Laboratory Information Management Software for genotyping workflows: Applications in high throughput crop genotyping

Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F7 Recombinant Inbred Lines (RILs) from cross H 77/833-2 9 PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available

Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

Highly endangered species like the Sumatran rhinoceros are at risk from inbreeding. Five historical and 16 modern genomes from across the species range show mutational load, but little evidence for local adaptation, suggesting that future inbreeding depression could be mitigated by assisted gene flow among populations. Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations

Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories

Similar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids

Conventional and Molecular Breeding Approaches for Biofortification of Pearl Millet

Pearl millet [Pennisetum glaucum (L.) R. Br.] is an essential diet of more than 90 million people in the semi-arid tropics of the world where droughts and low fertility of soils cause frequent failures of other crops. It is an important nutri-rich grain cereal in the drier regions of the world grown on 26 mha by millions of farmers (IFAD 1999; Yadav and Rai 2013). This makes pearl millet the sixth most important crop in the world and fourth most important food crop of the India, next to rice, wheat, and maize with annual cultivation over an area of ~8 mha. Pearl millet is also primary food crop in sub-Saharan Africa and is grown on 15 mha (Yadav and Rai 2013). The significant increase in productivity of pearl millet in India is attributed to development and adoption of hybrids of early to medium duration maturity. More than 120 diverse hybrids/varieties have been released till date for various production environments. The heterosis breeding and improved crop management technologies increased productivity substantially achieving higher increased production of 9.80 mt in 2016–2017 from 2.60 mt in 1950–1951 in spite of declined of area under the crop by 20–30% over last two decades (Yadav et al. 2012)

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security

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Severe Central Sleep Apnea in Vici Syndrome

Vici syndrome is a rare congenital multisystem disorder due to recessive mutations in the key autophagy regulator EPG5. Vici syndrome is characterized by agenesis of the corpus callosum, hypopigmentation, immunodeficiency, cataracts, and cardiomyopathy, with variable additional multisystem involvement. Here we report on a 5-year-old girl who presented with global developmental delay, seizures, callosal agenesis, cataracts, sensorineural hearing loss, hypopigmentation, and immunodeficiency with a low CD4 count and recurrent infections. EPG5 sequencing (prompted by suggestive clinical features) revealed a homozygous missense mutation, c.1007A&gt;G (p.Gln336Arg). The patient was referred to our center for evaluation of nocturnal apnea. Overnight polysomnography showed severe central sleep apnea (CSA) with an overall apnea-hypopnea index of 100.5 events per hour of sleep (central apnea index of 97.5, mixed apnea index of 2, and obstructive hypopnea index of 1). The patient responded to bilevel positive airway pressure therapy with a backup rate with normalization of the apnea-hypopnea index and maintenance of oxygen saturation &gt;90%. Despite successful control of the severe CSA, the patient was eventually started on nocturnal oxygen therapy due to excessive upper airway secretions and the high risk of possible aspiration with positive airway pressure therapy. This is the first report of EPG5-related Vici syndrome associated with CSA. We discuss the polysomnographic findings in our patient in the context of a brief literature review of the reported sleep abnormalities in Vici syndrome.</p

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Not AvailableThe present study was undertaken with the objective to determine the degree of association between yield and it`s component characters and their direct, indirect effects on seed yield in sesame (Sesamum indicum L.). 41 genotypes were evaluated for identifying their efficiency with respect to 10 quantitative characters. Character association studies revealed significant positive association of seed yield per plant with plant height, number of branches per plant, first capsule height, capsules per plant, and 1000-seed weight. This indicated the possibility of simultaneous selection of all these characters for yield improvement. A critical path analysis revealed that the number of capsules per plant, diameter of stem, capsule length, number of branches per plant and plant height directly affected the seed yield per plant. This indicated that direct selection for yield improvement via these traits would be possibleNot Availabl

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Not AvailableGenetic diversity study was carried out among 41 sesame genotypes using seed yield and its component characters. Based on the present investigation the 41sesame genotypes were grouped into seven clusters suggesting that considerable amount of genetic diversity present across genotypes. The maximum diversity was contributed by capsules per plant followed by number of branches per plant, plant height and days to maturity. Cluster II was the largest one comprising of 17 genotypes followed by cluster I with 12 genotypes, cluster IV with five genotypes, cluster III with four genotypes, cluster V, VI, and VII, were represented by each single genotype indicating high degree of heterogeneity among the genotypes. The maximum inter cluster distance was observed between IV and VI clusters followed by clusters IV and V and clusters VI and VII while it was low between clusters V and VI, followed by clusters I and V, clusters II and VII. Maximum intra cluster distance was observed in cluster VI, followed by cluster IV, cluster III, cluster II and cluster I. The inter cluster distance in most of the cases were higher than the intra-cluster distance indicating wider genetic diversity among the genotypes of different groups. Four characters viz., capsules per plant, followed by number of branches, plant height and days to maturity contributed more than 90% towards genetic divergence. Hence, these four characters are very important for selection indices.Not Availabl