Tag: plant breeding genomics

Introduction

Pyramiding genes on the same chromosome is a special case of gene pyramiding. This case study describes the use of molecular markers to pyramid two disease resistance genes on tomato chromosome 5: Rx-3 (resistance to tomato bacterial spot) and Pto (resistance to bacterial speck).

Bacterial spot and bacterial speck, two diseases with worldwide economic importance, can impact tomato crops simultaneously. Figure 1 shows a field affected by bacterial spot. Yang and Francis (2005) sought to combine resistance genes for both diseases. Although Yang and Francis (2005) knew from previous studies (Yang et al., 2005; Martin et al., 1993) that both resistance genes were on chromosome 5, they didn’t know the genetic distance between the two genes.

To combine Rx-3 and Pto, Yang and Francis (2005) crossed two inbred parents (see video): one homozygous for Rx-3 but susceptible to bacterial speck and the other homozygous for Pto but susceptible to bacterial spot. The video below outlines the general procedure for making crosses. The F₁ progeny were self-pollinated to obtain F₂ seed.

Figure 1. Tomato plot that includes tomato plants that are resistant (left) and susceptible (mid-right) to bacterial spot. Photo courtesy of David Francis, The Ohio State University.

In the F₂ generation, Yang and Francis (2005) wanted to identify individuals resistant to bacterial spot and bacterial speck, and to calculate the genetic distance between Rx-3 and Pto. To achieve these objectives, Yang and Francis (2005) genotyped a population of 419 individuals with two molecular markers (one associated with Pto and one associated with Rx-3) to identify individuals with alleles that confer resistance to both diseases. In the case of Pto, the molecular marker was within the Pto gene, so Francis and Yang did not have to worry about recombination between the marker and gene. However, in the case of Rx-3, the molecular marker used to select for bacterial spot resistance was not within Rx-3, so recombination between the marker and Rx-3 was possible. This meant that selection based on the marker alone wouldn’t be perfect. In some cases, individuals with the resistant allele would be susceptible. Yang and Francis conducted phenotypic screenings to confirm that individuals expected to be resistant based on their genotype were, in fact, resistant.

Individuals with resistance to both bacterial spot and bacterial speck could only be obtained if a recombination event occurred between Pto and Rx-3, because each parent carried only one of the resistance genes. The chance of a recombination event depends on the genetic distance between Pto and Rx-3. Of the 419 F₂ individuals genotyped, Yang and Francis identified 13 plants that were homozygous for bacterial spot and bacterial speck resistance alleles and 94 individuals that were heterozygous.

Yang and Francis estimated that Pto and the Rx-3 marker were 36.8 ± 2.2 cM apart. See the animation about genetic mapping to learn more about the principles of genetic mapping. The loose linkage between Pto and the Rx-3 marker means that breeders must take care to ensure that they maintain resistance conferred by Pto and Rx-3 when making crosses with individuals that have both these resistance genes.

References Cited

• Martin, G. B., M. C. de Vicente, and S. D. Tanksley. 1993. High-resolution linkage analysis and physical characterization of the PTO bacterial-resistance locus in tomato. Molecular Plant-Microbe Interactions 6: 26–34. (Available online at: http://www.apsnet.org/publications/mpmi/BackIssues/Documents/1993Abstracts/Microbe06-026.htm) (verified 30 Aug 2012).
• Yang, W., and D. M. Francis. 2005. Marker-assisted selection for combining resistance to bacterial spot and bacterial speck in tomato. Journal of the American Society for Horticultural Science 130: 716–721. (Available online at: http://journal.ashspublications.org/cgi/content/abstract/130/5/716) (verified 30 Aug 2012).
• Yang, W. C., E. J. Sacks, M.L.L. Ivey, S. A. Miller, and D. M. Francis. 2005. Resistance in Lycopersicum esculentum intraspecific crosses to race T1 strains of Xanthomonas campestris pv. vesicatoria causing bacterial spot of tomato. Phytopathology 95: 519–527. (Available online at: dx.doi.org/10.1094/PHYTO-95-0519) (verified 30 Aug 2012).

External Links

• Shermin, J., and D. Quinn. Genetic mapping [online lesson] Wheat CAP: Wheat Coordinated Agricultural Project. Available at: http://maswheat.ucdavis.edu/Education/animations/anim_mapping.htm (verified 30 Aug 2012).

Funding Statement

Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

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This session will focus on highly parallel genotyping tools. We are moving away from scoring sequence polymorphism as a “band on a gel”. We will present the design of the SolCAP/Illumina consortium tool, discuss the resulting data format, and discuss quality control.

You can view the webinar below or at the SolCAP website.

View the webinar transcript.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

 Presenter: Allen Van Deynze, University of California, Davis

View other SolCAP webinars

External Links

• Van Deynze, A. 2010. Working with Infinium genotype data. [Online seminar]. Solanaceae Coordinated Agricultural Project. Available at: solcap.msu.edu/infinium_genotype_webinar.shtml (verified 11 May 2012).

Funding Statement

Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

Mention of specific companies is not intended for promotional purposes.

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Photo credit: Patrick Hayes, BarleyWorld.org, Crop and Soil Science Department, Oregon State University

In the United States, barley is grown in 25 states, but the bulk of the production is in seven states. Each of these states hosts at least one checkoff organization, which collects money from producers to promote and support barley production, marketing, and research. As with most crops, certain information is critical for growers to optimize their chances to maximize production. Organizations, universities, and affiliated research and extension centers in each state provide such information on optimal variety selection, as well as state-specific information on marketing; economics; and prevalent diseases, insects, and weeds.

• Idaho
• Minnesota
• Montana
• North Dakota
• Washington
• Maryland
• Oregon
• Wisconsin
• United States

Idaho

Idaho Barley Commission is a self-governed state checkoff organization that works for Idaho barley producers to improve production and profitability of barley in the state. This site provides information on management practices, market reports, newsbriefs, nutrition, and publications.

Idaho Grain Producers Association represents Idaho grain producers at county, state, and federal levels to ensure the viability and profitability of their farming operations. This site provides information on markets, research, and state agricultural agencies, and it links to the Idaho Grain Magazine.

University of Idaho Extension. Provides information on crops, fertilizers and soils, direct seeding and conservation tillage, and pests and pesticides. This site also has information on insect pollinators and irrigation.

USDA/ARS Aberdeen National Small Grains Collection. Maintains collections representing global diversity of small grains, including barley. The site houses the Barley Genetic Stock Collection, which contains over 2,000 germplasm lines of diverse geographic origin.

Minnesota

The Minnesota Barley Research and Promotion Council is a state checkoff organization that works with Small Grains.org to support barley research and interests. The Small Grains site provides information on markets, policy, and production issues.

University of Minnesota Agricultural Experiment Station is responsible for up-to-date research information, showcasing yearly evaluations of yield, agronomic, and disease characteristics of multiple barley varieties in Minnesota.

Montana

Montana Wheat and Barley Committee is a Montana Department of Agriculture organization, funded and directed by producers through a checkoff program. Their goal is to protect the interests and viability of wheat and barley production in Montana. The site provides information on rail rates, weather, and news.

Montana Grain Growers Association is an association of grain producers that works to represent Montana grain growers through legislation efforts that affect farming. This site contains information on policy, research, news, and local events.

Montana State University Agricultural Research Centers are located throughout the state. This site provides localized information on research related to varieties, pest and disease control, and other barley production issues. 

North Dakota

North Dakota Barley Council is a producer-run organization, supported by checkoff funds, that provides information on barley utilization, research, marketing, and legislation. North Dakota is the top-ranked barley production state in the U.S.

North Dakota Grain Growers Association provides marketing and weather information, as well as the Gleaning newsletter, which contains information on grain yields, market prices, and other regional information of interest to growers.

NDSU Agricultural Experiment Station provides information on variety trial results, insect pest reports and management recommendations, and information on weeds and weed resistance.

North Dakota Irrigation Association has a publication that provides recommendations for irrigated malt barley production. Posted with permission by North Dakota Irrigation Association.

Institute of Barley and Malt Sciences. This institute provides information on the 2008, 2009, and 2010 American Malting Barley Association (AMBA) list of approved malting barley varieties. A detailed malting production calendar is also available.

Washington

Washington Grain Alliance provides funded research project summaries, as well as marketing and general crop information.

Washington State University Cereal Variety Testing Program provides weather data, variety brochures, and monthly rust updates.

Maryland

Maryland Grain Producers provides information on their checkoff grant program, general information on biofuels, and a speakers bureau established to raise awareness of agriculture.

University of Maryland’s Research and Extension Centers provide information on the use hulless barley for ethanol production and screening barley cultivars for ethanol production.

Oregon

Barley World, operated out of Oregon State University, offers an image gallery, information on barley food and straw and winter malting/food/forage barley breeding.

Oregon Wheat Growers League provides up-to-date local weather conditions.

Oregon State University, Crop and Soil Science Department barley page. This site contains information on varieties, diseases, nutrient management, and weeds.

Wisconsin

USDA-ARS-Cereal Crops Research Unit, located in Madison, WI. This site contains information about research programs and projects, barley quality analysis, and news.

United States

National Barley Growers Association is a national barley advocacy organization that works to ensure that US barley producers’ concerns are heard both nationally and internationally. This organization works closely with federal policymakers, congressional offices, and regulatory agencies to ensure barley producers’ concerns are addressed.

National Barley Improvement Committee is a national coalition representing barley producers, researchers, and end-users that works to address and discuss important national and regional barley research issues, and to ensure adequate funding for these areas. This site provides data on the economic significance of barley.

U.S. Grains Council is a private, nonprofit organization that works to build export markets for barley, corn, and sorghum. This site provides a database of grain suppliers and the Grains News newsletter.

U.S. Wheat and Barley Scab Initiative is an USDA–ARS-funded research project with the aim of developing effective control measures against Fusarium head blight (scab); the website provides links to a FHB risk assessment tool, Regional FHB Management Sites, and grain sampling for DON analysis.

International

Barley in China

. Article regarding the the Chinese barley industry and the cultural and national economic changes in recent years. Hertsgaard, K. and Wang, X. 2011. Barley in China. Institute of Barley and Malt Sciences Newsletter, Issue 14, April 2011. 

Funding Statement

Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Barley Coordinated Agricultural Project, agreement 2009-85606-05701, administered by the University of Minnesota. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

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