DNA ‣ Data Nuggets

8.2.24

A plant breeder’s quest to improve perennial grain

Hannah takes notes on the date of flowering in a Kernza® field in Southwest Minnesota.

The activities are as follows:

Kernza^® is a new grain crop that is similar to wheat. It can be ground into flour and used in bread, cookies, crackers and more! Unlike wheat, the rest of the plant can be eaten by livestock such as cattle. Another difference is that Kernza^® is a perennial, meaning it grows in the ground for multiple years, whereas annual wheat only grows for one year. However, the challenge is that annual wheat makes more grain and is easier to harvest and sell. This means farmers currently prefer growing annual wheat over Kernza^®.

One way to address this mismatch between annual and perennial crops is through selective breeding. This is when humans select individual plants with traits that are desirable for a specific reason. This group of individuals are strategically bred together. The breeder’s goal is to shift the traits over generations. Scientists have only been working on breeding Kernza^® for the past few decades; in comparison, humans started selecting annual wheat traits over 10,000 years ago! That is a lot of time to get the traits we are looking for.

Kernza^® breeders are working on improving the same traits that have already been improved in annual wheat, including larger seed size. Kernza^® scientists follow two main steps to breed plants 1) they select the best individuals from the population and 2) they intercross those individuals to create the next generation, or breeding cycle. With each breeding cycle, plant breeders see a slight improvement in the traits they selected.

Breeders can select plants based on phenotypes, genotypes, or both. Historically, plant breeders have selected based on desired phenotypes, or visible traits, only. Modern plant breeding can take advantage of the fact that we can now look at genotypes, or the genetic makeup, of individual plants quickly and at low costs. Scientists can use this information to make quicker breeding improvements, so we don’t have to wait another 10,000 years for high-yielding Kernza^®!

Hannah is a scientist currently working on Kernza^®. Hannah’s passion for plant breeding was ignited during her high school years. She discovered the captivating world of genetics in her AP Biology class. It was then that she first realized the potential for breeding crop plants to make them more productive and viable for human consumption.

Hannah decided to join other scientists who work on Kernza^®at the University of Minnesota. Here, scientists have completed four breeding cycles and are about to start the fifth. Hannah wanted to see whether different genetic makeups (genotypes) lead to differences in seed size (phenotypes). Her goal was to look at each plants’ phenotype and genotype for seed size.

To genotype a plant, scientists collect a small piece of leaf tissue, extract the DNA, and send the DNA to a lab for sequencing. This process tells scientists the genetic makeup that ultimately leads to the traits that we see. Specifically, sequencing data identifies nucleotides, or genetic building blocks of each plant’s DNA. Plants have thousands of genes, which are made up of the DNA nucleotides A, T, C, and G.

Sequencing data can be recorded in several ways. One common way is as SNP data, or Single Nucleotide Polymorphism data. You can think of SNP data as the recipe for proteins. In a SNP dataset, each SNP represents a difference in a nucleotide. Similar to using a different ingredient in a recipe, different nucleotides can result in a different phenotype.

By looking at SNP data, plant breeders can identify differences in genotypes that lead to certain phenotypes. Hannah started by evaluating 1,000 Kernza^® plants from the first four breeding cycles. Data on phenotypes had already been recorded for these plants. Hannah then collected SNP data to determine their genotypes as well. She was looking for a pattern between genotypes and phenotypes. If she sees that different genotypes have different phenotypes, scientists can then rely on genotypes to select individuals to breed in future breeding cycles.

Featured scientist: Hannah Stoll (she/her) from the University of Minnesota

Flesch–Kincaid Reading Grade Level = 8.9

Additional teacher resources related to this Data Nugget include:

Hannah, the scientist, made a slideshow to go along with this activity.
Check out this overview of translation and transcription by Khan Academy.

12.20.19

Fishy origins

The activities are as follows:

Striped bass, or stripers, make up one of the most important fisheries for seafood and sport fishing on the East Coast of the United States. Carleigh and Chelsea, biology teachers in New Jersey, were at the beach one day when they saw a couple of stripers in the Barnegat Bay Inlet. Both teachers have always been interested in research and even met while participating in a summer research program as undergraduate students. Since then, both have gone on to complete more research projects in biology and education. Their curiosity about striper populations led them to work together yet again!

They headed to Monmouth University in New Jersey, where they began working with two scientists, Megan and John. They learned that locations where fish reproduce are called spawning grounds. Young stripers spend 2-3 years developing in the spawning ground before moving downstream. When stripers become adults, they return to the same location to breed.

There are four main spawning grounds for stripers on the East coast: the Hudson River, the Chesapeake Bay, Delaware River, and the Albermarle Sound. Stripers from these areas are considered to be different stocks. Stripers are migratory fish, and generally move north in the spring and south in the fall. Because they all migrate to New Jersey, fish from different stocks combine, which results in a mixed stock. When there is a population that has a mixed stock, we don’t know which spawning ground the fish originally came from. Conservation and management of New Jersey’s striper fishery requires knowing where the fish come from. Understanding which spawning grounds stripers are using helps managers make sure we are not overfishing or damaging these important environments. So, Carleigh and Chelsea joined a project that is working to find out how we can identify where mixed stock stripers come from.

For their study, the scientists caught stripers in three different locations off the New Jersey coast in 2017. The fish were sampled by clipping off a small portion of the right pelvic fin. The scientists then extracted the DNA from each sample in the lab. They used polymerase chain reaction (PCR) to then copy regions of the DNA, called microsatellites. Microsatellites are small, repeating sections of DNA that can be variable enough to distinguish even close relatives. These data were then used to compare DNA samples from the unknown mixed stocks to the known spawning ground stocks. The scientists also recorded whether each fish was young or mature. The scientists then used the age data to tell whether the spawning grounds might be changing over time.

Featured scientists: Carleigh Engstrom, Chelsea Barreto, Megan Phifer-Rixey, and John Tiedemann from Monmouth University

Flesch–Kincaid Reading Grade Level = 9.2

11.2.17

When whale I sea you again?

Image of a humpback whale tail from the Palmer Station LTER. Photo credit Beth Simmons.

The activities are as follows:

People have hunted whales for over 5,000 years for their meat, oil, and blubber. In the 19^th and 20^th centuries, pressures on whales got even more intense as technology improved and the demand for whale products increased. This commercial whaling used to be very common in several countries, including the United States. Humpback whales were easy to hunt because they swim slowly, spend time in bays near the shore, and float when killed. Before commercial whaling, humpback whales were one of the most visible animals in the ocean, but by the end of the 20^th century whaling had killed more than 200,000 individuals.

Today, as populations are struggling to recover from whaling, humpback whales are faced with additional challenges due to climate change. Their main food source is krill, which are small crustaceans that live under sea ice. As sea ice disappears, the number of krill is getting lower and lower. Humpback whale population recovery may be limited because their main food source is threatened by ongoing ocean warming.

One geographic area that was over-exploited during times of high whaling was the South Shetland Islands along the Western Antarctic Peninsula (WAP). The WAP is in the southern hemisphere in Antarctica. Humpback whales migrate every year from the equator towards the south pole. In summer they travel 25,000 km (16,000 miles) south to WAP’s nutrient-rich polar waters to feed, before traveling back to the equator in the winter to breed or give birth. Today the WAP is experiencing one of the fastest rates of regional climate change with an increase in average temperatures of 6^° C (10.8^° F) since 1950. Loss of sea ice has been documented in recent years, along with reduced numbers of krill along the WAP.

Logan is a scientist who is studying how humpback whales are recovering after commercial whaling. Logan’s work helps keep track of the number of whales that visit the WAP in the summer. He also determines the sex ratio, or ratio of males to females, which is important for reproduction. The more females in a population compared to males, the greater the potential for having more baby whales born into the next generation. Logan predicts there may be a general trend of more females than males along the WAP as the season progresses from summer to fall. Logan thinks that female humpback whales stay longer in the WAP because they need to feed more than males in order to have extra nutrients and energy before they birth their babies later in the year. This extra energy will be needed for their milk supply to feed their babies.

The Palmer LTER station when Logan and others scientists live while they conduct research on whales.

Humpback whales only surface for air for a short period of time, making it difficult to determine their sex. In order to identify surfacing whales as female or male, scientists need to collect a biopsy, or a sample of living tissue, in order to examine the whale’s DNA. Logan worked with a team of scientists at Oregon State University and Duke University to engineer a modified crossbow that could be used to collect samples. Logan uses this crossbow to collect a biopsy sample each time they spot a whale. To collect a sample, Logan aims the crossbow at the whale’s back, taking care to avoid the dorsal fin, head, and fluke (tail). He mounts each arrow with a 40mm surgical stainless steel tip and a flotation device so the samples will bounce off the whale and float for collection. The samples are then frozen so they can be stored and brought back to the lab for analysis. Logan also takes pictures of each whale’s fluke because each has a pattern unique to that individual, just like the human fingerprint. Additionally, at the time of biopsy, Logan records the pod size (number of whales in the area) and GPS location.

Logan’s data are added to the long-term datasets collected at the WAP. To address his question he used data from 2010-2016 along the WAP and other feeding grounds. Logan’s data ranges from January to April because those are the months he is able to spend at the research station in the WAP before it gets too cold. Logan has added to the scientific knowledge we have about whales by building off of and using data collected by other scientists.

Featured scientist: Logan J. Pallin from Oregon State University. Written by: Alexis Custer

Flesch–Kincaid Reading Grade Level = 10.7

Additional teacher resources related to this Data Nugget:

To see more images of humpback whales, and the Palmer Research Station in the WAP where Logan works, check out this PowerPoint. This can be shared with students in class after they read the Research Background and before they move on to the data.
More data from this region can be found on the DataZoo, Palmer LTER’s online data portal. To access data on this portal, follow instructions found on this “cheat sheet”. For files that have been compiled for educators, check out this Google Drive folder.
For his research, Logan has traveled to United States Antarctic Programs’ Palmer Research Station on the WAP during the austral summer and fall and will be departing again for the WAP in January 2018. He is part of a team of scientists interested in Palmer Long Term Ecological Research, which is funded through the National Science Foundation, documenting changes on in the Antarctic ecosystem.
For more information on whale research at Palmer Station LTER and the WAP, check out this website.
For additional classroom activities dealing with Palmer Station LTER data, check out this website.
The International Whaling Commission (IWC) was created in
1946 in Washington D.C. in hopes to provide conservation to whale stocks around the world. In 1982, the IWC placed a moratorium on commercial whaling. Fore more information on the IWC and humpback whales, check out their website.

About Logan: Logan is interested in determining how humpback whales are recovering after commercial whaling. Logan first got interested in working with marine mammals when he was an undergraduate student at Duke University and had the opportunity to work as a field technician on a project with some scientists at Duke. He quickly realized this was what he wanted to do and that studying humpbac whales was particularly interesting as they appear to have all rebounded quite heavily in the Southern Hemisphere. Assessing why this recovery was happening so fast and why now, was something Logan really wanted to look at. After graduating from college, he continued to work with marine mammologists as a graduate student to receive his Masters in Science from Oregon State University. In the fall of 2017, he started his work on a PhD from University of California, Santa Cruz continuing asking questions and learning more about whales around Antarctica.
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