Domestication and improvement genes reveal the differences of seed size- and oil-related traits in soybean domestication and improvement.

To address domestication and improvement studies of soybean seed size- and oil-related traits, a series of domesticated and improved regions, loci, and candidate genes were identified in 286 soybean accessions using domestication and improvement analyses, genome-wide association studies, quantitative trait locus (QTL) mapping and bulked segregant analyses in this study. As a result, 534 candidate domestication regions (CDRs) and 458 candidate improvement regions (CIRs) were identified in this study and integrated with those in five and three previous studies, respectively, to obtain 952 CDRs and 538 CIRs; 1469 loci for soybean seed size- and oil-related traits were identified in this study and integrated with those in Soybase to obtain 433 QTL clusters. The two results were intersected to obtain 245 domestication and 221 improvement loci for the above traits. Around these trait-related domestication and improvement loci, 7 domestication and 7 improvement genes were found to be truly associated with these traits, and 372 candidate domestication and 87 candidate improvement genes were identified using gene expression, SNP variants in genome, miRNA binding, KEGG pathway, DNA methylation, and haplotype analysis. These genes were used to explain the trait changes in domestication and improvement. As a result, the trait changes can be explained by their frequencies of elite haplotypes, base mutations in coding region, and three factors affecting their expression levels. In addition, 56 domestication and 15 improvement genes may be valuable for future soybean breeding. This study can provide useful gene resources for future soybean breeding and molecular biology research.

Penicillium fungi mediate behavioral responses of the yellow peach moth, Conogethes punctiferalis (Guenée) to apple fruits via altering the emissions of host plant VOCs.

Plant-associated microbes have been reported as important but overlooked drivers of plant-herbivorous insect interactions. Influence of plant-associated microbes on plant-insect interactions is diverse, including beneficial, detrimental, and neutral. Here, we determined the effects of three Penicillium fungi, including Penicillium citrinum, Penicillium sumatrense, and Penicillium digitatum, on the oviposition selection and behavior of the yellow peach moth (YPM), Conogethes punctiferalis (Guenée). Compared with fungi noninfected apples (NIA), mechanically damaged apples (MDA), and P. citrinum in potato dextrose agar medium (PC), the oviposition selection and four-arm olfactometer experiments both showed that mated YPM females preferred to P. citrinum-infected apples (PCA). For P. sumatrense or P. digitatum, we also found that mated YPM females preferred to P. sumatrense-infected apples (PSA) or P. digitatum-infected apples (PDA), respectively. Among three Penicillium fungi-infected apples, the selection rates including oviposition and olfactometer behavior of mated YPM females on PDA were both higher than those on PSA and PCA. Further analyses of host plant volatile organic compounds (VOCs) by GC-MS showed that the absolute contents of ethyl hexanoate and (Z, E)-α-farnesene in PCA, PSA, and PDA were all higher than those in NIA, and a total of 16 novel VOCs were detected in fungi-infected apples (PCA, PSA, and PDA), indicating that fungi infection changed the components and proportions of apple VOCs. Taken together, three Penicillium fungi play significant roles in mediating the host selection of YPMs via altering the emissions of VOCs. These findings will be beneficial for developing formulations for field trapping of YPMs in the future.

A Cas6-based RNA tracking platform functioning in a fluorescence-activation mode.

Given the fact that the localization of RNAs is closely associated with their functions, techniques developed for tracking the distribution of RNAs in live cells have greatly advanced the study of RNA biology. Recently, innovative application of fluorescent protein-labelled Cas9 and Cas13 into live-cell RNA tracking further enriches the toolbox. However, the Cas9/Cas13 platform, as well as the widely-used MS2-MCP technique, failed to solve the problem of high background noise. It was recently reported that CRISPR/Cas6 would exhibit allosteric alteration after interacting with the Cas6 binding site (CBS) on RNAs. Here, we exploited this feature and designed a Cas6-based switch platform for detecting target RNAs in vivo. Conjugating split-Venus fragments to both ends of the endoribonuclease-mutated Escherichia coli Cas6(dEcCas6) allowed ligand (CBS)-activated split-Venus complementation. We name this platform as Cas6 based Fluorescence Complementation (Cas6FC). In living cells, Cas6FC could detect target RNAs with nearly free background noise. Moreover, as minimal as one copy of CBS (29nt) tagged in an RNA of interest was able to turn on Cas6FC fluorescence, which greatly reduced the odds of potential alteration of conformation and localization of target RNAs. Thus, we developed a new RNA tracking platform inherently with high sensitivity and specificity.

Peri-implant keratinized gingiva augmentation using xenogeneic collagen matrix and platelet-rich fibrin: A case report.

BACKGROUND: Keratinized gingival insufficiency is a disease attributed to long-term tooth loss, can severely jeopardizes the long-term health of implants. A simple and effective augmentation surgery method should be urgently developed. CASE SUMMARY: A healthy female patient, 45-year-old, requested implant restoration of the her left mandibular first molar and second molar. Before considering a stage II, as suggested from the probing depth measurements, the widths of the mesial, medial, and distal buccal keratinized gingiva of second molar (tooth #37) were measured and found to be 0.5 mm, 0.5 mm, and 0 mm, respectively. This suggested that the gingiva was insufficient to resist damage from bacterial and mechanical stimulation. Accordingly, modified apically repositioned flap (ARF) surgery combined with xenogeneic collagen matrix (XCM) and platelet-rich fibrin (PRF) was employed to increase the width of gingival tissue. After 1 mo of healing, the widths of mesial, medial, and distal buccal keratinized gingiva reached 4 mm, 4 mm, and 3 mm, respectively, and the thickness of the augmented mucosa was 4.5 mm. Subsequently, through the second-stage operation, the patient obtained an ideal soft tissue shape around the implant. CONCLUSION: For cases with keratinized gingiva widths around implants less than 2mm，the soft tissue width and thickness could be increased by modified ARF surgery combined with XCM and PRF. Moreover, this surgery significantly alleviated patients' pain and ameliorated oral functional comfort.

Identification of QTNs and their candidate genes for flowering time and plant height in soybean using multi-locus genome-wide association studies.

Flowering time (FT) and plant height (PH) are important agronomic traits in soybean. However, their genetic foundations are not fully understood. Thus, in this study, a total of 106,013 single nucleotide polymorphisms in 286 soybean accessions were used to associate with the first and full FT (FT1 and FT2) and PH in 4 environments and their BLUP values using 6 multi-locus genome-wide association study methods. As a result, 38, 43, and 27 stable quantitative trait nucleotides (QTNs) were identified, respectively, for FT1, FT2, and PH across at least 3 methods and/or environments. Among these QTNs for FT1, FT2, and PH, 31, 36, and 21 were found to have significant phenotype differences across 2 alleles; 22, 18, and 13 were consistent with the corresponding loci in previous studies; 13 and 8 genes, with more than average expression level, around 64 FT and 27 PH QTNs were predicted as their corresponding candidate genes. Among these candidate genes, GmPRR3b, and GmGIa for FT, and GmTFL1b for PH were known, while some were new, e.g., GmPHYA4, GmVRN5, GmFPA, and GmSPA1 for FT, and Glyma.02g300200, GmFPA, and Glyma.13g339800 for PH. All the validated QTNs were used to design the best cross-combinations in 2 FT directions. In each FT direction, the best 5 cross-combinations were predicted, such as Heihe 54 × Qincha 1 for early FT, and Yingdejiadou × Wuhuabayuehuang for late FT. This study provides solid foundations for genetic basis, molecular biology, and breeding by design of soybean FT and PH. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01230-3.

Identification of QTNs and Their Candidate Genes for 100-Seed Weight in Soybean (Glycine max L.) Using Multi-Locus Genome-Wide Association Studies.

100-seed weight (100-SW) in soybeans is a yield component trait and controlled by multiple genes with different effects, but limited information is available for its quantitative trait nucleotides (QTNs) and candidate genes. To better understand the genetic architecture underlying the trait and improve the precision of marker-assisted selection, a total of 43,834 single nucleotide polymorphisms (SNPs) in 250 soybean accessions were used to identify significant QTNs for 100-SW in four environments and their BLUP values using six multi-locus and one single-locus genome-wide association study methods. As a result, a total of 218 significant QTNs were detected using multi-locus methods, whereas eight QTNs were identified by a single-locus method. Among 43 QTNs or QTN clusters identified repeatedly across various environments and/or approaches, all of them exhibited significant trait differences between their corresponding alleles, 33 were found in the genomic region of previously reported QTLs, 10 were identified as new QTNs, and three (qHSW-4-1, qcHSW-7-3, and qcHSW-10-4) were detected in all the four environments. The number of seed weight (SW) increasing alleles for each accession ranged from 8 (18.6%) to 36 (83.72%), and three accessions (Yixingwuhuangdou, Nannong 95C-5, and Yafanzaodou) had more than 35 SW increasing alleles. Among 36 homologous seed-weight genes in Arabidopsis underlying the above 43 stable QTNs, more importantly, Glyma05g34120, GmCRY1, and GmCPK11 had known seed-size/weight-related genes in soybean, and Glyma07g07850, Glyma10g03440, and Glyma10g36070 were candidate genes identified in this study. These results provide useful information for genetic foundation, marker-assisted selection, genomic prediction, and functional genomics of 100-SW.

Single-nucleotide polymorphisms of APE1 associated with risk and prognosis of vitiligo in a Han Chinese population.

BACKGROUND: The single-nucleotide polymorphisms (SNPs) of apurinic/apyrimidinicendonuclease 1 (APE1), which has been implicated in cancers and the DNA base excision repair (BER) process, have not been thoroughly investigated in association with the risks of oxidative stress-related vitiligo. OBJECTIVES: The aim of this study is to investigate associations between APE1 single-nucleotide polymorphisms 141T >G and 1349T >G and risk and prognosis of vitiligo. MATERIAL AND METHODS: From June 2013 to June 2015, a total of 460 vitiligo patients were randomly recruited as a case group; 200 of these patients received narrow bound ultraviolet B (NB-UVB) treatment. Meanwhile, 460 healthy controls were included as a control group. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to explore the distribution frequencies of genotypes. RESULTS: Significant differences were detected between the case group and the control group in the frequencies of the 141T >G and 1349T >G genotypes. At 141T >G, compared with patients carrying the TG + GG genotype, male patients carrying the TT genotype aged more than 20 years with active non-segmental vitiligo, without a family history of vitiligo or other autoimmune diseases, exhibited an increased risk of vitiligo. Binary logistic regression analysis demonstrated that the TT genotype at 141T >G and the non-TT genotype at 1349T >G were independent risk factors for vitiligo development. At 1349T >G, compared with patients carrying the TT genotype, male patients carrying the TG + GG genotype aged more than 20 years with active non-segmental vitiligo, without a family history of vitiligo or other autoimmune diseases, exhibited an increased risk of vitiligo. Moreover, patients carrying 141TG + GG or 1349 TT genotypes had better photochromic effects, lower cumulative radiation doses, shorter treatment times, and earlier first photochromic times.

Sex-specific responses to winter flooding, spring waterlogging and post-flooding recovery in Populus deltoides.

Winter flooding events are common in some rivers and streams due to dam constructions, and flooding and waterlogging inhibit the growth of trees in riparian zones. This study investigated sex-specific morphological, physiological and ultrastructural responses to various durations of winter flooding and spring waterlogging stresses, and post-flooding recovery characteristics in Populus deltoides. There were no significant differences in the morphological, ultrastructural and the majority of physiological traits in trees subjected to medium and severe winter flooding stresses, suggesting that males and females of P. deltoides were winter flooding tolerant, and insensitive to winter flooding duration. Males were more tolerant to winter flooding stress in terms of photosynthesis and chlorophyll fluorescence than females. Females displayed greater oxidative damage due to flooding stress than males. Males developed more efficient antioxidant enzymatic systems to control reactive oxygen species. Both sexes had similarly strong post-flooding recovery capabilities in terms of plant growth, and physiological and ultrastructural parameters. However, Males had better recovery capabilities in terms of pigment content. These results increase the understanding of poplars's adaptation to winter flooding stress. They also elucidate sex-specific differences in response to flooding stress during the dormant season, and during post-flooding recovery periods.

[BEX2 regulates cell cycle through the interaction with INI1/hSNF5].

BEX2 (Brain expressed X-linked protein 2), a 13 kDa protein, is highly expressed in brain and testis. It is reported that the protein expression of BEX2 dramatically alters during the embryo development, but little is known about its function. By means of yeast two-hybrid screening, we isolated that INI1/hSNF5 was a binding partner for BEX2, a key component of SWI/SNF chromosome remolding complex. GST Pull-down experiment interaction is physical and specific. Further analysis using truncated mutations demonstrated that the two partner for BEX2, a key component of SWI/SNF chromosome remolding complex. GST Pull-down experiment confirmed that BEX2 can interact with INI1/hSNF5 directly and specifically. Truncated mutations analysis further demonstrated that the two conserved reverse repeats sequences within INI1/hSNF5 were necessary for the interaction. Sub-cellular localization showed that both BEX2 and INI1/hSNF5 mainly localized in cell nucleus, which indicated that the interaction may be involved in the regulation of gene expression. Our experiments also showed that co-overexpressing of the two proteins affected cell cycle by increasing the cells in S phase, indicating that BEX2 could regulate cell cycle by interacting with INI1/hSNF5.