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Genomic Regions and Key Genes Linked to Oocyte and Embryo Production in Gir Cattle Sire Families: A Daughter Design Study

Discover key genomic regions and genes linked to oocyte and embryo production in Gir cattle. How do these findings impact breeding strategies? Explore this study now.

Imagine revolutionizing cattle breeding by pinpointing genetic markers that boost oocyte and embryo production. Recent genomic advances promise just that. Our study explores the inheritance patterns of key genomic regions and genes in Gir cattle sire families, using daughter designs to reveal crucial insights. 

Focusing on genomic regions linked to viable oocytes (VO), total oocytes (TO), and embryos (EMBR) could transform cattle breeding. Understanding these genetic factors enhances reproductive efficiency and economic value. By examining 15 Gir sire families, each with 26 to 395 daughters, we aimed to identify specific genetic markers contributing to these traits. 

“Identifying QTLs through daughter designs may unlock remarkable advancements in cattle breeding.” — Lead Researcher. 

This research holds significant practical potential. Pinpointing genomic windows on BTA7—home to genes like EDIL3, HAPLN1, and VCAN—enables breeders to make informed decisions, boosting reproductive performance and economic returns. Our findings could lead to more robust and fertile cattle herds, ushering in a new era of genetically informed breeding practices.

Introduction to Genomic Regions and Key Genes in Gir Cattle

Identifying genomic regions linked to oocyte quality and embryo development is crucial for cattle breeding advancements. Through extensive Genome-Wide Association Studies (GWAS) on 15 Gir sire families, significant regions associated with viable oocytes (VO), total oocytes (TO), and embryos (EMBR) were discovered. These regions, notably concentrated on BTA7, highlight the heritable nature of these traits. In-depth analysis revealed significant genetic variations within these regions. 

This genetic mapping is essential for selecting sires with optimal reproductive traits, enabling targeted breeding programs to improve reproductive efficiency. Pinpointing specific regions allows breeders to leverage genetic predispositions for desirable outcomes. 

Essential genes like EDIL3, HAPLN1, and VCAN are vital in regulating oocyte maturation and embryo viability, impacting the developmental processes crucial for reproduction. Their involvement in ensuring oocyte and embryo quality underlines their importance in reproductive success. 

Discussions on gene expression patterns highlight the significance of these markers. Differential expression of genes such as EDIL3, HAPLN1, and VCAN influences reproductive outcomes and presents potential targets for genetic interventions. Technologies like CRISPR-Cas9 offer promising avenues for enhancing reproductive traits by precisely modifying specific genomic regions. This can improve oocyte quality and embryo development, leading to more efficient breeding strategies. 

For further insights into genetic selection and its implications, resources like Genomic Selection: Doubling of the Rate of Genetic Gain in the US Dairy Industry and Leveraging Herd Genotyping & Sexed Semen: A Game-Changer in the Livestock Industry are valuable.

Identifying QTL: Key Findings and Implications

The rigorous GWAS analysis using GBLUP revealed crucial genomic regions associated with reproductive traits in Gir cattle. Among these, BTA7 consistently emerged as a critical chromosomal region affecting VO, TO, and EMBR traits, highlighting its potential influence on reproductive efficiency. 

 VCAN, XRCC4, TRNAC-ACA, HAPLN1, and EDIL3 stand out among the identified genes.  VCAN and EDIL3 on BTA7 seem integral to cellular matrix interactions and endothelial cell function. These genes are likely crucial for enhancing oocyte and embryo yields, essential for genetic advancement, and economic benefits in cattle breeding. 

Furthermore, genomic windows found on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA23, and BTA27 for VO, and those on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA26, and BTA27 for TO, underline the complex genetic foundation of these traits. Overlaps among these regions hint at loci with pleiotropic effects, suggesting that targeted selection could improve multiple characteristics simultaneously. 

Additionally, the QTLs on BTA4, BTA5, BTA6, BTA7, BTA8, BTA13, BTA16, and BTA17 related to EMBR highlight the intricate genetic interplay in reproductive success. Overlapping and distinct QTLs across various chromosomes point to a nuanced genetic network. 

Overall, this study confirms the value of daughter design in QTL mapping, uncovering critical genetic insights into oocyte and embryo production. These findings lay a robust groundwork for future research. They targeted breeding strategies, with BTA7 identified as a primary focus for enhancing reproductive efficiency in Gir cattle.

Implications for Breeding and Genetic Improvement

Genomic information has the potential to enhance breeding strategies in Gir cattle. By identifying key genes like EDIL3, HAPLN1, and VCAN, breeders can improve reproductive traits with precision. Incorporating this data into selection programs allows for targeted breeding, focusing on individuals with favorable alleles. This can boost the number of viable oocytes and embryos, improving production efficiency and profitability. 

Moreover, integrating genetic data into selection programs is vital for sustained improvements. Genome-wide markers enable breeders to predict reproductive success early, accelerating genetic gains. This method enhances selection and reduces resources on less productive animals, optimizing herd performance. 

Finally, ongoing research is essential. Identifying more genomic regions and genes related to oocyte and embryo production maintains genetic diversity and refines breeding strategies. Incorporating new markers into programs ensures Gir cattle genetic improvement evolves with dairy production challenges. Advanced genomic tools and traditional practices promise robust, high-yielding cattle meeting growing dairy demands.

The Bottom Line

The discovery of genomic regions and essential genes tied to reproductive traits in Gir cattle significantly enhances our grasp of these crucial economic traits. This research highlights QTL across various chromosomes by examining 15 Gir sire families through a daughter design approach, particularly the vital genes EDIL3, HAPLN1, and VCAN on BTA7. These findings offer a genetic blueprint for improving oocyte and embryo production efficiency. 

These results call for further investigation to dissect the complexities of the bovine genome. Applying these insights in breeding programs can refine genetic selection strategies, optimize reproductive performance, and enhance the productivity and profitability of Gir cattle herds. 

The potential impact on the cattle industry is immense. Livestock producers can expect better herd fertility and efficiency, leading to higher yields and lower costs. Consumers may benefit from more sustainable and ethically managed cattle production systems, producing higher quality and potentially more affordable beef products. This study marks a crucial step in livestock genetic refinement, encouraging stakeholders to leverage these findings for future advancements.

Key Takeaways:

  • Identification of genomic regions and candidate genes related to reproductive traits in Gir cattle families has been achieved.
  • BTA7 was found to have the genomic windows with the highest QTL concentration, including genes like VCAN, XRCC4, TRNAC-ACA, HAPLN1, and EDIL3.
  • A total of 42 genes were associated with embryo production (EMBR), and 42 genes were linked to both viable oocytes (VO) and total oocytes (TO).
  • The study utilized a daughter design approach, focusing on 15 Gir sire families to map the inheritance of these key traits.
  • Genomic regions for VO were identified on multiple chromosomes, with BTA8 being the most frequent within families.
  • For EMBR, significant genomic windows were found on several chromosomes, with BTA7 being the most frequently occurring within families.
  • The research indicates a heritable nature of these reproductive traits, emphasizing the importance of targeted breeding strategies for genetic improvement.

Summary: A study on the inheritance patterns of key genomic regions and genes in Gir cattle sire families has revealed significant insights. The research focuses on genomic regions linked to viable oocytes (VO), total oocytes (TO), and embryos (EMBR) and aims to identify specific genetic markers contributing to these traits. The study holds practical potential, as pointing genomic windows on BTA7, home to genes like EDIL3, HAPLN1, and VCAN, enables breeders to make informed decisions, boosting reproductive performance and economic returns. The study highlights the heritable nature of these traits, with significant genetic variations within these regions. This genetic mapping is essential for selecting sires with optimal reproductive traits, enabling targeted breeding programs to improve reproductive efficiency. Technologies like CRISPR-Cas9 offer promising avenues for enhancing reproductive traits by precisely modifying specific genomic regions.

SEXING TECHNOLOGIES: Gender Vendors in a Changing Marketplace

Predetermined sex in offspring is the brass ring that dairy breeders seek in managing in the ever more competitive marketplace. Most definitely this control is becoming more achievable.  Sexed semen end user price has dropped to one third of the price it was when it was first introduced.

Sexing Technologies (ST) is a well known, worldwide provider of sexed semen and embryos. Juan Moreno, who is co-owner of ST with Maurice Rosenstein, outlines the business that has been built by this company.


Sexing Technologies owes its origin to a company called Genetic Resources International (GRI) which got started 22 years ago as a Custom Semen and Embryo collection facility and Genetics Exporter servicing the Southern US.  While considering expansion into the IVF world 12 years ago.  They discovered that sexed semen, although technologically possible, was not commercially available because it was consider too expensive and of lower fertility and therefore did not have commercial viability. He outlines the steps taken in forming Sexing Technologies. “The partners in the business 11 years ago went heavily into debt to obtain a license from XY Inc., additional partners came into the business and Sexing Technologies started its commercial sexed semen production 10 years ago having Select Sires as its first large commercial customer.”

AT YOUR SERVICE: The Rising Tide of Technology

“Our philosophy is to generate value for the end user.” Explains COCEO Moreno, who is excited about the growing possibilities. “High genetic level bulls are available now. For example the #1 Proven Jersey bull in the world is available in sexed semen. There is every reason for the same to be available in Holsteins. Producers are using sexed semen in both heifers and cows.  Sexed semen has become part of modern management strategies on the farm.”  Today ST sexed semen is in every day use on thousands of farms (both beef and dairy) in 15 countries around the world confirms Sexing Technologies COCEO. “ It is being produced by more than 25 bull studs. Our production is estimated at 10 million straws annually and over 30 million calves have been born.”  The ST co-owner lists five of the many services it provides to breeder customers:

  • As a commercial service we are one of the largest exporters of dairy heifers having shipped over 40,000 animals in two years.
  • We offer custom semen collection services for both conventional and sexed semen and reproductive services in Embryo Transfer and IVF.
  • We process sexed semen in Deer, Elk, Sheep, Goats and soon in Horses and Pigs.
  • We service the industry by progeny testing Holstein, Jersey and Brown Swiss bulls.


Juan speaks with both pride and humility when sharing the growth of Sexing Technologies. “ Today more than 28 families have ownership in Sexing Technologies and the ST family team of over 500 men and women proudly services an industry that feeds the world. We are very thankful to our customers and to the ST team that has provided us with the support to improve the fertility of the product and reduce the cost to the end user.”  What he feels in unique about this undertaking is that the entire team has a common goal. “We believe in team effort and being part of an industry that includes, breeders, farmers, bull studs, breed associations, testing services, researchers and others, all working for a common effort of producing in milk, a nutritious quality product, at a fair price that the end consumer can enjoy.”


Potential users of sexing technology are always hungry for advice from those who have experience. Moreno shares his viewpoint. “ The technology has changed dramatically, especially in the last 5 years. A considerable amount of resources and time has gone into developing new generations of equipment, changing procedures, media improvements and user awareness. For example in the last 5 years we have gone through 5 different new models of sperm sorters, each one an improvement on the previous one. Thus production efficiency has improved considerably and the end user has benefitted by seeing a significant price reduction in the cost for their sexed semen since ST introduced it in the market place 10 years ago.”


It’s important to use sexed semen as part of an overall management strategy on the dairy farm.  It facilitates the allocation of resources by allowing for the selection of higher quality replacement females. It allows you to significantly reduce calving difficulties. It allows for greater income  by marketing extra heifers or even introducing cross breeding with beef bulls to produce a product of a higher value in the market and, most importantly,  fertility is improving.  We are expecting the publication of several articles on large trials ran by independent researchers in different countries corroborating the improved fertility. It’s time to use it for first service in cows.”

“What`s In It For Me?”

With any leading edge tool that requires adapting to change, breeders are concerned about how it can work for them. “That is a tough question.” Asserts Juan Moreno. “Markets are always changing and unpredictable. My crystal ball has failed me many times in the past. However, I do believe that many technologies are coming together at this point” As Moreno looks to the best impact of sexing technologies, he points out 3 specifically.

  1. Sexed semen can be used to generate female only embryos 99% of buyers don’t really care about having bulls. Only bull studs care about the bulls, most breeders would like to improve their female base. Making embryos with conventional semen makes 50% of the resulting product (bulls) non marketable. Produce for the 99% not the 1%.
  2. Genomic testing allows targeting embryo production for different niche makers like higher protein, A2 milk, Show, Polled, Color, Milk, Fertility or Net Merit or TPI.
  3. New Technologies will drive the market to the selection for traits such as fertility, health, feed efficiency, robot adaptability, etc.


A full consideration of sexing technologies must not overlook InVitro Feriliaztion. Moreno provides particularly interesting statistics and suggestions for their use.

  1. 30% of the donors make 80% of the embryos. Don’t keep on trying with low embryo producers.
  2. make an assessment of the marketability or value within your own herd of the resulting offspring 24 months down the road. Don’t measure today expecting to forecast tomorrow.
  3. Producing 90%-95% females gives you a much better chance of maximizing your investment . Almost all females from top donors will have a place in your herd. Only 1% or less  of the bulls born will ever find a home. Therefore the investment does not compensate the return if you continue producing 50% bulls.


According to Juan Moreno, it’s not the technology that floods the market, it’s the users that choose to produce embryos from a higher number of donors. “I believe the success of IVF provides the opportunity to be more selective as to the genetic quality of donors being used. Technologies such as IVF provide the greatest benefit when used only on elite cattle. Maybe the excitement of Genomics has lead to a definition of “Elite” that is too relaxed.”


Moreno suggests definite steps in using IVF. “First and foremost the genetic value of the animal today and a year down the road needs to be evaluated.  The statistical possibility of that donor generating an offspring that will have market viability 18 to 24 months down the road must also be forecasted. Secondly animals must go through a very thorough schedule of vaccinations and heath testing. Donors are then placed on optimized nutritional regimens based on age and reproductive status. Thirdly reproductive examinations and evaluations on the animal are performed prior to her start in the donor program and they are continued through her life as a donor. The most important fourth step is that the animal must be evaluated after the first three aspirations to determine her ability to produce sufficient number of oocytes and embryos to compensate the investment.” Moreno concludes with a key statistic. “Breeders must always keep in mind that 30% of the donors produce 80% of the embryos.”


ST confirms that IVF results are influenced by breed, age of the donor, reproductive status of the donor, aspiration frequency, nutritional status and hormonal treatments. “We favor a more natural and conservative approach with no hormonal treatments. This approach benefits the long term well being of the animal. In Bos Indiscus breeds like Brahman we average over 7 embryos per aspiration and on Holstein cows  3.3 embryos per aspiration, dropping to 2.2 embryos in heifers. Embryo pregnancies depending on the time of the year range from 43% to 55%.”


ST has been doing IVF for more than 10 years and embryo transfer since the original company was created 20 years ago. ST operates 2 IVF labs in Brazil and 4 in the United States. Two of the US labs are operated as Research and Development laboratories which have been fundamental in testing procedures for sexed semen, leading to a series of improvements in the process that have lead to increased fertility in sexed semen.


“We dedicate a considerable amount of funds and resources to Research and Development in Animal Reproduction from heat detection devices, estrus synchronization technology, sexed semen, in vitro fertilization and genetic development programs.” reports Moreno adding that, “  A great deal of emphasis is being dedicated to genetic advancement programs researching new economically significant traits for which prior genetic pressure has not been applied.”


Once again as breeders, we are being urged to recognized that putting different technology tools together can provide advantages that they couldn’t deliver alone. Moreno says the list is long on the technologies  and we should look at in combination. “Some of the technologies have been around for a long time but they will become more relevant in the future because, when paired with new technologies, they lead to greater value.  For example: Genomics, Embryo Transfer, IVF, Sexed Semen, Robot Milkers, compliance data systems, Universal Animal Identification, Gene identification , they all have to lead to milk being produced in a more efficient manner so that dairying can be a profitable business for generations to come.”


Technology is not a tool that you can choose to do without. As is always the case with technology driven evolution those who choose to ignore it may be ignoring their own sustainable business. Sexing Technologies is on the leading edge. At the end of the dairy day, those who readily and effectively adapt to the “new world” will succeed and those who don’t won’t!


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Mapel Wood Farms – Invest in the Best! Forget the Rest!


Len Vis, owner of Mapel Wood Farms, says his motto has always been:  “Invest in the best and forget the rest”. It was the driving force behind his first investment in 1991 in Mark Diamonds who became the brood mare of Mapel Wood Farms and it is what led him and his partners to invest in Bombi and Lilac.  “Investing in top cow families never lets you down.  You may not get it this generation or the next generation but those genetics always breed through eventually.” On any measurement scale, records, show ring, progeny or the bottom line these two families represent where Len sees his farm going in the future!


Len points to the dramatic changes happening in the dairy industry not only in the past five years, but in the last year.  He says, “The biggest change is that 90% of people coming to Mapel Wood are interested in heifers.” This was not previously the case when people wanted to look at cows. “I have never flushed so many virgin heifers as I have in the last year and we are getting big money for their embryo’s.”  Knowing what the market wants and providing it for them is another part of aiming for the best!




In every area of running the Mapel Wood operation, Len relies on getting his homework done right.  This means investing in the right people to work with. He speaks with pride about his full-time employees, Chris Naves and brother Harold Vis and that he can rely on them 100% to keep things running smoothly and sale or show ready every day. Choosing the right investing partners is more homework done right that pays off.  Len says it is important for partners “to have the same philosophy, goals and commitment.” For him it has been a great experience.  “My two best partners have been GenerVations, Dave Eastman, and the O’Connor Brothers, Sean and Kelly.”


When you get to the real homework behind success in the cattle business Len is emphatic. “I never go to a sale on a whim.  If I’m in the market I have animals that I’ve got premarked in my catalogue.”  This is only the start of the decision-making process. For him the next thing is conformation. “I look at the ones I’m interested in.  If they don’t make it on conformation, they’re scratched!”  He has the steps clearly prioritized. “Cow families first.  Then sire stack. Then I start doing history on flush history.” Vis says there is nothing worse than buying something that doesn’t flush. You can be sure he always asks the seller about the flush history of the family. He looks at records. He thinks Holstein Canada’s free service is great. “A lot of times you just go on Holstein Canada. If you see 10 daughters from one mating, you know the family flushes.” Homework isn’t finished until he has checked out pictures. “For marketability, I like to see the dam and granddam all pictured.” Having said all that, the real test of getting your homework right is that final decision, to buy or not to buy. Len cautions, “Remember the Calf in the sales ring has to look the part. Conformation is still the most important thing when it comes down to the final bid. If she’s in the ring and you gut says something isn’t exactly right. Pull back. You’ve got to love that calf 100%!”

GEN-I-BEQ SHOTTLE BOMBI VG-89-6YR-CAN 2*, Shottle x Champion x Baler Twine, GLPI +2750


Success for Len Vis and Mapel Wood Farms means making sure that all the numbers add up! Years of experience have given him some benchmarks for investing.  Investment benchmarks have changed pretty dramatically. “It used to take 1 kilo of quota to buy a good animal.  Today it takes 3 or 4 kilos of quota.” He feels the right animal will pay for your quota.  “When I started out in the business, if the right animal came across I would be willing to sell a kilo of quota to buy her.” He explains, “Your investment can triple in one year. A lot of guys don’t know that. Quota takes forever to pay off but buy into the right cow family you can have it paid off in no time.” That’s MapelWood math.


For better or worse, Genomics is on everybody’s page these days.  “You can’t be in the dairy business without genomics affecting you.” Regardless of all the controversy Len hears and wonders about he says, “Genomics have helped every farmer because hopefully Semex or your semen company is not buying those bulls that don’t have a chance ever to make it.” That’s the good news. He goes on, “Five years ago I did not sense Genomics was going to be this big. I don’t think anybody did.  What studs thought they would be selling young sire semen for $100?”  He knows it is the ongoing debate.  “There are so many different army camps of people… some are all for it …. Some are sitting on the fence waiting to see.” Waiting is not a key part of Len’s goal setting.


Len’s goal is that people will come to Mapel Wood Farms as the “one stop to shop”.  He aims to be the “Wal-Mart of the cattle investing world.” The aim is to offer the best in several areas. “We want to have high genomic cows and heifers, show cows, red and white genetics, and polled genetics.” Aiming to have the best he is very enthusiastic.  ”Currently we’re buying embryos from Europe and still buying heifers and cows. Just recently we just sold a six year old cow for big money.” It pays to do your homework!


Len is looking forward but he points to his own history. “Diamonds was a good investment but it was three generations later that I realized what a great investment that was. Sometimes when you invest you don’t reap the benefits the next day. That doesn’t mean you just sit and wait.” Obviously Len feels you must have a timeline like he and his partners did with Bombi and Lilac. “Five years ago we had a game plan. Today we are up to 300 head. We have been buying recipients.  We’re constantly flushing.”  From the beginning there was a target. “We are gearing up for a sale in November 2012.  Nothing has been done on a whim. We are going to see the results of our five-year game plan.” 

BOTTOM LINE:  Aim to be the Best!

“When you invest in the best – cow families, embryos, and heifers – your farm will rise to the top.” Len Vis, Mapel Wood Farms. 




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