Comparative Genomics of Different Races of Columbia Root-knot Nematode and Development of Molecular Markers Linked to Corky Ringspot Resistance in Potato

On a global scale, potato (Solanum tuberosum L.) plays an important role in tackling the threat of food insecurity due to its high yield and broad global acceptance. However, pathogens threaten potato production, causing direct yield loss and rendering potatoes tubers unmarketable. Breeding new cultivars that carry multiple resistances is an efficient way for sustainable potato production. Columbia root-knot nematode (CRKN, Meloidogyne chitwoodi) parasitizes potato plants and causes small brown dots in the tuber flesh that dramatically reduce the market value of the crop. In the Pacific Northwest (PNW) two races of M. chitwoodi exist, Race 1 and Race 2; a pathotype of Race 1, Race 1Roza also occurs. The races of M. chitwoodi are primarily identified based on a differential host test. In order to understand the phylogeny of M. chitwoodi and develop molecular markers to identify the different races, we sequenced the genomes of M. chitwoodi Race 1, Race 2 and Race 1Roza using Illumina and PacBio sequencing. Each genome was assembled and annotated. Comparisons of syntenies and orthologs elucidate the complex evolutionary history of this species and facilitate molecular marker development and analysis of host plant resistance to these root-knot nematodes. Based on the genome comparisons of M. chitwoodi Race 1, Race 2 and Race 1Roza, we developed 36 pairs of PCR primers for SSR markers and 17 pairs of PCR primers for INDEL markers. Four of those molecular markers, HSINDEL8, HSINDEL5, HSINDEL9 and HSINDEL10, can successfully differentiate the three pathotypes of M. chitwoodi used in this study on agarose gel electrophoresis. These markers have application in plant disease diagnostics. Corky ringspot (CRS) disease caused by tobacco rattle virus (TRV) and vectored by stubby root nematodes, can render 6-55% of potatoes in an infested field unmarketable. Previous studies identified 22 SNP markers that are significantly associated with CRS resistance from ‘Castle Russet’ using a progeny of 48 seedlings. In this study we developed 44 pairs of PCR primers around previously identified significant SNPs. SNP marker PotVar0108448 on chromosome 9 shows polymorphisms on agarose gel electrophoresis and explains the highest percentage of phenotypic variance. Based on the initial marker screening, we developed 36 pairs of SSR primers, 72 pairs of primers for short INDELs and 36 pairs of primers for long INDELs on the upstream and downstream of SNP marker PotVar0108448. We screened them on 48 seedlings of progeny POR15V001 and 170 seedlings of progeny POR16V001. Markers INDEL20, INDEL490-7, Potvar008448 are linked to CRS resistance from ‘Castle Russet’. Of these, marker INDEL490-7 was robust and able to identify resistance from diverse germplasm. It has the potential for use in marker-assisted selection (MAS)

Disability-Free Life Expectancy among People Over 60 Years Old by Sex, Urban and Rural Areas in Jiangxi Province, China

Objective: To estimate and compare age trends and the disability-free life expectancy (DFLE) of the population over 60 years old in 2018 in Jiangxi Province, China, by sex and urban–rural areas. Methods: The model life table was employed to estimate the age-specific mortality rate by sex and urban–rural areas, based on the Summary of Health Statistics of Jiangxi Province in 2018 and the Sixth National Health Service survey of Jiangxi Province. DFLE and its ratio to life expectancy (LE) were obtained by the Sullivan method. Results: In 2018, the DFLE among people over 60 is 17.157 years for men and is 19.055 years for women, accounting for 89.7% and 86.5% of their LE respectively. The DFLE/LE of men is higher than that of women at all ages. LE and DFLE are higher for the population in urban areas than in rural areas. For women, DFLE/LE is higher in urban areas than in rural areas (except at ages 75 and 80). Urban men have a higher DFLE/LE than rural men (except at age 85). The difference in DFLE between men and women over 60 years is 1.898 years, of which 2.260 years are attributable to the mortality rate, and 0.362 years are due to the disability-free prevalence. In addition, the difference in DFLE between urban–rural elderly over 60 years old is mostly attributed to the mortality rate by gender (male: 0.902/1.637; female: 0.893/1.454), but the impact of the disability-free rate cannot be ignored either (male: 0.735/1.637; female: 0.561/1.454). Conclusions: The increase in DFLE is accompanied by the increase in LE, but with increased age, DFLE/LE gradually decreases. With advancing age, the effect of disability on elderly people becomes more severe. The government administration must implement some preventive actions to improve health awareness and the life quality of the elderly. Rural elderly; rural women in particular, need to be paid more attention and acquire more health care

Sheep 7SK promoter for short hairpin RNA expression

Background: Gene silencing mediated by small interfering RNA (siRNA) has become a powerful biological tool for the regulation of gene expression. For the synthesis of siRNA by vector-based expression systems, several mammalian small nuclear RNA (snRNA) promoters have been cloned and shown different transcriptional efficiencies. Results: In this study, we identified a sheep 7SK snRNA (s7SK) promoter based on the highly conserved polymerase III promoter elements. Promoter activity was measured by promoter-driven shRNA expression to suppress expression of an exogenous reporter gene and endogenous sheep gene. Conclusions: The knock down assay demonstrated that the s7SK induced more stronger inhibition effect than human U6 and H1 promoters. The use of this native sheep 7SK promoter for shRNA expressionis an important component for development of RNAi-based gene therapy and production of transgenic animals in sheep species

Spatial Congruence or Mismatch Between Phylogenetic and Functional Structure of Seed Plants Along a Tropical Elevational Gradient: Different Traits Have Different Patterns

Compared to species richness, few studies have investigated the patterns and relationship of phylogenetic and functional structures along elevational gradients. Here, we used the general additive models to determine the trends of taxonomic diversity (species richness, SR), phylogenetic and functional diversity (PD and FD), phylogenetic structure net relatedness index (NRI), and functional structure net functional relatedness index (NFRI) of seed plants along the elevational gradient in Mount Kenya, a tropical mountain in Africa. We measured growth form, fruit type, maximum height, and maximum leaf size of each species, calculated the phylogenetic signal of each trait, and tested the Pearson correlation coefficients between NRI and NFRI of each trait. Our results showed that SR, PD, and FD decreased gradually along the elevational gradient. NRI exhibited a fluctuating pattern along the elevational gradient, while NFRI of the four functional traits showed noticeably different patterns. We concluded that the relationship between the phylogenetic and functional structures in different functional traits could be congruent or mismatched along the elevational gradient. Compared with relatively conservative categorical traits (e.g., growth form and fruit type), continuous traits (e.g., height and leaf size) have a random or convergent evolutionary pattern. Therefore, they could be more easily affected by the environment and possibly have higher phenotypic plasticity

An annotated checklist of vascular plants of Cherangani hills, Western Kenya

Cherangani hills, located in Western Kenya, comprises of 12 forest blocks, maintaining great plant diversity. However, little attention to plant diversity studies has been paid to it in the past years. Here, we present a checklist of the vascular plants of this region obtained through intensive field investigations and matching of herbarium specimens. In total, 1296 species, including 17 endemic species are documented, belonging to 130 families and 608 genera. This flora represents 18.50%, 43.83% and 54.17% of the Kenyan species, genera and families, respectively. The habit, habitat and voucher specimens, as well as brief notes on the distribution of each taxon recorded are presented in this checklist. It is the first exhaustive inventory of the terrestrial vascular plants in Cherangani hills which is a significant regional centre for plant diversity

Complex origins indicate a potential bridgehead introduction of an emerging amphibian invader (Eleutherodactylus planirostris) in China

Identifying the origins of established alien species is important to prevent new introductions in the future. The greenhouse frog (Eleutherodactylus planirostris), native to Cuba, the Bahamas, and the Cayman Islands, has been widely introduced to the Caribbean, North and Central America, Oceania and Asia. This invasive alien amphibian was recently reported in Shenzhen, China, but the potential introduction sources remain poorly understood. Based on phylogenetic analysis using mitochondrial 16S, COI and CYTB sequences, we detected a complex introduction origin of this species, which may be from Hong Kong, China, the Philippines, Panama and Florida, USA, all pointing to a bridgehead introduction. In addition, the nursery trade between the four countries or regions and mainland China from 2011 to 2020 was also significantly higher than other areas with less likelihood of introductions, which supported the molecular results. Our study provides the first genetic evidence of the potential sources of this emerging amphibian invader in mainland China, which may help develop alien species control strategies in the face of growing trade through globalization

CRISPR-Cas13a-Based Detection for Bovine Viral Diarrhea Virus

Bovine Viral Diarrhea Virus (BVDV) is the main pathogen of bovine viral diarrhea disease (BVD), which leads to enormous economic losses in the cattle industry. A sensitive and specific detection for BVDV is advantageous to the control of BVDV. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have been used for detecting virus RNA. In this study, the expression and purification of LwCas13a protein was optimized and the RNase activity of LwCas13a in vitro was verified. CRISPR-LwCas13a system could detect BVDV virus and BVDV RNA with high specificity and simplicity. The detection limit of the LwCas13a system was 103 pM, and there were no cross-reactions with HEK293T and MDBK. In summary, a sensitive, specific, and simple nucleic acid detection method based on CRISPR-Cas13a was developed for BVDV. This method provides a new detection strategy for early diagnosis of BVDV

Expression profiles of microRNAs in skeletal muscle of sheep by deep sequencing

Objective MicroRNAs are a class of endogenous small regulatory RNAs that regulate cell proliferation, differentiation and apoptosis. Recent studies on miRNAs are mainly focused on mice, human and pig. However, the studies on miRNAs in skeletal muscle of sheep are not comprehensive. Methods RNA-seq technology was used to perform genomic analysis of miRNAs in prenatal and postnatal skeletal muscle of sheep. Targeted genes were predicted using miRanda software and miRNA-mRNA interactions were verified by quantitative real-time polymerase chain reaction. To further investigate the function of miRNAs, candidate targeted genes were enriched for analysis using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment. Results The results showed total of 1,086 known miRNAs and 40 new candidate miRNAs were detected in prenatal and postnatal skeletal muscle of sheep. In addition, 345 miRNAs (151 up-regulated, 94 down-regulated) were differentially expressed. Moreover, miRanda software was performed to predict targeted genes of miRNAs, resulting in a total of 2,833 predicted targets, especially miR-381 which targeted multiple muscle-related mRNAs. Furthermore, GO and KEGG pathway analysis confirmed that targeted genes of miRNAs were involved in development of skeletal muscles. Conclusion This study supplements the miRNA database of sheep, which provides valuable information for further study of the biological function of miRNAs in sheep skeletal muscle