and free asparagine in the developing seed. These results provided pointed information on seed protein-related genes influenced by environment. This information is valuable for breeding programs and genetic engineering of geographically optimized soybeans

Soybean Yield and Seed Composition Changes in Response to Increasing Atmospheric CO2 Concentration in Short-Season Canada

From 1993, we have conducted trials with the same set of old to newer soybean cultivars to determine the impact of plant breeding on seed yield, physiological and agronomic characteristics, and seed composition. Since 1993, global atmospheric [CO2] increased by 47 ppm. The objective of our current analysis with this data set was to determine if there were changes in soybean seed yield, quality or phenology attributable to elevated atmospheric CO2 concentration (eCO2), temperature or precipitation. Additionally, we estimated genetic gain annually. Over 23 years, there was a significant increase in atmospheric [CO2] but not in-season average maximum or minimum temperatures, or average in-season precipitation. Seed yield was increased significantly by eCO2, higher precipitation and higher minimum temperatures during flowering and podding. Yield decreased with higher minimum temperatures during vegetative growth and seed filling. Seed oil and also seed protein plus oil concentrations were both reduced with eCO2. Phenology has also changed, with soybean cultivars spending less time in vegetative growth, while time to maturity remained constant. Over the 23 years of the study, genetic improvement rates decreased as [CO2] increased. Newer cultivars are not better adapted to eCO2 and soybean breeders may need to intentionally select for favourable responses to eCO2 in the future

A Broad Review of Soybean Research on the Ongoing Race to Overcome Soybean Cyst Nematode

Plant pathogens greatly impact food security of the ever-growing human population. Breeding resistant crops is one of the most sustainable strategies to overcome the negative effects of these biotic stressors. In order to efficiently breed for resistant plants, the specific plant–pathogen interactions should be understood. Soybean is a short-day legume that is a staple in human food and animal feed due to its high nutritional content. Soybean cyst nematode (SCN) is a major soybean stressor infecting soybean worldwide including in China, Brazil, Argentina, USA and Canada. There are many Quantitative Trait Loci (QTLs) conferring resistance to SCN that have been identified; however, only two are widely used: rhg1 and Rhg4. Overuse of cultivars containing these QTLs/genes can lead to SCN resistance breakdown, necessitating the use of additional strategies. In this manuscript, a literature review is conducted on research related to soybean resistance to SCN. The main goal is to provide a current understanding of the mechanisms of SCN resistance and list the areas of research that could be further explored

Patterns of Genetic Variation in a Soybean Germplasm Collection as Characterized with Genotyping-by-Sequencing

Genomic characterization is playing an increasing role in plant germplasm conservation and utilization, as it can provide higher resolution with genome-wide SNP markers than before to identify and analyze genetic variation. A genotyping-by-sequencing technique was applied to genotype 541 soybean accessions conserved at Plant Gene Resources of Canada and 30 soybean cultivars and breeding lines developed by the Ottawa soybean breeding program of Agriculture and Agri-Food Canada. The sequencing generated an average of 952,074 raw sequence reads per sample. SNP calling identified 43,891 SNPs across 20 soybean chromosomes and 69 scaffolds with variable levels of missing values. Based on 19,898 SNPs with up to 50% missing values, three distinct genetic groups were found in the assayed samples. These groups were a mixture of the samples that originated from different countries and the samples of known maturity groups. The samples that originated from Canada were clustered into all three distinct groups, but 30 Ottawa breeding lines fell into two groups only. Based on the average pairwise dissimilarity estimates, 40 samples with the most genetic distinctness were identified from three genetic groups with diverse sample origin and known maturity. Additionally, 40 samples with the highest genetic redundancy were detected and they consisted of different sample origins and maturity groups, largely from one genetic group. Moreover, some genetically duplicated samples were identified, but the overall level of genetic duplication was relatively low in the collection. These findings are useful for soybean germplasm management and utilization

Photoperiod Affects Node Appearance Rate and Flowering in Early Maturing Soybean

The photoperiod plays a critical role in the control of flowering timing in soybean (Glycine max (L.) Merr.) with long days increasing the time to flowering. Early flowering cultivars have been developed from breeding programs for environments with long photoperiods; however, this effect is challenging to isolate in field experiments because of other environmental influences. Our experiment examined the effect of photoperiod on the node appearance rate and time to flower for 13 early maturing soybean cultivars ranging in maturity group (MG) between 000.9 and 1.3. Growth chambers were programmed to 14, 15, 16, and 17 h photoperiods and temperature was kept at 25 °C. The date of emergence and main stem node appearance were recorded until flowering. The node appearance rate was slowest for the first node and increased thereafter. All cultivars required more time to flowering in the longer photoperiod treatments and the later rated MG had the greatest sensitivity to photoperiod. A delay in time to flower from a longer photoperiod can delay maturity and expose the crop to fall frost that can reduce seed yield and quality. Understanding and documentation of soybean photoperiod sensitivity will help plant breeders develop suitable cultivars for environments with long photoperiods

Tillage and crop rotation effects on the yield of corn, soybean and wheat in eastern Canada

Farmers in Canada are adopting no till (NT) production at a high frequency. Conventional tillage (CT) was compared to no till (NT) with corn (Zea mays L.), soybean [Glycine max (L.) Merr.], and wheat (Triticum aestivum L.) grown in monoculture or annual rotation in a long term study established in Ottawa (1990). From 1996 to 2000 all plots reverted to NT conditions to study the transition effects from CT to NT. In transition from CT to NT, new-NT corn plots yielded significantly more than established-NT plots in the first year of transition only, while there were no transition effects for soybean or wheat. In 2001 the experiment was changed back to CT and NT. Over 15 years of the tillage-rotation trial (2001 to 2015) CT corn yields were ~20% higher than NT corn across all three rotations but the differences were not significant at the 5% level (p values 0.11 to 0.15). Fertilizer was not incorporated in all NT corn and wheat and may have limited NT yields. Yields did not differ between CT and NT for either soybean or wheat in any of the rotations. Wheat yielded 22% and CT corn yielded 8% more when grown in rotation than in monoculture. Soybean yield did not differ between rotation and monoculture. Crop order in the rotation (corn-soybean-wheat vs. corn-wheat-soybean) did not result in significant yield differences. An economic, agronomic or environmental advantage will be needed to justify NT corn production, in high-yielding environments of a humid continental agroecosystem.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Species-specific microRNA discovery and target prediction in the soybean cyst nematode

Abstract The soybean cyst nematode (SCN) is a devastating pathogen for economic and food security considerations. Although the SCN genome has recently been sequenced, the presence of any miRNA has not been systematically explored and reported. This paper describes the development of a species-specific SCN miRNA discovery pipeline and its application to the SCN genome. Experiments on well-documented model nematodes (Caenorhabditis elegans and Pristionchus pacificus) are used to tune the pipeline’s hyperparameters and confirm its recall and precision. Application to the SCN genome identifies 3342 high-confidence putative SCN miRNA. Prediction specificity within SCN is confirmed by applying the pipeline to RNA hairpins from known exonic regions of the SCN genome (i.e., sequences known to not be miRNA). Prediction recall is confirmed by building a positive control set of SCN miRNA, based on a limited deep sequencing experiment. Interestingly, a number of novel miRNA are predicted to be encoded within the intronic regions of effector genes, known to be involved in SCN parasitism, suggesting that these miRNA may also be involved in the infection process or virulence. Beyond miRNA discovery, gene targets within SCN are predicted for all high-confidence novel miRNA using a miRNA:mRNA target prediction system. Lastly, cross-kingdom miRNA targeting is investigated, where putative soybean mRNA targets are identified for novel SCN miRNA. All predicted miRNA and gene targets are made available in appendix and through a Borealis DataVerse open repository ( https://borealisdata.ca/dataset.xhtml?persistentId=doi:10.5683/SP3/30DEXA )

Variability in Maturity, Oil and Protein Concentration, and Genetic Distinctness among Soybean Accessions Conserved at Plant Gene Resources of Canada

Soybean (Glycine max (L.) Merr.) is one of the important crops in Canada and has the potential to expand its production further north into the Canadian Prairies. Such expansion, however, requires the search for adapted soybean germplasm useful for the development of productive cultivars with earlier maturity and increased protein concentration. We initiated several research activities to characterize 848 accessions of the soybean collection conserved at Plant Gene Resources of Canada (PGRC) for maturity, oil and protein concentration, and genetic distinctness. The characterization revealed a wide range of variations present in each assessed trait among the PGRC soybean accessions. The trait variabilities allowed for the identification of four core subsets of 35 PGRC soybean accessions, each specifically targeted for early maturity for growing in Saskatoon and Ottawa, and for high oil and protein concentration. The two early maturity core subsets for Saskatoon and Ottawa displayed days to maturity ranging from 103 to 126 days and 94 to 102 days, respectively. The two core subsets for high oil and protein concentration showed the highest oil and protein concentration from 25.0 to 22.7% and from 52.8 to 46.7%, respectively. However, these core subsets did not differ significantly in genetic distinctness (as measured with 19,898 SNP markers across 20 soybean chromosomes) from the whole PGRC soybean collection. These findings are useful, particularly for the management and utilization of the conserved soybean germplasm