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.     

Reproductive resilience: a paradigm shift in understanding spawner‐recruit systems in exploited marine fish

A close relationship between adult abundance and stock productivity may not exist for many marine fish stocks, resulting in concern that the management goal of maximum sustainable yield is either inefficient or risky. Although reproductive success is tightly coupled with adult abundance and fecundity in many terrestrial animals, in exploited marine fish where and when fish spawn and consequent dispersal dynamics may have a greater impact. Here, we propose an eco‐evolutionary perspective, reproductive resilience, to understand connectivity and productivity in marine fish. Reproductive resilience is the capacity of a population to maintain the reproductive success needed to result in long‐term population stability despite disturbances. A stock's reproductive resilience is driven by the underlying traits in its spawner‐recruit system, selected for over evolutionary timescales, and the ecological context within which it is operating. Spawner‐recruit systems are species specific, have both density‐dependent and fitness feedback loops and are made up of fixed, behavioural and ecologically variable traits. They operate over multiple temporal, spatial and biological scales, with trait diversity affecting reproductive resilience at both the population and individual (i.e. portfolio) scales. Models of spawner‐recruit systems fall within three categories: (i) two‐dimensional models (i.e. spawner and recruit); (ii) process‐based biophysical dispersal models which integrate physical and environmental processes into understanding recruitment; and (iii) complex spatially explicit integrated life cycle models. We review these models and their underlying assumptions about reproductive success vs. our emerging mechanistic understanding. We conclude with practical guidelines for integrating reproductive resilience into assessments of population connectivity and stock productivity.     

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 social learning video method: Identifying and sharing successful transformation knowledge for sustainable soil management in Switzerland

To enhance sustainable land use, a From Farmer to Farmer project was conducted in Switzerland (2001–2010). A multi‐stakeholder discussion group co‐produced nine videos with experienced farmers and wine producers showing sustainable soil management practices. We analysed the video audio‐visual content and drew on reflections of the co‐production process, referring to concepts of system, target and transformation knowledge, as well as on social learning. The analysis showed a broad range of means (or actions) for sustainable soil management in arable land management, fodder production and wine growing that are aligned to transformation knowledge. The research showed that farmers refer to three phases of social learning, light‐bulb moments, coping with challenges and gaining successful expertise. These are not just linear processes of individuals. Four types of social learning were found in the video analysis: (a) learning from observing actions of others, (b) sharing experiences with storytelling, (c) informal social interactions and (d) being a role model with a large social network. Videos enable transformation knowledge to be shared with peers using storytelling; this powerful narrative communication style provides credibility and respects the ‘thought style’ of the target audience group. We conclude that for successful implementation of sustainable actions, it is important to address a specific target group and share their transformation knowledge built upon system and target knowledge. The social learning video method is a viable way to enable social learning between science, administration and practice and has potential for fostering change in sustainable soil management.     

The neglected role of religion in fisheries management

Religion and spirituality have long played important roles in fishery systems around the world, and yet are often neglected in modern fisheries management and research. We review current literature and analyse the major small‐scale fishery on Lake Tanganyika, Africa, to highlight how religion may mediate fishing behaviours. Our study surveyed 154 fishers across 11 landing sites in Tanzania, followed by 15 semi‐structured interviews with key informants including fishery officers and local religious leaders. We identified key connections between religious beliefs/practices and fisher perceptions, behaviour and compliance with harvest restrictions and regulations. We demonstrate that better understanding and accounting for religious dimensions is critical for engaging with fishery stakeholders more effectively and managing global fisheries more sustainably.     

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.     

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.