Molecular identification of blast resistance genes in rice landraces from northeastern India

Rice blast disease caused by the fungus Magnaporthe oryzae is one of the most devastating diseases causing huge losses worldwide. In the present study, major blast resistance genes were investigated in landraces originating from northeastern India. Based on phenotypic evaluation, 288 landraces were classified into three distinct groups: resistant (75), moderately resistant (127) and susceptible (86). The genetic frequencies of the 18 major blast resistance genes were between 6.2% and 27.4%, with only two genotypes possessing a maximum of nine blast resistance genes. The cluster and population structure analysis grouped the landraces into two groups. Through principal coordinate analysis, the scatter plots partitioned the resistant and moderately resistant landraces into different groups. Analysis of molecular variance showed maximum (96%) diversity within populations and least (4%) diversity between populations. Association analysis identified six markers, CRG4_2, RM72, tk59-2, pi21_79-3, RM1233 and RM6648, that are significantly associated with blast disease and explained a phenotypic variance of 1.1–6.5%. The associated genes could be used in marker-assisted rice breeding programmes for gene pyramiding to develop rice varietal resistance against blast disease. The present study represents a valuable blast resistance genetic resource that could be used for identification of new R genes, donors for blast resistance, and genomic studies.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

A histological evaluation of pansteatitis-affected Mozambique tilapia,Oreochromis mossambicus (Peters 1852), from different geographical locations in South Africa

Pansteatitis is the leading cause for the decline in Nile crocodile populations and the sporadic mortality of fish in the Olifants River System, South Africa. To determine the prevalence of this disease in lentic systems, Mozambique tilapia, Oreochromis mossambicus, were collected from Lake Loskop, Lake Flag Boshielo, Phalaborwa Barrage and Lake Luphephe-Nwanedi. The former three impoundments are located within the main stem of the Olifants River, while the latter, which is geographically isolated and situated in the Limpopo River System, served as a reference site. Mesenteric adipose, liver, serosa of the swim bladder, gill and the skeletal muscle of fish sampled were examined for gross and microscopic evidence of pansteatitis. Microscopically observed changes were used to statistically compare pansteatitis prevalence between samples and sites. Based on histopathological evaluation, the adipose tissue in the liver, swim bladder serosa and coelom from severely debilitated individuals showed the most significant pathological changes. Lesions indicative of steatitis were observed in fish collected from Lake Loskop (75%), Lake Flag Boshielo (22%) and Lake Luphephe-Nwanedi (15%). Further investigation is warranted to understand the pervasiveness and mechanisms driving pathological changes of pansteatitis at Lake Flag Boshielo, Phalaborwa Barrage and Lake Luphephe-Nwanedi.     

The face of conservation responding to a dynamically changing world

In its 40‐year history, the science of conservation has faced unprecedented challenges in terms of environmental damage and rapid global change, and environmental problems are only increasing as greater demands are placed on limited natural resources. Conservation science has been adapting to keep pace with these changes. Here, we highlight contemporary and emerging trends and innovations in conservation science that we believe represent the most effective responses to biodiversity threats. We focus on specific areas where conservation science has had to adjust its approach to address emerging threats to biodiversity, including habitat destruction and degradation, climate change, declining populations and invasive species. We also document changes in attitudes, norms and practices among conservation scientists. A key component to success is engaging and maintaining public support for conservation, which can be facilitated through the use of technology. These recent trends in conservation and management are innovative and will assist in optimizing conservation strategies, increasing our leverage with the general public and tackling our current environmental challenges.     

Onchocerca sp. in an imported Zangersheide gelding causing suspensory ligament desmitis

A 5-year-old imported Zangersheide gelding was evaluated for SC swellings over both forelimbs and lameness localized to the distal metacarpus. Ultrasound examination of the SC masses was compatible with verminous granulomas. Linear hyperechoic foci were present within the suspensory ligament branches of both forelimbs, suggestive of ligamentous parasitic infiltrates. A diagnosis of onchocerciasis was confirmed on biopsy of a SC mass. The gelding was treated with ivermectin and a tapering course of PO dexamethasone but was eventually euthanized. Necropsy confirmed the presence of SC eosinophilic granulomas and degenerative suspensory ligament desmitis, both with intralesional nematodes. Given the location and appearance of the nematode, a diagnosis of Onchocerca sp., most likely O. reticulata, was made. Onchocerciasis should be included as a differential diagnosis for multifocal suspensory ligament desmitis with these sonographic characteristics when paired with SC masses in imported European Warmbloods.     

Intracranial medulloblastoma as the cause of progressive ataxia in a 6-month-old draft horse cross gelding

We describe the unique clinical presentation of a central nervous system neoplasm in a 6-month-old draft horse cross gelding. Based on the neurologic examination at admission, neurolocalization was most consistent with a mildly asymmetric cervical, multifocal, or diffuse myelopathy. Mild vestibular involvement also was considered, but no cranial nerve deficits were observed. The gelding was negative for Sarcocystis neurona or Neospora hughesi based on paired serum and cerebrospinal fluid (CSF) samples analyzed, with no evidence of cervical compression based on contrast myelography. The horse was euthanized because of progression of clinical signs. At necropsy, a mass was identified associated with the cerebellum, and histopathology was consistent with medulloblastoma, which has not been reported previously in the horse.