SoySNP618K array: A high-resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding.

Innovations in genomics have enabled the development of low-cost, high-resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high-confidence genes. Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research.

Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS.

Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS® . Based on 99 085 high-quality SNPs, landraces were classified into three sub-populations which exhibit geographical genetic differentiation. Clustering was inferred from STRUCTURE, principal component analyses and neighbour-joining tree analyses. Using phenotypic data collected at two locations separated by 10 degrees of latitude, 17 trait-associated SNPs (TASs) for flowering time were identified, including a stable locus Chr12:5914898 and previously undetected candidate QTL/genes for flowering time in the vicinity of the previously cloned flowering genes, E1 and E2. Using passport data associated with the collection sites of the landraces, 27 SNPs associated with adaptation to three bioclimatic variables (temperature, daylength, and precipitation) were identified. A series of candidate flowering genes were detected within linkage disequilibrium (LD) blocks surrounding 12 bioclimatic TASs. Nine of these TASs exhibit significant differences in flowering time between alleles within one or more of the three individual sub-populations. Signals of selection during domestication and/or subsequent landrace diversification and adaptation were detected at 38 of the 44 flowering and bioclimatic TASs. Hence, this study lays the groundwork to begin breeding for novel environments predicted to arise following global climate change.

Identification of the dwarf gene GmDW1 in soybean (Glycine max L.) by combining mapping-by-sequencing and linkage analysis.

KEY MESSAGE: GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean. Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length. The bioactive GA1 (gibberellin A1) and GA4 (gibberellin A4) were not detectable in the stem of dw, and the dwarf phenotype could be rescued by treatment with exogenous GA3. Genetic analysis showed that the dwarf trait of dw was controlled by a recessive nuclear gene. By combining linkage analysis and mapping-by-sequencing, we mapped the GmDW1 gene to an approximately 460-kb region on chromosome (Chr.) 8, containing 36 annotated genes in the reference Willliams 82 genome. Of these genes, we identified two nonsynonymous single nucleotide polymorphisms (SNPs) that are present in the encoding regions of Gmdw1 and Glyma.08G165100 in dw, respectively. However, only the SNP mutation (T>A) at nucleotide 1224 in Gmdw1 cosegregated with the dwarf phenotype. GmDW1 encodes an ent-kaurene synthase, and was expressed in various tissues including root, stem, and leaf. Further phenotypic analysis of the allelic variations in soybean accessions strongly indicated that GmDW1 is responsible for the dwarf phenotype in dw. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding.

Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean.

BACKGROUND: The relative abundance of five dominant fatty acids (FAs) (palmitic, stearic, oleic, linoleic and linolenic acids) is a major factor determining seed quality in soybean. METHODS: To clarify the currently poorly understood genetic architecture of FAs in soybean, targeted association analysis was conducted in 421 diverse accessions phenotyped in three environments and genotyped using 1536 pre-selected SNPs. RESULTS: The population of 421 soybean accessions displayed significant genetic variation for each FA. Analysis of the molecular data revealed three subpopulations, which reflected a trend depending on latitude of cultivation. A total of 37 significant (p < 0.01) associations with FAs were identified by association mapping analysis. These associations were represented by 33 SNPs (occurring in 32 annotated genes); another four SNPs had a significant association with two different FAs due to pleiotropic interactions. The most significant associations were cross-verified by known genes/QTL or consistency across cultivation year and subpopulations. CONCLUSION: The detected marker-trait associations represent a first important step towards the implementation of molecular-marker-based selection of FA composition with the potential to substantially improve the seed quality of soybean with benefits for human health and for food processing.

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing.

BACKGROUND: Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed. RESULTS: A total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits. The selection regions were not distributed randomly or uniformly throughout the genome. Instead, clusters of selection hotspots in certain genomic regions were observed. Moreover, a set of candidate genes (4.38% of the total annotated genes) significantly affected by selection underlying soybean domestication and genetic improvement were identified. CONCLUSIONS: Given the uniqueness of the soybean germplasm sequenced, this study drew a clear picture of human-mediated evolution of the soybean genomes. The genomic resources and information provided by this study would also facilitate the discovery of genes/loci underlying agronomically important traits.

Synthesis and degradation of the major allergens in developing and germinating soybean seed.

Gly m Bd 28K, Gly m Bd 30K and Gly m Bd 60K are the major soybean (Glycine max (L.) Merr.) allergens limiting the consumption of a good protein source for sensitive individuals. However, little is known about their temporal-spatial expression during seed development and upon germination. The present data shows that soy allergens accumulated in both the embryonic axes and cotyledon, but expression patterns differed depending on the specific allergen. Allergens accumulated sooner and to a greater level in cotyledons than in embryonic axes. Gly m Bd 28 began at 14 d after flowering, 7 to 14 d earlier than Gly m Bd 30K and Gly m Bd 60K. Comparatively, their degradation was faster and more profound in embryonic axes than in cotyledons. Gly m Bd 60K began to decline at 36 h after imbibition and remained detectable up to 108 h in cotyledons. In contrast, the Glym Bd 60K protein was reduced at 24 h, and eventually disappeared at 96 h . In cotyledons Gly m Bd 28K first declined at 24 h, then increased from 36 h to 48 h, followed by its large reduction at 72 h after seed germination. These findings provide useful information on soy allergen biosynthesis and will help move forward towards developing a hypoallergenic soybean for safer food.

Genome-wide association mapping of QTL underlying seed oil and protein contents of a diverse panel of soybean accessions.

To investigate the genetic basis of variation in oil and protein contents in soybean seeds, a diverse collection of 421 mainly Chinese soybean cultivars was genotyped using 1536 SNPs, mostly from candidate genes related to acyl-lipid metabolism and from regions harboring known QTL. Six significant associations were identified for each of seed oil and protein contents which individually explained 2.7-5.9% of the phenotypic variance. Six associations occurred in or near known QTL and the remaining are putative novel QTL. Ten significant associations influenced the oil content without decreasing protein content, and vice versa. One SNP was pleiotropic, with opposite effects on oil and protein contents. The genetic region covering Map-6076 and-6077 was shown to be involved in controlling oil content in soybean by integrating the results of association mapping with information on known QTL and tissue-specific expression data. This region was subject to strong selection during the genetic improvement of soybean. Our results not only confirm and refine the map positions of known QTL but also contribute to a further elucidation of the genetic architecture of protein and oil contents in soybean seeds by identifying new associations exhibiting pleiotropic effects on seed protein and oil contents.

[The mechanism of root hair development and molecular regulation in plants].

The formation of the root epidermis in Arabidopsis thaliana provides a simple model to study mechanisms underlying patterning in plants. Root hair increases the root surface area and effectively increases the root diameter, so root hair is thought to aid plants in nutrient uptake, anchorage and microbe interactions. The determination of root hair development has two types, lateral inhibition with feedback and position-dependent pattern of cell differentiation. The initiation and development of root hair in Arabidopsis provide a simple and efficacious model for the study of cell fate determination in plants. Molecular genetic studies identify a suite of putative transcription factors which regulate the epidermal cell pattern. The homeodomain protein GLABRA2 (GL2), R2R3 MYB-type transcription factor WEREWOLF (WER) and WD-repeat protein TRANSPARENTT TESTA GLABRA (TTG) are required for specification of non-hair cell type. The CAPRICE (CPC) and TRYPTICHON (TRY) are involved in specifying the hair cell fate.

[Genetic diversity and recombination of soybean cultivar Suinong 14 and its pedigree].

In this study, 14 agronomic traits and 139 SSR loci, distributed on 20 linkage groups of soybean (Glycine max L.) cultivar Suinong 14 and its pedigree were analyzed to explain the genetic diversity and recombination of Suinong 14 and to provide useful information for breeding. The cluster analysis based on SSR makers agreed with the pedigree information. The Shannon-Weaver index of each SSR locus ranged from 0 to 1.677. The average genetic similarity coefficient among cultivars was 0.6380, ranged from 0.538 to 0.799. At least three SSR loci were needed to discriminate Suinong 14 from its pedigree, for example a combination of Satt543, Sat_130 and Satt218. These loci have more alleles. No significant difference was observed between the end portion and the mid-portion within a linkage group, which indicates that the distribution of recombination occurred randomly in each linkage group. No polymorphism was detected within 39 of 139 SSR loci between Suinong 14 and its 8 parents. It implys their importance during cultivar improvement. Satt168, a marker on LGB2, was the only locus transmitted from Zihua 4 to Suinong 14, which indicates that the genetic constitute of Suinong 14 is greatly changed compared with Zihua 4 through five generations of recombination.

Dissecting the Genetic Basis of Resistance to Soybean Cyst Nematode Combining Linkage and Association Mapping.

A set of 585 informative single-nucleotide polymorphism (SNP) loci was used to genotype both a panel of diverse accessions and a set of recombinant inbred lines (RILs) bred from the cross Zhongpin03-5373 (ZP; resistant to SCN) × Zhonghuang13 (ZH; susceptible). The SNP loci are mostly sited within genic sequence in regions of the soybean [ (L.) Merr.] genome thought to harbor genes determining resistance to the soybean cyst nematode (SCN, Ichinohe). The three strongest quantitative trait nucleotides (QTNs) identified by association mapping (AM) involved the genes (a component of the multigene locus ), and (an paralog), as well as some other loci with smaller effects. The linkage mapping (LM) analysis performed using the RILs revealed two putative quantitative trait loci (QTL): one mapping to and the other to an paralog; both of these loci were also identified by AM. The former locus explained 25.5% of the phenotypic variance for SCN resistance and the latter 5.8%. In combination, the two major loci acted nonadditively, providing a high level of SCN resistance.

[Studies of genetic analysis and SSR linked marker location of gene resistance to southern rust in inbred line P25 of maize].

Using P25 (immune inbred line), F349 (susceptible inbred line) and the derived population F1, F2, B1 and B2 as materials, we investigated the heredity the of disease resistance gene to maize southern rust (Puccinia polysora Underw.) through the major-gene and polygene inheritance model. The results indicate that a major resistance gene exists in the inbred line P25 and expresses with additive effect. We didn't find any multi-genes. The inheritabilities of this major resistant gene among F2, B1 and B2 were 81.88%, 38.14% and 55.1%, respectively. We constructed a maize SSR linkage map using P25 x F349 F2:3 population, and located the resistant gene on chromosome 10. The genetic distance between this gene and phi059 marker was 5.8 cM.

Biparental resequencing coupled with SNP genotyping of a segregating population offers insights into the landscape of recombination and fixed genomic regions in elite soybean.

Identification of genes underlying agronomic traits is dependent on the segregation of quantitative trait loci (QTL). A popular hypothesis is that elite lines are becoming increasingly similar to each other, resulting in large genomic regions with fixed genes. Here, we resequenced two parental modern elite soybean lines [ZhongHuang13 (ZH) and ZhongPin03-5373 (ZP)] and discovered 794,876 SNPs with reference to the published Williams82 genome. SNPs were distributed unevenly across the chromosomes, with 87.1% of SNPs clustering in 4.9% of the soybean reference genome. Most of the regions with a high density of SNP polymorphisms were located in the chromosome arms. Moreover, seven large regions that were highly similar between parental lines were identified. A GoldenGate SNP genotyping array was designed using 384 SNPs and the 254 recombinant inbred lines (F8) derived from the cross of ZP × ZH were genotyped. We constructed a genetic linkage map using a total of 485 molecular markers, including 313 SNPs from the array, 167 simple sequence repeats (SSRs), 4 expressed sequence tag-derived SSRs, and 1 insertion/deletion marker. The total length of the genetic map was 2594.34 cM, with an average marker spacing of 5.58 cM. Comparing physical and genetic distances, we found 20 hotspot and 14 coldspot regions of recombination. Our results suggest that the technology of resequencing of parental lines coupled with high-throughput SNP genotyping could efficiently bridge the genotyping gap and provide deep insights into the landscape of recombination and fixed genomic regions in biparental segregating populations of soybean with implications for fine mapping of QTL.

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.

Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

DNA sequence polymorphism of the Rhg4 candidate gene conferring resistance to soybean cyst nematode in Chinese domesticated and wild soybeans.

Rhg4 is one of the major resistant genes conferring resistance to soybean cyst nematode races 1, 3 and 4. In order to better understand its sequence diversity among different Chinese soybean populations and the impact of human activities on it, we designed 5 primer sets based on its sequence deposited in Genbank (Genbank accession No. AF506518) to obtain the Rhg4 sequence from 104 Chinese cultivated and wild soybean genotypes, and then analyzed the DNA sequence polymorphism in different Chinese soybean populations. The alignment of Rhg4 sequence included 5,216 nucleotide base pairs. A total of 67 single nucleotide polymorphisms (SNPs) including 59 single base changes and 8 DNA insertion-deletions (InDels) were identified with a SNP frequency of 1/78. Except for a 14-base InDel, there were 29 SNPs in coding regions, and among them, 13 were non-synonymous (9 in functional domains with 1 in a leucine-rich repeats region, 2 in a transmembrane region and 6 in a Ser/Thr kinase domain). The probability of substitution at each site was not the same, there were two hot spots, one was in the 5'-untranslated region between positions 124 and 804, and the other was in the region between positions 2520 and 3733. Sequence diversity analysis among 104 soybean genotypes showed π = 0.00102 and θ = 0.00218 for Rhg4. A domestication bottleneck was found because of lower sequence diversity and 58% unique SNPs loss in landraces compared with Glycine soja. Intensive selection increased the sequence diversity of cultivars, which had higher diversity and more unique SNPs than landraces. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-012-9703-1) contains supplementary material, which is available to authorized users.