Tomato late blight caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary is a major threat to tomato production in cool and wet environments. Intensified outbreaks of late blight have been observed globally from the 1980s, and are associated with migration of new and more aggressive populations of P. infestans in the field. The objective of this study was to reassess late blight resistance in the wild tomato accession L3708 (Solanum pimpinellifolium L.) against pathogens of different aggressiveness. An F2:3 genetic mapping population was developed using L3708 as the paternal parent. Two isolates of P. infestans, Pi39A and Pi733, were used for inoculation. Pi733 is a highly aggressive genotype that defeats three known late blight resistance genes, Ph-1, Ph-2, and Ph-5t in tomato. In contrast, Pi39A is a less aggressive genotype that defeats only Ph-1. Restriction site Associated DNA Sequencing (RAD-Seq) technology was used to massively sequence 90 bp nucleotides adjacent to both sides of PstI restriction enzyme cutting sites in the genome for all individuals in the genetic mapping population. The RAD-seq data were used to construct a genetic linkage map containing 440 single nucleotide polymorphism markers. Quantitative trait locus (QTL) analysis identified a new disease-resistant QTL specific to Pi733 on chromosome 2. The Ph-3 gene located on chromosome 9 could be detected whichever isolates were used. This study demonstrated the feasibility and efficiency of RAD-Seq technology for conducting a QTL mapping experiment using an F2:3 mapping population, which allowed the identification of a new late blight resistant QTL in tomato.

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To mine new favorable alleles for tomato breeding, we investigated the feasibility of utilizing Solanum pimpinellifolium as a diverse panel of genome-wide association study through the restriction site-associated DNA sequencing technique. Previous attempts to conduct genome-wide association studies using S. pimpinellifolium were impeded by an inability to correct for population stratification and by lack of high-density markers to address the issue of rapid linkage disequilibrium decay. In the current study, a set of 24,330 SNPs was identified using 99 S. pimpinellifolium accessions from the Tomato Genetic Resource Center. Approximately 84% of Pst I site-associated DNA sequencing regions were located in the euchromatic regions, resulting in the tagging of most SNPs on or near genes. Our genotypic data suggested that S. pimpinellifolium were divided into three single-ancestry subpopulations and four mixed-ancestry subpopulations. Additionally, our SNP genotypic data consistently confirmed the genetic differentiation, achieving a relatively reliable correction of population stratification. Previous studies utilized the 8K tomato SNP array, SolCAP, to investigate the genetic variation of S. pimpinellifolium and we performed a meta-analysis of these genotypes. The result suggested SolCAP array was less appropriate to profile the genetic differentiation of S. pimpinellifolium when more accessions were involved because the samples belonging to the same accession demonstrated different genome patterns. Moreover, as expected, rapid linkage disequilibrium decay was observed in S. pimpinellifolium , especially in euchromatic regions. Approximately two-thirds of the flanking SNP markers did not display linkage disequilibrium based on r 2 = 0.1. However, the 18-Kb linkage disequilibrium decay indeed reveals the potential of single-gene resolution in GWAS when markers are saturated.

Secondary branch number (SBN) is an important component affecting spikelet number per panicle (SPP) and yield in rice. During recurrent backcross breeding, four BC2F4 populations derived from the high-yield donor parent IR65598-112-2 and the recurrent parent Tainan 13 (a local japonica cultivar) showed discontinuous variations of SPP and SBN within populations. Genetic analysis of 92 BC2F4 individuals suggested that both SPP and SBN are controlled by a single recessive allele. Two parents and 37 BC2F4 individuals showing high- and low-SBN type phenotypes were analyzed by restriction-site associated DNA sequencing (RAD-seq). Based on 2,522 reliable SNPs, the qSBN7 was mapped to a distal region of the long arm of chromosome 7. Trait-marker association analysis with an additional 166 high-SBN type BC2F4 individuals and 8 newly developed cleaved amplified polymorphic sequence markers further delimited the qSBN7 locus to a 601.4-kb region between the markers SNP2788 and SNP2849. Phenotype evaluation of two BC2F5 backcross inbred lines revealed that qSBN7 increased SPP by 83.2% and SBN by 61.0%. The qSBN7 of IR65598-112-2 could be used for improving reproductive sink capacity in rice.

Background Comorbidities in patients undergoing total hip arthroplasty (THA) and total knee arthroplasty (TKA) may compromise outcomes with increased hospital stays, readmission and mortality rates. We aimed to determine whether chronic kidney disease (CKD) affects postoperative outcomes of patients undergoing total joint arthroplasty (TJA).Methods To identify studies for this review and meta-analysis, two independent reviewers searched PubMed, Cochrane, EMBASE and Google Scholar until April 1, 2019, and identi ed additional studies by manual search of reference lists. Prospective or retrospective studies with quantitative outcomes for patients undergoing TJA were selected. Outcomes were compared between patients with underlying CKD stage >=3 or eGFR< 60 mL/min/1.73 m2 versus mild/non-CKD as controls. Main endpoints were mortality, re-operation and re-admission rates.Results Among 59 studies reviewed, 19 meeting the eligibility criteria were included, providing data of 2,141,393 patients. After THA or TKA, CKD was associated with higher mortality risk than non-CKD (pooled OR 2.20, 95%CI = 1.90 to 2.54; P < 0.001); no signi cant differences were seen in re-operation between CKD and non-CKD patients (pooled OR 1.26, 95%CI = 0.84 to 1.88; P=0.266); and CKD patients had higher any-cause re-admission rates (pooled OR= 1.57, 95%CI = 1.27 to 1.94, P<0.001). ConclusionUnderlying CKD predicts adverse outcomes after elective TJA with increased risk of mortality, re-admission, surgical site infection, and perioperative transfusion. Findings of this review and meta-analysis highlight CKD as a critical contributor to complications after TJA and may be helpful to surgeons when advising patients about associated risks of TJA.