Search

Genetic adaptation of soybean phenological stages to high‐latitude long‐day environments is the major pre‐requisite for enhancing regional plant‐based protein production. Both E‐genes controlling flowering and growing environment determine timing of flowering and maturity, and E‐gene composition might differ between Chinese and European soybeans bearing the potential for improving adaptability. Therefore, 140 early maturity elite soybean cultivars of either Chinese or European origin were genotyped for the E1 to E4 flowering loci, and genotypes were tested across 17 European environments spanning a latitude range from 45 to 52°N in order to determine effects of various E‐allele combinations. Differences in E‐allele composition between Chinese and European cultivars were largest for the loci E1 and E3. Wild‐type alleles significantly delayed flowering, and effects of particular E‐alleles were depending on geographic latitude. Consequently, photoperiod‐insensitive E‐haplotypes carrying several non‐functional alleles proved to be suitable for cultivation in higher latitudes, whereas photoperiod‐sensitive late‐maturity E‐haplotypes are adapted to lower latitudes only. Thus, breeding for new E‐haplotypes through combining Chinese and European alleles could enhance the potential for further soybean adaptation to northern growing regions. [ABSTRACT FROM AUTHOR]

Summary: Soybean is a short‐day plant that typically flowers earlier when exposed to short‐day conditions. However, the identification of genes associated with earlier flowering time but without a yield penalty is rare. In this study, we conducted genome‐wide association studies (GWAS) using two re‐sequencing datasets that included 113 wild soybeans (G. soja) and 1192 cultivated soybeans (G. max), respectively, and simultaneously identified a candidate flowering gene, qFT13‐3, which encodes a protein homologous to the pseudo‐response regulator (PRR) transcription factor. We identified four major haplotypes of qFT13‐3 in the natural population, with haplotype H4 (qFT13‐3H4) being lost during domestication, while qFT13‐3H1 underwent natural and artificial selection, increasing in proportion from 4.5% in G. soja to 43.8% in landrace and to 81.9% in improve cultivars. Notably, most cultivars harbouring qFT13‐3H1 were located in high‐latitude regions. Knockout of qFT13‐3 accelerated flowering and maturity time under long‐day conditions, indicating that qFT13‐3 functions as a flowering inhibitor. Our results also showed that qFT13‐3 directly downregulates the expression of GmELF3b‐2 which is a component of the circadian clock evening complex. Field trials revealed that the qft13‐3 mutants shorten the maturity period by 11 days without a concomitant penalty on yield. Collectively, qFT13‐3 can be utilized for the breeding of high‐yield cultivars with a short maturity time suitable for high latitudes. [ABSTRACT FROM AUTHOR]

Abstract 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.

Functional identification of salt-tolerant genes is crucial for the improvement of soybean varieties and the development and utilization of saline-alkali land. Under salt stress, crops reduce the effect of salt damage on crop yield by synthesizing and accumulating betaine as osmotic protective agent. BADH gene is been proved to regulate plant response to stress in many plants, but the regulation mechanism in soybean is not clear. In this study, GmBADH1 gene was cloned, and qRT-PCR showed that the gene was expressed stems and leaves, especially in roots. The expression vector constructed by CRISPR/Cas9 system was transferred into soybean variety JACK by Agrobacterium-mediated soybean genetic transformation technology, and three targeted mutations that could regulate the salt tolerance of soybean were produced. They all occurred in the coding region, which had three difference of deletion 19 bp, insertion 1 bp, and insertion 9 bp to replace 2 bp. The first two, premature termination codons, resulting in truncated BADH1 protein, the latter occurred frameshift mutation. The mutant homozygous plants were treated with salt at the emergence stage and seedling stage, respectively. The results showed that the salt tolerance of the mutant homozygous plants was significantly lower than that of the wild type at seedling stage, and there was no significant difference compared with the wild type at seeding stage, which indicating that GmBADH1 gene may mainly regulate the salt tolerance of seedling stage. This study provides a basis for further excavation of soybean salt-tolerant genes and cultivation of soybean salt-tolerant varieties. [ABSTRACT FROM AUTHOR]

Salinity greatly affects the production of soybeans in arid and semi-arid lands around the world. The responses of soybeans to salt stress at germination, emergence, and other seedling stages have been evaluated in multitudes of studies over the past decades. Considerable salt-tolerant accessions have been identified. The association between salt tolerance responses during early and later growth stages may not be as significant as expected. Genetic analysis has confirmed that salt tolerance is distinctly tied to specific soybean developmental stages. Our understanding of salt tolerance mechanisms in soybeans is increasing due to the identification of key salt tolerance genes. In this review, we focus on the methods of soybean salt tolerance screening, progress in forward genetics, potential mechanisms involved in salt tolerance, and the importance of translating laboratory findings into field experiments via marker-assisted pyramiding or genetic engineering approaches, and ultimately developing salt-tolerant soybean varieties that produce high and stable yields. Progress has been made in the past decades, and new technologies will help mine novel salt tolerance genes and translate the mechanism of salt tolerance into new varieties via effective routes. [ABSTRACT FROM AUTHOR]

Advances in plant phenotyping technologies are dramatically reducing the marginal costs of collecting multiple phenotypic measurements across several time points. Yet, most current approaches and best statistical practices implemented to link genetic and phenotypic variation in plants have been developed in an era of single‐time‐point data. Here, we used time‐series phenotypic data collected with an unmanned aircraft system for a large panel of soybean (Glycine max (L.) Merr.) varieties to identify previously uncharacterized loci. Specifically, we focused on the dissection of canopy coverage (CC) variation from this rich data set. We also inferred the speed of canopy closure, an additional dimension of CC, from the time‐series data, as it may represent an important trait for weed control. Genome‐wide association studies (GWASs) identified 35 loci exhibiting dynamic associations with CC across developmental stages. The time‐series data enabled the identification of 10 known flowering time and plant height quantitative trait loci (QTLs) detected in previous studies of adult plants and the identification of novel QTLs influencing CC. These novel QTLs were disproportionately likely to act earlier in development, which may explain why they were missed in previous single‐time‐point studies. Moreover, this time‐series data set contributed to the high accuracy of the GWASs, which we evaluated by permutation tests, as evidenced by the repeated identification of loci across multiple time points. Two novel loci showed evidence of adaptive selection during domestication, with different genotypes/haplotypes favored in different geographic regions. In summary, the time‐series data, with soybean CC as an example, improved the accuracy and statistical power to dissect the genetic basis of traits and offered a promising opportunity for crop breeding with quantitative growth curves. [ABSTRACT FROM AUTHOR]

The soybean aphid poses a severe threat to soybean quality and yield by sucking phloem sap and transmitting plant viruses. An early-maturing and highly resistant soybean landrace, Fangzheng Moshidou, with markedly reduced aphid colonization has been identified by screening of aphid-resistant soybean accessions. In a population derived from the cross of Fangzheng Moshidou with the susceptible cultivar Beifeng 9, resistance was conferred by a single dominant gene. Three linked markers, Satt114, Satt334, and Sct_033, on chromosome 13 were identified by bulked-segregant analysis. Additional simple-sequence repeat and single-nucleotide polymorphism (SNP) markers were developed for gene mapping. The resistance of Fangzheng Moshidou was fine-mapped to the interval between the SNP markers YCSNP20 and YCSNP80, corresponding to 152.8 kb in the Williams 82 assembly 2 genome. This region was near the reported loci Rag2 and Rag5 but did not overlap the interval containing them. A unique haplotype is described for Fangzheng Moshidou that distinguishes it from soybean accessions PI 587972, PI 594879, and PI 567301B in the interval containing Rag2 and Rag5. These results indicate that Fangzheng Moshidou harbors a novel gene at a tightly linked resistance locus, designated as RagFMD. Fourteen candidate genes were annotated in the fine-mapping region, including seven NBS-LRR genes, which are usually considered resistance genes in plant defense. Most of these candidate genes showed variations distinguishing the resistant and susceptible parents and some genes also showed differences in expression between the two parental lines and at several times after aphid infestation. Isolation of RagFMD would advance the study of molecular mechanisms of soybean aphid resistance and contribute to precise selection of resistant soybeans. [ABSTRACT FROM AUTHOR]

Purpose: This study aimed to examine the relationship between anxiety, depression, sleep quality and health-related quality of life among systemic lupus erythematosus (SLE) patients in China. Patients and Methods: After ethical approval and obtaining participants' informed consent, a cross-sectional study was conducted in The First Affiliated Hospital of Anhui Medical University between October 1, 2021 and January 30, 2022. The data comprised demographic information, number of SLE symptoms, Hospital Anxiety and Depression Scale (HADS), Pittsburgh Sleep Quality Index (PSQI) and Systemic Lupus Erythematosus-Specific Quality of Life Questionnaire (SLEQoL). We performed descriptive statistics, Spearman or Pearson correlations, and multiple linear regression. And Path analysis was performed to examine direct and indirect associations between these variables and health-related quality of life. Results: A total of 580 patients were recruited and 513 met our target criteria. Our final model fitted the data well: goodness-of-fit index (GFI) =0.996; adjusted goodness-of-fit index (AGFI) =0.974; comparative fit index (CFI) =0.998; root mean square error of approximation (RMSEA) =0.043. This model explained 57.3% of the variance on health-related quality of life (HRQoL) in patients with SLE and all the hypothesized paths reached significance (P< 0.05). Anxiety, depression, sleep quality, income/family, and number of SLE symptoms were related to health-related quality of life, and anxiety had the most influence on HRQoL (β=0.561). Conclusion: The study model helps to explain the relation among anxiety, depression, sleep quality and health-related quality of life in patients with SLE. It also suggests that health care professionals should be aware of factors such as anxiety, sleep quality, number of SLE symptoms, and depression in their care for HRQoL of SLE patients. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Asthma is observationally associated with an increased risk of COVID-19, but the causality remains unclear. We aim to determine whether there is a casual role of asthma in susceptibility to SARS-CoV-2 infection or COVID-19 severity. Methods: Instrumental variables (IVs) for asthma and moderate-to-severe asthma were obtained from publicly available summary statistics from the most recent and largest genome-wide association study (GWAS), including 394 283 and 57 695 participants of European ancestry, respectively. The corresponding data for COVID-19 susceptibility, hospitalization and severe-disease were derived from the COVID-19 Host Genetics Initiative GWAS meta-analysis of up to 1 683 768 individuals of European descent. Causality was inferred between correlated traits by Mendelian Randomization analyses. Inverse-variance weighted method was used as the primary MR estimates and multiple alternate approaches and several sensitivity analyses were also conducted. Results: Our MR analysis revealed no causal effects of asthma on COVID-19 susceptibility, hospitalization or severe disease, with odds ratio (OR) of 0.994 (95% CI: 0.962–1.027), 1.020 (95% CI: 0.955–1.089), and 0.929 (95% CI: 0.836–1.032), respectively. Furthermore, using genetic variants for moderate-to-severe asthma, a similar pattern of results was observed for COVID-19 susceptibility (OR: 0.988, 95% CI: 0.946–1.031), hospitalization (OR: 0.967, 95% CI: 0.906–1.031), and severe disease (OR: 0.911, 95% CI: 0.823–1.009). The association of asthma and moderate-to-severe asthma with COVID-19 was overall robust to sensitivity analyses. Conclusion: Genetically predicted asthma was not associated with susceptibility to, or severity of, COVID-19 disease, indicating that asthma is unlikely to be a causal factor in the development of COVID-19. [ABSTRACT FROM AUTHOR]