A Modified Roger's Distance Algorithm for Mixed Quantitative-Qualitative Phenotypes to Establish a Core Collection for Taiwanese Vegetable Soybeans

Genetic profiles and phenotypic patterns in Taiwanese Phalaenopsis orchids: a two-step phenotype and genotype strategy using modified genetic distance algorithms

This study establishes the first core collection (CC) for Taiwanese Phalaenopsis orchids to preserve genetic diversity and key traits essential for breeding and research, thereby enhancing breeding efficiency without the need for a large maintained parent population. We examined 207 commercial orchid cultivars from ten nurseries, characterized by two phenotypes and genotypic data from eight simple sequence repeat markers. Multiple imputation was applied to estimate missing phenotypes, minimizing potential uncertainties and ensuring the reliability of population structure analysis. Weighted k-means clustering identified seven distinct clusters, highlighting substantial genetic diversity. We proposed a two-step phenotype and genotype strategy and modified genetic distance algorithms to effectively preserve both phenotypic and genetic diversity while retaining key features. Consequently, 22 core accessions were selected, distributed across seven clusters, and representing the orchid germplasm collection. Our evaluation revealed significant diversity preservation, particularly in distinct characteristics and rare features, outperforming other methodologies. Pedigree background analysis further confirmed the representativeness of the CC in maintaining diverse genetic materials. We emphasized the importance of evaluating the CC by detailing the criteria and statistical analyses used to ensure the quality, representativeness, and effectiveness of the selected accessions. This study contributes to orchid breeding, conservation efforts, and sustainable agricultural practices by providing a valuable and comprehensive resource. In conclusion, our research establishes a groundbreaking CC, offering insights into the genetic landscape of Taiwanese Phalaenopsis orchids and highlighting potential advancements in breeding commercially desirable varieties.

Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean

Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties. However, the complex correlation patterns among quantitative traits with genetic architecture pose a challenge for improving vegetable soybean through breeding. Herein, a genome-wide association study (GWAS) was applied to 6 yield-related traits in 188 vegetable soybean accessions. Using a BLINK model, a total of 116 single nucleotide polymorphisms (SNPs) were identified for plant height, pod length, pod number, pod thickness, pod width, and fresh pod weight. Furthermore, a total of 220 genes were found in the 200 kb upstream and downstream regions of significant SNPs, including 11 genes encoding functional proteins. Among them, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed for significant haplotype variations and to be in LD block, which encode MYB-related transcription factor, auxin-responsive protein, F-box protein, and CYP450, respectively. The relative expression of candidate genes in V030 and V071 vegetable soybean (for the plant height, pod number, and fresh pod weight of V030 were lower than those of the V071 strains) was significantly different, and these genes could be involved in plant growth and development via various pathways. Altogether, we identified four candidate genes for pod yield and plant height from vegetable soybean germplasm. This study provides insights into the genomic basis for improving soybean and crucial genomic resources that can facilitate genome-assisted high-yielding vegetable soybean breeding.

Global Status of Vegetable Soybean

Vegetable soybean, popularly known as edamame in Japan and mao dou in China is a specialty soybean. Green pods with physiologically mature beans are harvested, and whole pods or shelled beans are used as a fresh or frozen vegetable. Vegetable soybeans are prepared in diverse ways, and they are highly nutritious, with excellent taste properties. Unlike grain soybeans, it is perishable. In this review, the chronological progression of area, production, export, import, and expansion of vegetable soybeans and potential for further expansion is discussed. Available information on current ongoing research and development activities in various countries around the world are presented, and their relevance is discussed. At present, the production and consumption of vegetable soybeans are mainly in East and Southeast Asia, with Japan as the largest importing country that dictates the global market. However, interest and trend in cultivation of this crop in other regions has increased significantly. Lack of germplasm or suitable varieties is a major constraint in vegetable soybean production and expansion in countries outside East and Southeast Asia. Most of the vegetable soybean varieties are genetically related and are susceptible to biotic and abiotic stresses. Extensive research and breeding of vegetable soybeans are still restricted in a few countries such as China, Japan, Taiwan and the USA. The need for focused research and development activities with concern for the environment, farmers' and processors' profit, consumers' preference, quality, and nutrition are emphasized.

Promoter of Vegetable Soybean GmTIP1;6 Responds to Diverse Abiotic Stresses and Hormone Signals in Transgenic Arabidopsis

Tonoplast intrinsic proteins (TIPs), a sub-family of aquaporins (AQPs), are known to play important roles in plant abiotic stress responses. However, evidence for the promoters of TIPs involvement in abiotic stress processes remains scarce. In this study, the promoter of the vegetable soybean GmTIP1;6 gene, which had the highest similarity to TIP1-type AQPs from other plants, was cloned. Expression pattern analyses indicated that the GmTIP1;6 gene was dramatically induced by drought, salt, abscisic acid (ABA), and methyl jasmonate (MeJA) stimuli. Promoter analyses revealed that the GmTIP1;6 promoter contained drought, ABA, and MeJA cis-acting elements. Histochemical staining of the GmTIP1;6 promoter in transgenic Arabidopsis corroborated that it was strongly expressed in the vascular bundles of leaves, stems, and roots. Beta-glucuronidase (GUS) activity assays showed that the activities of the GmTIP1;6 promoter were enhanced by different concentrations of polyethylene glycol 6000 (PEG 6000), NaCl, ABA, and MEJA treatments. Integrating these results revealed that the GmTIP1;6 promoter could be applied for improving the tolerance to abiotic stresses of the transgenic plants by promoting the expression of vegetable soybean AQPs.

A multiple phenotype imputation method for genetic diversity and core collection in Taiwanese vegetable soybean

Establishment of vegetable soybean (edamame) [Glycine max (L.) Merr.] germplasms has been highly valued in Asia and the United States owing to the increasing market demand for edamame. The idea of core collection (CC) is to shorten the breeding program so as to improve the availability of germplasm resources. However, multidimensional phenotypes typically are highly correlated and have different levels of missing rate, often failing to capture the underlying pattern of germplasms and select CC precisely. These are commonly observed on correlated samples. To overcome such scenario, we introduced the "multiple imputation" (MI) method to iteratively impute missing phenotypes for 46 morphological traits and jointly analyzed high-dimensional imputed missing phenotypes (EC impu ) to explore population structure and relatedness among 200 Taiwanese vegetable soybean accessions. An advanced maximization strategy with a heuristic algorithm and PowerCore was used to evaluate the morphological diversity among the EC impu . In total, 36 accessions (denoted as CC impu ) were efficiently selected representing high diversity and the entire coverage of the EC impu . Only 4 (8.7%) traits showed slightly significant differences between the CC impu and EC impu . Compared to the EC impu , 96% traits retained all characteristics or had a slight diversity loss in the CC impu . The CC impu exhibited a small percentage of significant mean difference (4.51%), and large coincidence rate (98.1%), variable rate (138.76%), and coverage (close to 100%), indicating the representativeness of the EC impu . We noted that the CC impu outperformed the CC raw in evaluation properties, suggesting that the multiple phenotype imputation method has the potential to deal with missing phenotypes in correlated samples efficiently and reliably without re-phenotyping accessions. Our results illustrated a significant role of imputed missing phenotypes in support of the MI-based framework for plant-breeding programs.

Genome-Wide Identification of Candidate Genes Underlying Soluble Sugar Content in Vegetable Soybean (Glycine max L.) via Association and Expression Analysis

Soluble sugar is a major indicator of the intrinsic quality of vegetable soybean [Glycine max (L.) Merr. ]. The improvement of soluble sugar content in soybean is very important due to its healthcare functions for humans. The genetic mechanism of soluble sugar in soybean is unclear. In this study, 278 diverse soybean accessions were utilized to identify the quantitative trait nucleotides (QTNs) for total soluble sugar content in soybean seeds based on a genome-wide association study (GWAS). A total of 25,921 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) ≥ 5% and missing data ≤ 10% were selected for GWAS. Totally, thirteen QTNs associated with total soluble sugar content were identified, which were distributed on ten chromosomes. One hundred and fifteen genes near the 200-kb flanking region of these identified QTNs were considered candidate genes associated with total soluble sugar content in soybean seed. Gene-based association analysis and haplotype analysis were utilized to further identify the effect of candidate genes on total soluble sugar content. Totally, 84 SNPs from seventeen genes across four chromosomes were significantly associated with the total soluble sugar content. Among them, three SNPs from Glyma.02G292900 were identified at two locations, and other eighty-one SNPs from sixteen genes were detected at three locations. Furthermore, expression level analysis of candidate genes revealed that Glyma.02G293200 and Glyma.02G294900 were significantly positively associated with soluble sugar content and Glyma.02G294000 was significantly negatively associated with soluble sugar content. Six genes (i.e., Glyma.02G292600, Glyma.02G292700, Glyma.02G294000, Glyma.02G294300, Glyma.02G294400, and Glyma.15G264200) identified by GWAS were also detected by the analysis of differential expression genes based on soybean germplasms with higher and lower soluble sugar content. Among them, Glyma.02G294000 is the only gene that was identified by gene-based association analysis with total soluble sugar content and was considered an important candidate gene for soluble sugar content. These candidate genes and beneficial alleles would be useful for improving the soluble sugar content of soybean.

Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean

Vegetable soybean is one of the most important vegetables in China, and the demand for this vegetable has markedly increased worldwide over the past two decades. Here, we present a high-quality de novo genome assembly of the vegetable soybean cultivar Zhenong 6 (ZN6), which is one of the most popular cultivars in China. The 20 pseudochromosomes cover 94.57% of the total 1.01 Gb assembly size, with contig N50 of 3.84 Mb and scaffold N50 of 48.41 Mb. A total of 55 517 protein-coding genes were annotated. Approximately 54.85% of the assembled genome was annotated as repetitive sequences, with the most abundant long terminal repeat transposable elements. Comparative genomic and phylogenetic analyses with grain soybean Williams 82, six other Fabaceae species and Arabidopsis thaliana genomes highlight the difference of ZN6 with other species. Furthermore, we resequenced 60 vegetable soybean accessions. Alongside 103 previously resequenced wild soybean and 155 previously resequenced grain soybean accessions, we performed analyses of population structure and selective sweep of vegetable, grain, and wild soybean. They were clearly divided into three clades. We found 1112 and 1047 genes under selection in the vegetable soybean and grain soybean populations compared with the wild soybean population, respectively. Among them, we identified 134 selected genes shared between vegetable soybean and grain soybean populations. Additionally, we report four sucrose synthase genes, one sucrose-phosphate synthase gene, and four sugar transport genes as candidate genes related to important traits such as seed sweetness and seed size in vegetable soybean. This study provides essential genomic resources to promote evolutionary and functional genomics studies and genomically informed breeding for vegetable soybean.

Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing

Vegetable soybean is a type of value-added specialty soybean, served as a fresh vegetable or snack in China. Due to the difference from other types, it is important to understand the genetic structure and diversity of vegetable soybean for further utilization in breeding programs. The four vegetable cultivars, Taiwan-75, Zhexiandou No. 8, Zhexian No. 9 and Zhexian No. 10 are popular soybean varieties planted in Zhejiang province, and have large pods and intermediate maturity. The clustering showed a close relationship of these four cultivars in simple sequence repeat analysis. To reveal the genome variation of vegetable soybean, these four improved lines were analyzed by whole-genome re-sequencing. The average sequencing depth was 7X and the coverage ratio of each cultivar was at least more than 94%. Compared with the reference genome, a large number of single-nucleotide polymorphisms, insertion/deletions and structure variations were identified with different chromosome distributions. The average heterozygosity rate of the single-nucleotide polymorphisms was 11.99% of these four cultivars. According to the enrichment analysis, there were 23,371 genes identified with putative modifications, and a total of 282 genes were related to carbohydrate metabolic processes. These results provide useful information for genetic research and future breeding, which can facilitate the selection procedures in vegetable soybean breeding.