Statistical model predicts performance of hybrid rice

Long-grain rice

Genomic prediction, a new field of quantitative genetics, is a statistical approach to predicting the value of an economically important trait in a plant, such as yield or disease resistance. The method works if the trait is heritable, as many traits tend to be, and can be performed early in the life cycle of the plant, helping reduce costs.

Now a research team led by plant geneticists at the University of California, Riverside and Huazhong Agricultural University, China, has used the method to predict the performance of hybrid rice (for example, the yield, growth-rate and disease resistance). The new technology could potentially revolutionize hybrid breeding in agriculture.

The study, published online in the Proceedings of the National Academy of Sciences, is a pilot research project on rice. The technology can be easily extended, however, to other crops such as maize.

"Rice and maize are two main crops that depend on hybrid breeding," said Shizhong Xu, a professor of genetics in the UC Riverside Department of Botany and Plant Sciences, who co-led the research project. "If we can identify many high-performance hybrids in these crops and use these hybrids, we can substantially increase grain production to achieve global food security."

Genomic prediction uses genome-wide markers to predict future individuals or species. These markers are genes or DNA sequences with known locations on a chromosome. Genomic prediction differs from traditional predictions in that it skips the marker-detection step. The method simply uses all markers of the entire genome to predict a trait.

"Classical marker-assisted selection only uses markers that have large effects on the trait," Xu explained. "It ignores all markers with small effects. But many economically important traits are controlled by a large number of genes with small effects. Because the genomic prediction model captures all these small-effect genes, predictability is vastly improved."

Without genomic prediction, breeders must grow all possible crosses in the field to select the best cross (hybrid). For example, for 1000 inbred parents, the total number of crosses would be 499500.

"It is impossible to grow these many crosses in the field," Xu said. "However, with the genomic prediction technology, we can grow only, say, 500 crosses, then predict all the 499500 potential crosses, and select the best crosses based on the predicted values of these hybrids."

Xu noted that genomic prediction is particularly useful for predicting hybrids because hybrid DNA sequences are determined by their inbred parents.

"More cost-saving can be achieved because we do not need to measure the DNA sequences of the hybrids," he said. "Knowing the genotypes of the parents makes it possible to immediately know the genotype of the hybrid. Indeed, there is no need to measure the genotype of the hybrid. It is fully predicted by the model."

When the researchers incorporated "dominance" and "epistasis" into their prediction model, they found that predictability was improved. In genetics, dominance describes the joint action of two different alleles (copies) of a gene. For example, if one copy of a gene has a value of 1 and the other copy has a value of 2, the joint effect of the two alleles may be 4, indicating that the two alleles are not additive. In this case, dominance has occurred. Epistasis refers to any type of gene-gene interaction.

"By incorporating dominance and epistasis, we took into account all available information for prediction," Xu said. "It led to a more accurate prediction of a trait value."

Genomic prediction can be used to predict heritable human diseases. For example, many cancers are heritable and genome prediction can be performed to predict disease risk for a person.

Xu was joined in the research by Qifa Zhang and his student Dan Zhu at Huazhong Agricultural University, China.

Next the research team, led by Xu and Zhang, will design a field experiment to perform hybrid prediction in rice.

Source: University of California - Riverside

Human faces are so variable because we evolved to look unique

The amazing variety of human faces -- far greater than that of most other animals -- is the result of evolutionary pressure to make each of us unique and easily recognizable. Credit: UC Berkeley

The amazing variety of human faces -- far greater than that of most other animals -- is the result of evolutionary pressure to make each of us unique and easily recognizable, according to a new study by University of California, Berkeley, scientists.

Our highly visual social interactions are almost certainly the driver of this evolutionary trend, said behavioral ecologist Michael J. Sheehan, a postdoctoral fellow in UC Berkeley's Museum of Vertebrate Zoology. Many animals use smell or vocalization to identify individuals, making distinctive facial features unimportant, especially for animals that roam after dark, he said. But humans are different.

"Humans are phenomenally good at recognizing faces; there is a part of the brain specialized for that," Sheehan said. "Our study now shows that humans have been selected to be unique and easily recognizable. It is clearly beneficial for me to recognize others, but also beneficial for me to be recognizable. Otherwise, we would all look more similar."

"The idea that social interaction may have facilitated or led to selection for us to be individually recognizable implies that human social structure has driven the evolution of how we look," said coauthor Michael Nachman, a population geneticist, professor of integrative biology and director of the UC Berkeley Museum of Vertebrate Zoology.

The study will appear Sept. 16 in the online journal Nature Communications.

In the study, Sheehan said, "we asked, 'Are traits such as distance between the eyes or width of the nose variable just by chance, or has there been evolutionary selection to be more variable than they would be otherwise; more distinctive and more unique?'"

As predicted, the researchers found that facial traits are much more variable than other bodily traits, such as the length of the hand, and that facial traits are independent of other facial traits, unlike most body measures. People with longer arms, for example, typically have longer legs, while people with wider noses or widely spaced eyes don't have longer noses. Both findings suggest that facial variation has been enhanced through evolution.

Finally, they compared the genomes of people from around the world and found 

more genetic variation in the genomic regions that control facial characteristics than in other areas of the genome, a sign that variation is evolutionarily advantageous.

"All three predictions were met: facial traits are more variable and less correlated than other traits, and the genes that underlie them show higher levels of variation," Nachman said. "Lots of regions of the genome contribute to facial features, so you would expect the genetic variation to be subtle, and it is. But it is consistent and statistically significant."

Using Army data

Sheehan was able to assess human facial variability thanks to a U.S. Army database of body measurements compiled from male and female personnel in 1988. The Army Anthropometric Survey (ANSUR) data are used to design and size everything from uniforms and protective clothing to vehicles and workstations.

A statistical comparison of facial traits of European Americans and African Americans -- forehead-chin distance, ear height, nose width and distance between pupils, for example -- with other body traits -- forearm length, height at waist, etc. -- showed that facial traits are, on average, more varied than the others. The most variable traits are situated within the triangle of the eyes, mouth and nose.

Sheehan and Nachman also had access to data collected by the 1000 Genome project, which has sequenced more than 1,000 human genomes since 2008 and catalogued nearly 40 million genetic variations among humans worldwide. Looking at regions of the human genome that have been identified as determining the shape of the face, they found a much higher number of variants than for traits, such as height, not involving the face.

Prehistoric origins

"Genetic variation tends to be weeded out by natural selection in the case of traits that are essential to survival," Nachman said. "Here it is the opposite; selection is maintaining variation. All of this is consistent with the idea that there has been selection for variation to facilitate recognition of individuals."

They also compared the human genomes with recently sequenced genomes of Neanderthals and Denisovans and found similar genetic variation, which indicates that the facial variation in modern humans must have originated prior to the split between these different lineages.

"Clearly, we recognize people by many traits -- for example their height or their gait -- but our findings argue that the face is the predominant way we recognize people," Sheehan said.

Source: University of California - Berkeley

John Lennon commemorated by naming a new tarantula species from South America after him

A newly described tarantula species from Western Brazilian Amazonia was named Bumba lennoni in honor of John Lennon, a founder member of the legendary band the Beatles. Credit: Doi: 10.3897/zookeys.448.7920, Image courtesy of Pensoft Publishers

A newly described tarantula species from Western Brazilian Amazonia was named Bumba lennoni in honor of John Lennon, a founder member of the legendary band the Beatles. The new species is part of the tarantula family Theraphosidae which comprises the largest spider species in the world. The study was published in the open access journal ZooKeys.

The name of the new species came across when the authors of the study Fernando Pérez-Miles, from the University of the Republic, Uruguay, and Alexandre Bonaldo and Laura Miglio, both from the Museu Paraense Emilio Goeldi, Brazil, found out that they are all great fans of the Beatles music.

The genus, Bumba, which is proposed as replacement of the old one Maraca, already taken and used for Orthoptera, also has a story behind the choice of name. The new name is taken from Brazilian theatrical folk tradition of the popular festival called Boi-bumbá (hit my bull), which takes place annually in North and Northeastern Brazil.

The new species, as other tarantulas, has defensive urticating hairs on the abdomen which produce irritation upon contact with the skin or sensible tissues.

The specimens used in the study were captured manually or in traps during the night in Caxiuaná, Pará, Brasil, which suggest they could be mainly nocturnal animals.

Source: Pensoft Publishers

A taxonomic toolkit ends a century of neglect for a genus of parasitic wasps

This is Ophion keala, one of the newly described species of Ophion." Credit: Dr. Marla Schwarzfeld; CC-BY 4.0

In 1912, three species in the parasitic wasp genus Ophion were described by two different entomologists, increasing the number of known species in North America to eleven. It has long been known that the actual diversity is much higher; however, it took 102 years for any additional species to be described.

"The main reason for this is that everyone has assumed that Ophion are just too difficult to tell apart. Museum collections are full of unidentified Ophion, but nobody has wanted to face the challenge of sorting them out" said Marla Schwarzfeld, an entomologist who recently completed her Ph.D. at the University of Alberta, Canada.

In fact, the author of one of the species described in 1912, Claude Morley, stated: "Without abundant material it were ridiculous to attempt a wide revision of these insects; and ... a mass of this material causes one's courage to sink at the sight of so uniform and apparently characterless a group."

However, with the advent of new taxonomic tools, it is no longer necessary to rely solely on the challenging morphology of the group. Schwarzfeld and her Ph.D. supervisor, Felix Sperling, used a combination of molecular and morphometric analyses to define a new species group within Ophion, and to delimit and describe six new species within this group. The molecular work involved the analysis of three different genetic markers, while the morphometric analyses included both an analysis of wing venation and a more traditional approach of measuring various body parts. The study, including the new descriptions, has recently been published in the open-access journal, ZooKeys.

"The exciting part about this work is that these techniques all gave remarkably congruent results, which gives us a lot of confidence in these new species. This takes a lot of the guesswork out of describing species, and will be a really valuable toolkit for studying additional species of Ophion, as well as species in other morphogically-challenging groups" declared Schwarzfeld.

Source:  Pensoft Publishers

Do women and men ride differently? Horses cannot tell the difference

Horses seem to be truly gender-neutral. It doesn't matter to them if their human partner is female or male.
Credit: Juliane Kuhl / Vetmeduni Vienna

Scientists at the Vetmeduni in Vienna have analysed how horses are affected by the sex of their riders. Various parameters of stress were determined in horses and their riders when they covered an obstacle course. The results were surprising: the level of stress on a horse is independent of whether a man or a woman is in the saddle. Furthermore, the stress responses of male and female riders are essentially the same. The results have been published in the Journal of Comparative Exercise Physiology.

For centuries, horse riding was largely restricted to males. The previous situation is in stark contrast to the present day, when nearly 80 percent of riders are women. Modern-day equestrian sports are unique in that men and women compete directly against one another at all levels, from beginners in gymkhanas to national champions in the Olympic Games. "For this reason it is interesting to consider whether a theory of riding that was developed exclusively for men can be applied to women," explains Natascha Ille, the first author of the recent publication.

A rider is a rider

As Ille notes, "It is often assumed that women are more sensitive towards their horses than men. If this is so, male and female riders should elicit different types of response from their horses." Ille, Christine Aurich and colleagues from the Vetmeduni Vienna´s Graf Lehndorff Institute tested this notion by examining eight horses and sixteen riders, including eight men and eight women. Each horse had to jump a standard course of obstacles twice, ridden once by a male and once by a female of similar equestrian experience. The scientists monitored the levels of stress in the horses and their riders, checking the amounts of cortisol in the saliva and the heart rates.

The results were unexpected. The level of cortisol in horses' saliva increased during the test but the increase was not affected by the sex of the rider. The horses' heart rates also increased as a result of taking the course but the increase was irrespective of the human partner in the saddle. The tests on the riders gave similar conclusions. Again, the level of cortisol in the saliva increased but there was no difference between men and women. The riders' pulses sped up when the horses switched from a walk to a canter and accelerated further during the jumping course. But the heart rate curves for male and female riders were close to identical.

The distribution of saddle pressure is the same for male and female riders
In a second experiment, Ille and her colleagues studied the pressure exerted on a horse's back via the saddle. As she explains, "Depending on the rider's posture and position, the pattern of pressure on the horse's back may change dramatically." A special pad placed directly under the saddle was used to analyse saddle pressure in walk, trot and canter. Because female riders are generally lighter than males, the saddle pressure was lower when horses were ridden by females. However, the distribution of pressure did not differ and there was no evidence of differences in the riding posture between males and females.

A fair chance for all

So what does all this mean for modern equestrian sports? Aurich is keen to reassure potential competitors that horses are truly gender-neutral. As she puts it, "Assuming that there is no difference in riding ability, from the horse's point of view, it does not seem to matter whether the human partner is male or female. Our results make it extremely unlikely that horses have a preference for riders of one sex over the other. And when male and female riders compete against one another in equestrian sports, all of them have similar chances of doing well."

Source: Veterinärmedizinische Universität Wien

Birth of four foals from genotyped, cryopreserved embryos: A first in Europe

Genotyping allows scientists to choose the embryos they want to use based on different criteria: sex, like in this experiment, the absence of known genetic disorders, or, perhaps in the future, other traits that are tied to behavior, such as emotivity or sociability. Credit: INRA/C. Maitre

IFCE and INRA announced that, for the first time ever in Europe, four foals were successfully born as the result of the transfer of genotyped and cryopreserved embryos. The goal of this work is to better understand embryonic development, control livestock reproduction, and maintain breed genetic diversity. Furthermore, it is advantageous for the horse industry to be able to determine the traits of a future foal.

The INRA Val de Loire center at Nouzilly is where the technology to maintain embryo viability following genotyping and cryopreservation was honed, and then, last summer, the transfer of several embryos took place at the IFCE Haras du Pin Stud Farm, located in the French department of Orne. The partnership between the two institutions has now been cemented by the birth of the healthy foals.

What were the steps leading up to the birth of these foals?

Seven days after fertilization, embryos were collected from Welsh B ponies that are part of INRA's livestock. The embryos were genotyped: scientists sampled some of the embryos' cells to analyze their genomes. In this experiment, embryos were selected based on sex, the idea being to use sex-based selection to test the technique's feasibility. The embryos were then cryopreserved in liquid nitrogen (at -196°). Last summer, they were transferred into saddlebred mares at the Haras du Pin center. After an 11-month gestation period, the foals were born in May. They were of the expected sex: two females and two males. This is the first time that such an event has taken place in Europe, and it is the product of more than 10 years of various types of embryonic research carried out by INRA and IFCE scientists.

What made it so difficult to apply this technique to horses?

Although embryo preservation techniques are already well developed for bovines, small ruminant species, and even humans, preserving horse embryos is a very complex process. For instance, horse embryos vary greatly in size: 7-day-old embryos range in diameter from 200 to 700 micrometers. It is very difficult to cryopreserve the largest embryos because the liquid inside them forms ice crystals when the embryos are frozen at very cold temperatures. What's more, horse embryos are surrounded by a capsule that interferes with successful cryopreservation.

What is the significance of this event, which is the first of its kind in Europe?

There are several reasons why being able to successfully cryopreserve embryos is important. For example, it allows us to maintain breed genetic diversity, particularly that of breeds with small population sizes, such as the Landais or the Poitevin Mulassier. Furthermore, the factor that currently limits the use of embryo transfer is its cost: the transfer center has to maintain a team of recipient mares that are reproductively synchronized with the donor mares. Cryopreservation means that the transfer doesn't have to take place immediately; it can wait until a recipient mare becomes available to receive the embryo. Finally, it may now be possible to directly repopulate horse herds that have experienced losses as a result of various issues, such as disease-related problems, instead of having to use the indirect technique of crossbreeding.

Why genotype the embryos?

Genotyping allows us to choose the embryos we want to use based on different criteria: sex, like in this experiment, the absence of known genetic disorders, or, perhaps in the future, other traits that are tied to behavior, such as emotivity or sociability. It is advantageous for the horse industry to be able to determine the traits of a future foal. We will next aim to simplify the process -- to make this technology more accessible and user friendly for those in the horse industry.

Source: INRA-France

Female frogs modify offspring development depending on reproduction date

Breeding male of Rana arvalis from the study area. Credit: Germán Orizaola

Global warming is altering the reproduction of plants and animals, notably accelerating the date when reproduction and other life processes occur. A study by the University of Uppsala (Sweden), including the participation of Spanish researcher Germán Orizaola, has discovered that some amphibians are capable of making their offspring grow at a faster rate if they have been born later due to the climate.

Over recent decades many organisms, both plants and animals, have experienced a notable advance in the date when many of their life processes (like reproduction, migration or flowering) occur, attributed to the impact of climate change. An article published in the journal Ecology examines the effects that these changes in the reproduction date have on the life cycles of the amphibians.

"We specifically examined whether changes in the reproduction date of a common amphibian species in the north of Europe, Rana arvalis, can condition the growth and development of their offspring," the Spanish researcher Germán Orizaola, from the University of Uppsala (Sweden) and co-author of the study, said.

Results revealed that female frogs have the ability to influence both the growth rate and the development of their offspring, and they adjust it depending on the date of reproduction.

According to Orizaola, "the mechanism by which the female frogs can condition the growth of their larvae could be due to the genes associated with the maintenance of their biological clock being transferred to the embryos and becoming active even before fertilisation. This would provide the larvae with the exact information regarding the progression of the growing season."

The later the birth, the faster the growth

One of the characteristics associated with climate change is an increase in the interannual variability of climatic conditions, so organisms are also exposed to greater uncertainty when it comes to determining the right time to reproduce. This explains why the existence of mechanisms adjusting growth and development rates depending on the variation in the start of breeding is highly advantageous for many species.

In particular, as part of this study they observed that by delaying the date of reproduction (which simulated a time of environmental instability), the result was an equivalent reduction in the growth period for the larvae. "That means the later this species of frog breeds, the faster the larvae develop," explains the scientist.

An interesting aspect of the study is that the acceleration in growth is produced under constant lab conditions. "The larvae were not exposed to any outside sign that would indicate the progression of the growing season," adds Orizaola.

"This result is very novel and demonstrates that the acceleration in the development of the larvae is conditioned by the breeding females, which reveals the existence of a 'transgenerational effect' in which the breeding adults are capable of altering key aspects of the life cycle for the following generations, to better prepare them to survive the environmental conditions that they are going to experience," concludes the expert.

Source: Plataforma SINC.

Boy moms more social in chimpanzees: Watching adult males in action may help youngsters prepare

Infant chimpanzee in Gombe National Park, Tanzania. Nearly four decades of observations of Tanzanian chimpanzees has revealed that the mothers of sons are about 25 percent more social than the mothers of daughters. Boy moms were found to spend about two hours more per day with other chimpanzees than the girl moms did. Credit: © Impala / Fotolia

Nearly four decades of observations of Tanzanian chimpanzees has revealed that the mothers of sons are about 25 percent more social than the mothers of daughters. Boy moms were found to spend about two hours more per day with other chimpanzees than the girl moms did.

Chimpanzees have a male-dominated society in which rank is a constant struggle and females with infants might face physical violence and even infanticide. It would be safer in general to just avoid groups where aggressive males are present, yet the mothers of sons choose to do so anyway.

"It is really intriguing that the sex of her infant influences the mother's behavior right from birth and that the same female is more social when she has a son than when she has a daughter," said Anne Pusey, chair of Evolutionary Anthropology at Duke.

The researchers believe that the mothers are giving the young males the opportunity to observe males in social situations, even while still clinging to their mothers. This gives the youngsters a start on developing the social skills they'll need to thrive in the competitive world of adults.

The findings are based on an analysis of 37 years of daily observations of East African chimpanzeess from the Gombe National Park in Tanzania. Duke University houses all of the data from the famous Kasekela chimpanzee community in the Jane Goodall Institute Research Center, which contains more than 50 years of observational data all the way back to Jane Goodall's first hand-written observations from the early 1960s.

The data largely consist of "follows," in which a researcher focuses on one chimpanzee and notes her behaviors and interactions with others throughout the day. Duke scholars led by Pusey are now working on digitizing the entire collection of Gombe data in the Goodall archive to enable more longitudinal studies of this kind.

"Drawing from the long-term datasets, we were able to investigate patterns within the same mother, examining how she behaved with her sons versus with her daughters," said lead author Carson Murray, an assistant professor at George Washington University, who was a PhD student under Pusey. "These results are even more compelling than a general pattern, demonstrating that the same female behaves very differently depending on the sex of her offspring."

For this study, researchers measured gregariousness based on three kinds of analyses. They looked at how much time a mother spent with other adults who were not immediate family members; the average size of the mother's party and its composition; and the proportion of time a mother spent in mixed-sex and female-only parties.

For the most part, mothers with offspring spend their time alone or with adult daughters and other dependents. Adult males are the more gregarious sex, forming coalitions with other males to assert rank, defend their territory and hunt as a group.

Mothers with sons were found to spend more time with others and to associate with more of their kin. During the first six months of an infant's life, mothers with sons spend significantly more time in mixed-sex parties than mothers with daughters.

At 30 to 36 months, chimpanzee infants start moving around more on their own without being carried and spend most of their time out of mother's reach. At this age, the male infants start having more interactions with unrelated chimpanzees, especially adult males. Their female counterparts are significantly less social.

As the offspring get older and range further from their mothers, the young males have more social partners over the course of the day. Juvenile and adolescent males watch their adult counterparts carefully and often mimic the behaviors they see, including charging displays and copulation.

"Mothers obviously increase social exposure for their young male infants," Murray said. "This finding leads to a larger question about how social exposure might shape gender-typical behavior in humans as well."

This study also suggests it is possible the sons themselves are driving the increased gregariousness later in life. In early infancy, the boy mothers spend about the same time in female-only groups that the girl moms do. But as their sons become older, boy moms spend more time in female-only, nursery groups, probably because the young males are attracted to the offspring of other females as playmates.

"One of the most surprising results to me was that mothers with young females still have lower association with their relatives," Murray said. "As we argue in the paper, this suggests that social exposure is less critical to females in general."

Social exposure has a potential downside too. Females with low rank are known to experience more social stress in large groups, and there is always a risk of infanticide against the young chimpanzees. Perhaps the best way to avoid having infants killed is to steer clear of groups, which the mothers do up to 70 percent of the time.

"Mothers with infant daughters were likely to be avoiding competitive and stressful situations," Murray said. "While mothers with sons seem willing to incur those costs for the benefit of having their sons socialized."

Source: Duke University.