A reference-grade wild soybean genome

Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci

A reference-grade wild soybean genome

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs

Neglecting legumes has compromised human health and sustainable food production

The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner 'nutritious seeds for a sustainable future'. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.We thank World University Network (WUN) and research collaboration awards (UWA and the University of Leeds) for financial support. CHF thanks the Biotechnology and Biological Sciences Research Council (BBSRC UK (BB/M009130/1) and the European Union (KBBE-2012-6-311840; ECOSEED) for financial support. JWC thanks BBSRC (UK) and Wherry and Sons, (UK) for an industrial CASE studentship (BB/K501839/1). H-ML was supported by the Hong Kong RGC Collaborative Research Fund (CUHK3/CRF/11G), the Lo Kwee-Seong Biomedical Research Fund and Lee Hysan Foundation. Ka-Ming Fung, Qianwen Wang, Lydia Kit-Wah Siu, and Yihan Jiang of The Chinese University of Hong Kong assisted in the production of Fig. 2, Table 1 and the associated webpage, highlight and cover design. We thank Hari Upadhyaya for the images shown in Fig. 4. TAM and JMH thank the Western Australian Government, Department of Industry and Resources for financial support. The authors thank Bodhi‟s Bakery, Fremantle, Western Australia, for baking the bread and biscuits and Belmar Foods, Balcatta, Western Australia, for manufacturing and providing the pasta. BNK and HB are supported by Australian Research Council (ARC), ITRH – Legumes for Sustainable Agriculture (IH140100013). MJC and CHF thank the ARC (DP150103211) for financial support. AJM is supported by grant funding (BB/JJ004553/1 and BB/L010305/1) from the BBSRC and the John Innes Foundation.http://www.nature.com/nplantshb2017Plant Production and Soil Scienc

The Seed Quality Assurance Regulations and Certification System in Soybean Production—A Chinese and International Perspective

Soybean is an important and valuable crop for global food and feed supply, providing high-quality nutrition. Globally, five countries—namely Brazil, the USA, Argentina, China and India—have dominated soybean production for many years. The intention of this paper is to review the reasons for their dominance, starting with seeds. High-quality seeds enable stress-free, high-density and even planting of soybean in the field. Seed quality assurance is essential for the successful expansion of soybean cultivation. The aim of this review is to compare and contrast the factors impacting soybean seed production in these top five soybean-producing countries, including the situations at different stages of the supply chain; research and development on new soybean varieties; and regulations, rules and quality assurance systems (seed testing, certification and labeling). Since the soybean supply chain involves many different operating parties, principles and practices, efforts on different fronts need to be well coordinated by a central authority to ensure successful production. Recently, China has implemented a revised national “Seed Law”. The possible impacts of this new legal framework on soybean seed development and trading in China are also discussed. The strengthened China Seed law to protect resources and encourage variety innovation, as well as the clearer China GM soybean commercial release policy, implies future soybean cultivation expansion with elite varieties. A continuous global production increase will require every party’s compliance to the sustainability principles

Data from: Improvement in nitrogen fixation capacity could be part of the domestication process in soybean

Biological nitrogen fixation (BNF) in soybeans is a complex process involving the interplay between the plant host and the symbiotic rhizobia. As nitrogen supply has a crucial role in growth and development, higher nitrogen fixation capacity would be important to achieve bigger plants and larger seeds, which were important selection criteria during plant domestication by humans. To test this hypothesis, we monitored the nitrogen fixation-related performance in 31 cultivated and 17 wild soybeans after inoculation with the slow-growing Bradyrhizobium diazoefficiens sp. nov. USDA110 and the fast-growing Sinorhizobium (Ensifer) fredii CCBAU45436. Our results showed that, in general, cultivated soybeans gave better performance in BNF. Electron microscopic studies indicated that there was an exceptionally high accumulation of poly-β-hydroxybutyrate bodies in bacteroids in the nodules of all wild soybeans tested, suggesting that the C/N balance in wild soybeans may not be optimized for nitrogen fixation. Furthermore, we identified new quantitative trait loci (QTLs) for total ureides and total nodule fresh weight by employing a recombinant inbred population composed of descendants from a cross between a cultivated and a wild parent. Using nucleotide diversity (θπ), divergence index (Fst) and distribution of fixed single-nucleotide polymorphisms as parameters, we found that some regions in the total ureides QTL on chromosome 17 and the total nodule fresh weight QTL on chromosome 12 exhibited very low diversity among cultivated soybeans, suggesting that these were traits specially selected during the domestication and breeding process

Development of a Set of Polymorphic DNA Markers for Soybean (<i>Glycine max</i> L.) Applications

Soybean (Glycine max L.) is gaining in importance due to its many uses, including as a food crop and a source of industrial products, among others. Increasing efforts are made to accelerate soybean research and develop new soybean varieties to meet global demands. Soybean research, breeding, identification, and variety protection all rely on precise genomic information. While DNA markers are invaluable tools for these purposes, the older generations, especially those developed before the advent of genome sequencing, lack precision and specificity. Thankfully, advancements in genome sequencing technologies have generated vast amounts of sequence data over the past decade, allowing precise and high-resolution analyses. However, making sense of the genomic information requires a certain level of professional training and computational power, which are not universally available to researchers. To address this, we generated a set of PCR-based DNA markers out of the existing genomic data from 228 popular soybean varieties that offer precise, unambiguous genomic information and can be easily adapted in various applications. A standard operating procedure (SOP) was also designed for these markers and validated on diverse soybean varieties to ensure their reproducibility. This user-friendly universal panel of DNA markers, along with the SOP, will facilitate soybean research and breeding programs through simple applications

Genotype and Phenotype of 96 Recombinant Inbred Lines

The data files contain the genotypic and phenotypic information of a recombinant inbred (RI) population. This population was obtained by crossing the cultivated Glycine max (C08) with the wild type Glycine soja (W05) was adopted from a previous study (Qi et al., 2014). In our previous research (Qi et al., 2014), a core panel of 96 RI lines was re-sequenced at ~1 X depth to generate high-quality single nucleotide polymorphism (SNP) information. An array of high-quality SNPs were grouped into 2,757 bin markers distributed on the 20 chromosomes. A bin map of 2,992.0 cM in the Kosambi mapping function was generated using the bin markers. Biological nitrogen fixation related phenotypes of the RILs were collected in controlled environment as mentioned in materials and methods