Monthly Archives: November 2020

Genetic progress has helped drive our industry forward and each segment along the value chain hasbenefited from technological advancements in genetics followed by breeder integration. But, have we moved the needle far enough with regard to total beef system profitability?

There are opportunities to take a step forward from the current one size fits all production models. Managers are seeking solutions to their constant struggle to balance getting cows bred while producing highly desirable feeder cattle. Any direction a manager leans, maternal or terminal, tends to leave them in a profitability-strapped state. Have balanced trait idealisms taken us as far as they can? Is it time to consider terminal breeding systems?

Frankly, average cow productivity simply isnt good enough to sustain profitability in most systems long-term. There is a real need for advancements in maternal productivity. Highly functional cows that last longer are simply hard to make while also trying to blend the genetics required for terminal performance.

If we truly believe in sustainable production moving forward, this must be accounted for in the environmental equation that supports progress in all areas. Therefore, is it time to examine the feasibility of focused maternal genetic inputs matched with a terminal genetic line to maximize heterosis and metric specific performance traits?

Moreover, why continue to fight the genetic balancing battle while simultaneously struggling with regional environmental challenges and other competing profit centers? If a tiger stripe is the Cadillac of your area, cultivate internal or external pipelines that will meet annual replacement rates. After that, simply use targeted terminal crosses to maximize value-based marketability. The same can be said for every region from coast to coast.

If large ranching systems coast to coast begin this transition into more defined approaches to production with clear efforts toward highly simplified maternal and terminal genetic lines, is that a step backward? Or, does it represent true progress in system processes that will ultimately drive successful ranching? I think it might be the next logical step. A transition made possible by technologies such as sexed semen and other advancements in genetics and forced by growing challenges to operational efficiencies.

It might represent a form of production that is simply a generation newer. Perhaps the time has come to finally effectively utilize purpose specific lines of genetics to achieve sustainable levels of profit through the right combination of simplicity and precision. Balanced trait genetic approaches have brought the national beef herd to the great place it is today. However, will its overarching effectiveness continue to diminish as our industry progresses?

Jared Wareham is the North American business development manager for ABS NuEra. He has been involved in the cattle industry for over two decades, in business development roles growing genetics-focused companies that service producers along the beef value chain by driving the integration of precision-based production.

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Jared Wareham: Are Balanced Trait Genetics a Long-Term Answer? - Drovers Magazine

Seed banks across the globe store and preserve the genetic diversity of millions of varieties of crops. This massive collection of genetic material ensures crop breeders access to a wealth of genetics with which to breed crops that yield better or resist stress and disease.

But, with a world of corn genetics at their disposal, how do plant breeders know which varieties are worth studying and which ones aren't? For most of history, that required growing the varieties and studying their performance in the real world. But innovative data analytics and genomics could help plant breeders predict the performance of new varieties without having to go to the effort of growing them.

Jianming Yu, a professor of agronomy at Iowa State University and the Pioneer Distinguished Chair in Maize Breeding, has devoted much of his research to "turbo charging" the seemingly endless amount of genetic stocks contained in the world's seed banks. Yu and his colleagues have published an article in the Plant Biotechnology Journal, a scientific publication, that details their latest efforts to predict traits in corn-based on genomics and data analytics.

Plant breeders searching for varieties to test might feel lost in a sea of genomic material. Yu said applying advanced data analytics to all those genomes can help breeders narrow down the number of varieties they're interested in much faster and more efficiently.

"We're always searching for the best genetic combinations, and we search the various combinations to see what varieties we want to test," said Xiaoqing Yu (no relation), a former postdoctoral research associate in Yu's lab and the first author of the study. "Having these predictions can guide our searching process."

The study focused on predicting eight corn traits based on the shoot apical meristem (SAM), a microscopic stem cell niche that generates all the above-ground organs of the plant. The researchers used their analytical approach to predict traits in 2,687 diverse maize inbred varieties based on a model they developed from studying 369 inbred varieties that had been grown and had their shoot apical meristems pictured and measured under the microscope.

The researchers then validated their predictions with data obtained from 488 inbreds to determine their prediction accuracy ranged from 37% to 57% across the eight traits they studied.

"We wanted to connect the research in foundational biological mechanisms of cell growth and differentiation with agronomic improvement of corn," said Mike Scanlon, a professor of developmental biology at Cornell University and the lead investigator of the multi-institutional team behind the study. "SAM morphometric measurements in corn seedlings allow a quick completion of the study cycle. It not only enables that connection, but also extends the practice of genomic prediction into the microphenotypic space."

Jianming Yu said plant breeders can bump up the accuracy of those genomic predictions by increasing the number of plants per inbred for measurement and findings-improved prediction algorithms. More importantly, plant breeders can finetune their selection process for which inbreds to study closely by leveraging the "U values," a statistical concept that accounts for the reliability of estimates. Yu said the study shows that implementing a selection process that accounts for prediction and statistical reliability can help plant breeders zero in on desirable crop genetics faster.

For instance, analytical models might predict a particular inbred to have modest potential for a given trait, but the U value, or the upper bound for reliability, might indicate a high degree of unreliability in those predictions. So plant breeders might elect to test inbreds that don't do as well in the predictive model simply because of their genetic uniqueness, being less related to those used in building the prediction models.

"We found that there can be a balance between selecting for optimizing short-term gain and mining diversity," Yu said. "It's a tricky balance for plant breeders. Those considerations sometimes go in different directions. Genetic improvement can be viewed as space exploration, either of the vast amount of existing genetic materials in seed banks or of the innumerable breeding progenies constantly being generated. We want to develop better tools to guide those decisions in the process."

Reference: Yu X, Leiboff S, Li X, et al.Genomic prediction of maize microphenotypes provides insights for optimizing selection and mining diversity.Plant Biotechnol. J. 2020. doi:10.1111/pbi.13420

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

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Turbo Charging the Genetic Stocks Contained in the Worlds Seed Banks - Technology Networks

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Sentiment is on the rise as the annus horribilis 2020 winds to an end. Theres a feeling, after all we have been through over the past ten months, that things just can not get worse. And so, investors are looking forward to 2021.Two big factors in market uncertainty are on their way to resolving themselves. First, COVID-19 vaccines are in the works, and two major drug companies have announced that vaccines will be available in a matter of months. And second, Democrat Joe Biden will take office in the White House, with a strengthened GOP opposition in Congress. The prospect of relief from the coronavirus and a divided government unable to enact extreme or controversial measures promises us a degree of stability that will be welcome.A feeling of optimism and a perception that there are opportunities available, have Wall Streets analysts tagging stocks for success. Weve pulled up theTipRanks dataon three stocks that high-rated analysts have tagged as potentially strong investments. These are buy-rated equities, with double-digit upside potential for the coming year.LendingTree, Inc. (TREE)First up is LendingTree, the online marketplace that connects borrowers and lenders. The company offers borrowers options to shop for competitive rates, loan terms, and various financing products. Among the offerings, from multiple financing sources, are credit cards, deposit accounts, and insurance products. LendingTree is based in North Carolina, with offices in New York, Chicago, and Seattle.In the third quarter, the company showed mixed fiscal results. Revenues were up sequentially, gaining 19% to reach $220 million but earnings were down, both sequentially and year-over-year. At minus $1.33, the EPS was net-negative, and far below the year-ago quarters $1.70.Covering this stock for Needham, 5-star analyst Mayank Tandon rated 66 overall out of more than 7,100 stock pros is upbeat despite the recent turndown after the Q3 results. Tandon noted, [We] remain positive on the shares of TREE LT as we believe that the company is well-positioned to generate strong and consistent revenue Consumer revenue dropped 68% Y/Y as the pandemic constrained consumer credit originations, but trends improved on a sequential basis due to better personal loan volumes and a seasonal boost from the student loan business""TREE's diversified portfolio of personal finance products and the strong secular trends driving the shift of personal finance advertising and shopping to digital channels will help the company achieve its LT growth targets, the analyst concluded. To this end, Tandon rates TREE a Buy, and sets a $375 price target. At current levels, his target suggests a 44% upside for the stock in 2021. (To watch Tandons track record, click here)LendingTree has a unanimous Strong Buy analyst consensus rating, based on 6 Buy reviews set in recent week. The stocks average price target, $362, implies it has room for 39% growth from the current share price of $260.09. (See TREE stock analysis on TipRanks)Allegro MicroSystems (ALGM)Allegro MicroSystems is a semiconductor company and fabless manufacturer of integrated circuits for sensor systems and analyst power technologies. The companys products are used in the automotive and industrial sectors, and include solutions for developing electric vehicle control systems. Allegros circuit chips can also be found in data centers and green energy applications.Allegro is new to the stock markets, having held its IPO just this past October. The stock debuted at $14 per share, and the company put 25 million shares up for offer. In its first day of trading, it closed at more than $17 per share, grossing over $440 million for the IPO. Since then, ALGM has gained 35% in less than four weeks of trading.Vijay Rakesh, 5-star analyst with Mizuho, is clearly bullish on this newly public company.We believe Allegro is leading the early stages of a multi-decade transformation in sensing, automotive electrification, and power distribution, with substantial upside from its industry leadership in magnetic sensors, a differentiated Power IC roadmap, and fabless operating model. Allegro's xMR sensors and power ICs drive technology platform leadership and enable better performance, accuracy, and control for the growing EV market and Industry 4.0 - key for next-generation electrified automotive powertrains, data centers, and factory automation, Rakesh wrote.Along with his upbeat comments, Rakesh gives this stock a Buy rating and a $28 price target. His target implies an upside potential of ~17% for the next 12 months. (To watch Rakeshs track record, click here)Overall, this chip maker is a Wall Street favorite. Out of 6 analysts polled in the last 3 months, all 6 are bullish on ALGM. With a return potential of ~18%, the stock's consensus target price stands at $28.29. (See ALGM stock analysis on TipRanks)American Well (AMWL)American Well, also called AmWell, connects patients, health care providers, and insurers to promote quality care outcomes in a digital world. The company boasts over 55 major insurers and more than 62,000 providers incorporating its service into their networks, giving access to more than 80 million potential patients.AmWell is another newcomer to the markets. This past September, the company held its IPO and raised more than $742 million. Over 41.2 million shares were sold, with the initial price of $18. This compared well to the 35 million shares and $14 to $16 price expected prior to the event. In its first quarter trading as a public company, AmWell reported several gains in key metrics. Revenue was up year-over-year, rising 80% to reach $62.6 million. The active provider total more than 62,000 represents a 930% increase in the past year, and shows strong growth for the company. And the company registered over 1.4 million patient visits during the quarter, a 450% increase from the year-ago quarter.Piper Sandlers 5-star analyst Sean Wieland notes the importance of network growth for AMWL, writing in his note on the stock: 62K providers are using the AMWL Network, up almost 10x from a year ago. The increase was driven primarily by providers employed by, or affiliated with, AMWL's health systems and payor clients As the number of providers on the network grows, so does the value of the network; network expansion makes it easier for patients to find the right provider and for providers to find the right patient.Wieland rates AMWL an Overweight (i.e. Buy), and his $44 price target indicates his confidence in an upside of 78% for the next 12 months. (To watch Wielands track record, click here)All in all, AMWL's Moderate Buy consensus rating is based on 8 reviews, including 5 Buys and 3 Holds. The shares are selling for $24.71 and their average price target, at $35.86, represents a 45% upside potential. (See AMWL stock analysis at TipRanks)To find good ideas for stocks trading at attractive valuations, visit TipRanks Best Stocks to Buy, a newly launched tool that unites all of TipRanks equity insights.Disclaimer: The opinions expressed in this article are solely those of the featured analysts. The content is intended to be used for informational purposes only. It is very important to do your own analysis before making any investment.

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Forecast: Analysts Think Fulgent Genetics, Inc.'s (NASDAQ:FLGT) Business Prospects Have Improved Drastically - Yahoo Finance

Africa is the cradle of humankind. All humans are descendants from this common pool of ancestors. Africa and its multitude of ethnolinguistic groups are therefore fundamental to learning more about humans and our origins.

A genome is the complete set of genetic information in a cell. We inherit our genomes from our parents. Studying the variations in peoples genomes gives clues to how genetic information influences peoples health and tells us about our ancestry.

Very few African individuals have been included in studies looking at genetic variation. Studying African genomes fills a gap in the current understanding of human genetic variation and gives new insights into the history of African populations.

My colleagues and I, who are all members of the Human Heredity and Health (H3Africa) consortium, contributed to a landmark genetics study, which focused on 426 individuals from 13 African countries. More than 50 different ethnolinguistic groups were represented, one of the most diverse groups of Africans ever to be included in such an investigation. We sequenced the whole genome of each of these individuals in other words, we could read every part of the genome to look for variation.

This study contributes a major new source of African genomic data, which shows the complex and vast diversity of African genetic variation.

One of the key outcomes was the discovery of more than three million new genetic variants. This is significant because we are learning about human genetic diversity in general, and discovering more differences that could be linked to disease or traits.

The study also adds details to what is known about the migration and expansion of groups across the continent. We were able to show that Zambia was probably an intermediate site on the likely route of migration from the west of the continent to east and southwards. Evidence supporting movement from east Africa to central Nigeria between 1 500 and 2 000 years ago was also revealed through the identification of east African ancestry in a central Nigerian ethnolinguistic group, the Berom.

The study enabled us to reclassify certain variants that were previously suspected to cause disease. Variants that cause serious genetic diseases are often rare in the general population, mostly because a person with such a variant often does not reach adulthood. The study showed that many of these variants are quite common in the studied populations, something one wouldnt expect in healthy adults. This finding helps to reclassify these variants for clinical interpretation.

Finally, we found a surprising number of regions with signatures of natural selection that have not previously been reported. Selection means that when individuals are exposed to environmental factors like a viral infection, or a drastic new dietary component, some gene variants may confer an added adaptive advantage to the humans that bear them in their genome.

Our best interpretation of these findings is that as humans across Africa were exposed to different environments, sometimes as a result of migration, these variants probably helped them survive in those new conditions. This has left an imprint on the genome and contributes to genomic diversity across the continent.

Our data has also shown that we have not yet found all the variation in the human genome. There is more to learn by looking at unstudied population groups. Less than a quarter of participants in genomics research are of non-European ancestry because most genetic data comes from just three countries the United Kingdom (40%), the United States (19%) and Iceland (12%).

It is essential to keep adding more genomic data from all populations to ensure that everyone can benefit from the advances in health that precision medicine offers. Precision medicine refers to the customisation of healthcare to fit the individual. Including personal genetic information could radically change the nature and scope of healthcare options that would work best for that individual.

The Human Heredity and Health consortium is now in its eighth year of existence and supports more than 51 projects. These include studies focusing on diseases such as diabetes, HIV and tuberculosis. The reference data generated through our study are already being put to use by many of the consortiums studies.

We are planning to take an even deeper look at the data to better understand what other types of genetic variation exist and to add unstudied populations to expand and enrich this data set.

Building capacity for genomics research on the African continent is a key goal of Human Heredity and Health. An important aspect of this study is that it was driven and conducted by researchers and scientists from 24 institutions in Africa participated and led this investigation.

Zan Lombard is principal medical scientist and associate professor at the University of the Witwatersrand. This is an edited version of an article first published by The Conversation. Read the original article here

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Africa study finds three million new genetic variations - Mail and Guardian

Africa is the cradle of humankind. All humans are descendants from this common pool of ancestors. Africa and its multitude of ethnolinguistic groups are therefore fundamental to learning more about humankind and our origins.

A human genome refers to the complete set of genetic information found in a human cell. We inherit our genomes from our parents. Studying the variations in different peoples genomes gives important clues to how genetic information influences peoples appearance and health. It can also tell us about our ancestry. To date, very few African individuals have been included in studies looking at genetic variation. Studying African genomes not only fills a gap in the current understanding of human genetic variation, but also reveals new insights into the history of African populations.

My colleagues and I, who are all members of the Human Heredity and Health (H3Africa) consortium, contributed to a landmark genetics study. This study focused on 426 individuals from 13 African countries. More than 50 different ethnolinguistic groups were represented in the study one of the most diverse groups of Africans ever to be included in such an investigation. We sequenced the whole genome of each of these individuals this means we could read every part of the genome to look for variation.

This study contributes a major, new source of African genomic data, which showcases the complex and vast diversity of African genetic variation. And it will support research for decades to come.

Our findings have broad relevance, from learning more about African history and migration, to clinical research into the impact of specific variants on health outcomes.

One of the key outcomes was the discovery of more than three million new genetic variants. This is significant because we are learning more about human genetic diversity in general, and discovering more differences that could be linked to disease or traits in the future.

This study also adds details to what is known about the migration and expansion of groups across the continent. We were able to show that Zambia was most probably an intermediate site on the likely route of migration from west Africa to east and south Africa. Evidence supporting movement from east Africa to central Nigeria between 1,500 and 2,000 years ago was also revealed, through the identification of a substantial amount of east African ancestry in a central Nigerian ethnolinguistic group, the Berom.

The study also enabled us to reclassify certain variants that were previously suspected to cause disease. Variants that cause serious genetic diseases are often rare in the general population, mostly because their effect is so severe that a person with such a variant often does not reach adulthood. But we observed many of these variants at quite common levels in the studied populations. One wouldnt expect that these types of disease-causing variants would be this common in healthy adults. This finding helps to reclassify these variants for clinical interpretation.

Finally, we found a surprising number of regions with signatures of natural selection that have not been previously reported. Selection means that when individuals are exposed to environmental factors like a viral infection, or a drastic new dietary component, some gene variants may confer an added adaptive advantage to the humans that bear them in their genome.

Our best interpretation of these findings is that as humans across Africa were exposed to different environments sometimes as a result of migration these variants were likely important to surviving in those new conditions. This has left an imprint on the genome and contributes to genomic diversity across the continent.

Our data has shown that we have not yet found all the variation in the human genome. There is more to learn by adding new, unstudied population groups. We know that less than a quarter of participants in genomics research are of non-European ancestry. Most available genetic data come from just three countries the UK (40%), the US (19%) and Iceland (12%).

It is essential to keep adding more genomic data from all global populations including Africa. This will ensure that everyone can benefit from the advances in health that precision medicine offers. Precision medicine refers to the customisation of healthcare to fit the individual. Including personal genetic information could radically change the nature and scope of healthcare options that would work best for that individual.

The Human Heredity and Health consortium is now in its eighth year of existence, and supports more than 51 diverse projects. These include studies focusing on diseases like diabetes, HIV and tuberculosis. The reference data generated through our study are already being put to use by many of the consortiums studies.

Read more: What we've learnt from building Africa's biggest genome library

Next, we are planning to take an even deeper look at the data to better understand what other types of genetic variation exist. We are also hoping to add further unstudied populations to grow and enrich this data set.

Building capacity for genomics research on the African continent is a key goal of Human Heredity and Health. An important aspect of this study is that it was driven and conducted by researchers and scientists from the African continent. Researchers from 24 institutions across Africa participated and led this investigation. This study showcases the availability of both infrastructure and skills for large-scale genomics research on the continent. It also highlights the prospect of future world-class research on this topic from Africa.

Continued here:
Major new study unveils complexity and vast diversity of Africa's genetic variation - The Conversation CA