Pan-Genome of Wild and Cultivated Soybeans.

Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.

High Precision Positioning and Rotation Angle Estimation of a Flatbed Truck Based on BDS and Vision.

Centimeter-level localization and precise rotation angle estimation for flatbed trucks pose significant challenges in unmanned forklift automated loading scenarios. To address this issue, the study proposed a method for high-precision positioning and rotation angle estimation of flatbed trucks using the BeiDou Navigation Satellite System (BDS) and vision technology. First, an unmanned forklift equipped with a Time-of-Flight (ToF) camera and a dual-antenna mobile receiver for BDS positioning collected depth images and localization data near the front and rear endpoints of the flatbed. The Deep Dual-Resolution Network-23-slim (DDRNet-23-slim) model was used to segment the flatbed from the depth image and extract the straight lines at the edges of the flatbed using the Hough transform. The algorithm then computed the set of intersection points of the lines. A neighborhood feature vector was designed to identify the endpoint of a flatbed from a set of intersection points using feature screening. Finally, the relative coordinates of the endpoints were converted to a customized forklift navigation coordinate system by BDS positioning. A rotation angle estimation was then performed using the endpoints at the front and rear. Experiments showed that the endpoint positioning error was less than 3 cm, and the rotation angle estimation error was less than 0.3°, which verified the validity and reliability of the method.

Exploring the relationship between digital transformation and green innovation: The mediating role of financing modes.

Green innovation is important and beneficial for the green development of enterprises. The development of digital technology could improve the asymmetry of information and affect the enterprise's financing modes. Currently, a definitive conclusion about the relationship between the digital transformation and green technology innovation has not reached. Additionally, studies have not yet fully explored the impact pathways of corporate digital transformation on green innovation through corporate financing modes. To fill this void, this study collected data of Chinese A-share listed companies from 2010 to 2020. The empirical analysis results showed that digital transformation significantly enhanced enterprises' green innovation abilities. Furthermore, mediating models were utilized to explore how enterprise financing modes mediate the impact of digital transformation on the enterprise green innovation. Results indicated that through internal financing and bank loans as "bridges", digital transformation promoted enterprise green innovation. However, digital transformation did not have a significant impact on enterprise green innovation through venture capital. Moreover, heterogeneity analyses revealed significant differences among different groups of enterprises. This study expands the research field related to digital transformation and enterprise green innovation by providing empirical evidence to uncover the impact of digital transformation on enterprise green innovation. Findings of this study contribute not only to enterprise managerial decision-makers to better leverage digital transformation through corporate financing to accelerate green innovation, but also to government policymakers to design policies to stimulate enterprise green innovation.

The Effects of Nutrition and Health Claim Information on Consumers' Sensory Preferences and Willingness to Pay.

As marketing tools, nutrition claims (NCs) and health claims (HCs) can be used to convey the nutritional properties and health benefits of food to consumers, but their respective effects on consumers' perceptions of healthier meat products are inconsistent in the literature. Using a physical prototype of omega-3-enriched sausages as a research interest, this paper explores how HCs and NCs differently influence consumers' sensory preferences and willingness to pay (WTP). Sensory tests were carried out among 330 participants, followed by a choice-based conjoint (CBC) experiment to measure consumers' WTP. Results indicate that, in comparison with the uninformed condition, labeling an omega-3 nutrition claim increased consumers' sensory liking for omega-3-enriched sausages in the attributes of appearance and texture. Moreover, consumers were willing to pay more for healthier sausages, but labeling HCs did not significantly improve participants' WTP for omega-3-enriched sausages more than NCs. Hence, HCs did not significantly outperform NCs, when it comes to positively influencing consumers' sensory liking and paying intentions for omega-3-enriched sausages. The findings of this study have implications for the meat industry in developing healthier sausage formulations with greater likelihood of success in the market.

Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references.

Even though the human reference genome assembly is continually being improved, it remains debatable whether a population-specific reference is necessary for every ethnic group. Here, we de novo assembled an individual genome (TJ1) from the Tujia population, an ethnic minority group most closely related to the Han Chinese. TJ1 provided a high-quality haplotype-resolved assembly of chromosome-scale with a scaffold N50 size >78 Mb. Compared with GRCh38 and other de novo assemblies, TJ1 improved short-read mapping, enhanced calling precision for structural variants, and detected rare and low-frequency variants. This revealed fine-scale differences between the closely related Han and Tujia populations, such as population-stratified variants of LCT and UBXN8, and improved screening for ancestry informative markers. We demonstrated that TJ1 could reduce false positives in clinical diagnosis and analyzed the PRSS1-PRSS2 locus as a test case. Our results suggest that population-specific assemblies are necessary for genetic and medical analysis, especially when closely related populations are studied. A record of this paper's transparent peer review process is included in the supplemental information.

The genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution.

Halophytes have evolved specialized strategies to cope with high salinity. The extreme halophyte sea lavender (Limonium bicolor) lacks trichomes but possesses salt glands on its epidermis that can excrete harmful ions, such as sodium, to avoid salt damage. Here, we report a high-quality, 2.92-Gb, chromosome-scale L. bicolor genome assembly based on a combination of Illumina short reads, single-molecule, real-time long reads, chromosome conformation capture (Hi-C) data, and Bionano genome maps, greatly enriching the genomic information on recretohalophytes with multicellular salt glands. Although the L. bicolor genome contains genes that show similarity to trichome fate genes from Arabidopsis thaliana, it lacks homologs of the decision fate genes GLABRA3, ENHANCER OF GLABRA3, GLABRA2, TRANSPARENT TESTA GLABRA2, and SIAMESE, providing a molecular explanation for the absence of trichomes in this species. We identified key genes (LbHLH and LbTTG1) controlling salt gland development among classical trichome homologous genes and confirmed their roles by showing that their mutations markedly disrupted salt gland initiation, salt secretion, and salt tolerance, thus offering genetic support for the long-standing hypothesis that salt glands and trichomes may share a common origin. In addition, a whole-genome duplication event occurred in the L. bicolor genome after its divergence from Tartary buckwheat and may have contributed to its adaptation to high salinity. The L. bicolor genome resource and genetic evidence reported in this study provide profound insights into plant salt tolerance mechanisms that may facilitate the engineering of salt-tolerant crops.

Investigating the Relationship Between Entity Financialization, Managers' Incentives, and Enterprise's Innovation: Fresh Evidence From China.

The current study examines the relationship between financialization, managers' incentives, and the enterprise's innovation. Based on the principal-agent and incentive theories, this study proposes a research model with two management incentives as moderating variables between financialization and the enterprise's innovation. First, we analyze the direct relationship between financialization and the enterprise's innovation. Second, we examine the moderating effect of managers' equity incentive and compensation incentives on the relationship between entity financialization and the enterprise's innovation in high-tech/non-high-tech enterprises and state-owned and non-state-owned enterprises. This study covers the most recent updated data from both A-share listed companies in the Shenzhen and Shanghai stock exchange in China from 2009 to 2019. This study's finding indicates a significant negative impact of entity financialization and the enterprise's innovation. It means that the entity financial has a significant "crowding-out" effect on the enterprise's innovation. This study also confirms that management incentives cannot effectively suppress a "crowding-out" impact of entity financialization on firm innovation because of the principal-agent severe problem in financialization. Finally, considering the heterogeneities of property rights and degrees of dependence on the enterprise's innovation, a "crowding-out" effect of entity financialization on the enterprise's innovation is more significant in high-tech and state-owned enterprises. Managers' equity incentive significantly affects the enterprise's innovation in high-tech enterprises, while the managers' compensation incentive affects the enterprise's innovation in state-owned enterprises. Our study could help the enterprise to improve the company manager's incentive and provide the optimal assets allocation to improve the enterprise's innovation ability. Lastly, this study provides significant policies and recommendations for the public sector high-tech enterprise and private sector high-tech enterprises. Moreover, policies and recommendations are fruitful for the public sector non-high-tech enterprise and private sector non-high-tech enterprise.

Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia.

Figs and fig pollinators are one of the few classic textbook examples of obligate pollination mutualism. The specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat changes. However, there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig pollinators. In fig syconia, there are also non-pollinator species. The non-pollinator species differ in their evolutionary and life histories from pollinators. We conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published genome. The pollinators colonized the figs approximately 66.9 million years ago, consistent with the origin of host figs. Compared with non-pollinators, many more genes in pollinators were subject to relaxed selection. Seven genes were absent in pollinators in response to environmental stress and immune activation. Pollinators had more streamlined gene repertoires in the innate immune system, chemosensory toolbox, and detoxification system. Our results provide genomic evidence for the differentiation between pollinators and nonpollinators. The data suggest that owing to the long-term adaptation to the fig, some genes related to functions no longer required are absent in pollinators.

Resequencing of 683 common bean genotypes identifies yield component trait associations across a north-south cline.

We conducted a large-scale genome-wide association study evaluation of 683 common bean accessions, including landraces and breeding lines, grown over 3 years and in four environments across China, ranging in latitude from 18.23° to 45.75° N, with different planting dates and abiotic or biotic stresses. A total of 505 loci were associated with yield components, of which seed size, flowering time and harvest maturity traits were stable across years and environments. Some loci aligned with candidate genes controlling these traits. Yield components were observed to have strong associations with a gene-rich region on the long arm of chromosome 1. Manipulation of seed size, through selection of seed length versus seed width and height, was deemed possible, providing a genome-based means to select for important yield components. This study shows that evaluation of large germplasm collections across north-south geographic clines is useful in the detection of marker associations that determine grain yield in pulses.

De novo assembly of a Chinese soybean genome.

Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding. Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome (cv. Williams 82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.

Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum.

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world's poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.