Other Plant Sciences Commons^™

An Integrative Approach To Genomic Introgression Mapping, Andrew J. Severin, Gregory A. Peiffer, Wayne W. Xu, D. L. Hyten, Bruna Bucciarelli, Jamie A. O'Rourke, Yung-Tsi Bolon, David Grant, Andrew Farmer, Gregory D. May, Carroll P. Vance, Randy C. Shoemaker, Robert M. Stupar

Department of Agronomy and Horticulture: Faculty Publications

Near-isogenic lines (NILs) are valuable genetic resources for many crop species, including soybean (Glycine max). The development of new molecular platforms promises to accelerate the mapping of genetic introgressions in these materials. Here, we compare some existing and emerging methodologies for genetic introgression mapping: single-feature polymorphism analysis, Illumina GoldenGate single nucleotide polymorphism (SNP) genotyping, and de novo SNP discovery via RNA-Seq analysis of next-generation sequence data. We used these methods to map the introgressed regions in an iron-inefficient soybean NIL and found that the three mapping approaches are complementary when utilized in combination. The comparative RNA-Seq approach offers …

Soydb: A Knowledge Database Of Soybean Transcription Factors, Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng

Department of Agronomy and Horticulture: Faculty Publications

Background: Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors.

Description: The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database …

Structural And Functional Divergence Of A 1-Mb Duplicated Region In The Soybean (Glycine Max) Genome And Comparison To An Orthologous Region From Phaseolus Vulgaris, Jer-Young Lin, Robert M. Stupar, Christian Hans, D. L. Hyten, Scott A. Jackson

Department of Agronomy and Horticulture: Faculty Publications

Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ~1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ~13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in …

Selecting Strawberry Cultivars For Winter Greenhouse Production, Ellen T. Paparozzi, Stacy A. Adams, George E. Meyer, M. Elizabeth Conley, Vicki L. Schlegel, Erin E. Blankenship, Paul E. Read

Department of Agronomy and Horticulture: Faculty Publications

Costs of transportation and food safety concerns have spawned an increase in public support of locally grown vegetables and fruit. With this in mind, a two-phase investigation was planned with the goal of combining low start up costs for sustainable greenhouse production with selection of strawberry cultivars that would provide the greatest number and largest size of berries. Additionally, berries from each cultivar will be analyzed for their beneficial nutraceutical properties to determine if there is a difference among cultivars.

Fine Mapping The Soybean Aphid Resistance Gene Rag1 In Soybean, Ki-Seung Kim, Stephanie Bellendir, Karen A. Hudson, Curtis B. Hill, Glen L. Hartman, D. L. Hyten, Matthew E. Hudson, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

The soybean aphid (Aphis glycines Matsumura) is an important soybean [Glycine max (L.) Merr.] pest in North America. The dominant aphid resistance gene Rag1 was previously mapped from the cultivar ‘Dowling’ to a 12 cM marker interval on soybean chromosome 7 (formerly linkage group M). The development of additional genetic markers mapping closer to Rag1 was needed to accurately position the gene to improve the effectiveness of markerassisted selection (MAS) and to eventually clone it. The objectives of this study were to identify single nucleotide polymorphisms (SNPs) near Rag1 and to position these SNPs relative to Rag1. …

A High Density Integrated Genetic Linkage Map Of Soybean And The Development Of A 1536 Universal Soy Linkage Panel For Quantitative Trait Locus Mapping, D. L. Hyten, Ik-Young Choi, Qijian Song, James E. Specht, Thomas E. Carter Jr., Randy C. Shoemaker, Eun-Young Hwang, Lakshmi K. Matukumalli, P. B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Single nucleotide polymorphisms (SNPs) are the marker of choice for many researchers due to their abundance and the high-throughput methods available for their multiplex analysis. Only recently have SNP markers been available to researchers in soybean [Glycine max (L.) Merr.] with the release of the third version of the consensus genetic linkage map that added 1141 SNP markers to the map. Our objectives were to add 2500 additional SNP markers to the soybean integrated map and select a set of 1536 SNPs to create a universal linkage panel for high-throughput soybean quantitative trait locus (QTL) mapping. The GoldenGate assay …

Crop Registration: The Pathway To Public Access Of Plant Genetic Materials To Build Crops For The Future, D. D. Ellis, K. A. Garland-Campbell, J. A. Grotenhuis, M. M. Jenderek, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

Starting in 1926 and continuing for 80+ yr, 11,241 crop genetic materials have been registered as of 31 Dec. 2008. The crop registration process is an important pathway to publically describe and document new and useful genetic materials and to incorporate these into the public domain via the National Plant Germplasm System (NPGS). Crop Registration materials are now searchable via the Germplasm Resources Information Network (GRIN) and demand for registered materials remains strong with more than 9150 registered accessions distributed in the past 26 yr by the NPGS. Guidelines continue to evolve to accommodate global factors effecting germplasm exchange such …

Efficacy Of Singular And Stacked Brown Midrib 6 And 12 In The Modification Of Lignocellulose And Grain Chemistry, Scott E. Sattler, Deanna L. Funnell-Harris, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

In sorghum, brown midrib (bmr) 6 and 12 impair the last two steps of monolignol synthesis. bmr genes were introduced into grain sorghum to improve the digestibility of lignocellulosic tissues for grazing or bioenergy uses following grain harvest. Near-isogenic grain sorghum hybrids (AWheatland X RTx430) were developed containing bmr6, bmr12, and the bmr6 bmr12 double mutant (stacked), and their impacts were assessed in a two-year field study. The bmr genes did not significantly impact grain or lignocellulosic tissue yield. Lignocellulosic tissue from bmr6, bmr12, and stacked hybrids had reduced lignin content and increased in …

Heterosis In Sweet Sorghum And Selection Of A New Sweet Sorghum Hybrid For Use In Syrup Production In Appalachia, T. W. Pfeiffer, M. J. Bitzer, J. J. Toy, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

Although heterosis is well established in grain and forage sorghum [Sorghum bicolor (L.) Moench], reports of heterosis in sweet sorghum are limited to results from grain sorghum × sweet sorghum hybrids. Recent development of cytoplasmic male-sterile sweet sorghum lines allows creation of sweet sorghum hybrids for research and industry. Male sterility may also affect allocation of photosynthate to plant parts, creating the potential to increase sugar content in stems by eliminating seed as a sink. The objectives of this study were to compare performance of A₃ cytoplasmic male-sterile lines and A₃ cytoplasmic male-sterile hybrids to fertile B …

Influences Of Wind And Sandblasting On The Endangered Blowout Penstemon, James Stubbendieck, Cheryl D. Dunn, Heidi L. Hillhouse, L. M. Landholt

Department of Agronomy and Horticulture: Faculty Publications

Blowout penstemon Penstemon haydenii is a federally endangered species growing only in areas with active wind erosion in sand dunes of the central United States. This early seral species declines as the blowout habitat stabilizes, allowing later seral species to increase. Blowout penstemon populations and plant size declined in the 1990s when precipitation was higher than normal, resulting in reduced sand movement. We conducted a greenhouse experiment to determine whether blowing sand influenced vigor and persistence of blowout penstemon seedlings. Treatments were wind, sandblasting, wind with sandblasting, and a control. The wind treatment was a constant 14 km h^{–1 …}

Fine Mapping Of The Scn Resistance Locus Rhg1-B From Pi 88788, Myungsik Kim, David L. Hyten, Andrew F. Bent, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is the most economically damaging soybean [Glycine max (L.) Merr.] pest in the USA and genetic resistance is a key component for its control. Although SCN resistance is quantitative, the rhg1 locus on chromosome 18 (formerly known as Linkage Group G) confers a high level of resistance. The objective of this study was to fi ne-map the rhg1-b allele that is derived from plant introduction (PI) 88788. F₂ and F₃ plants and F_3:4 lines from crosses between SCN resistant and susceptible genotypes were tested with genetic markers to …

High-Throughput Snp Discovery And Assay Development In Common Bean, David L. Hyten, Qijian Song, Edward W. Fickus, Charles V. Quigley, Jong-Sung Lim, Ik-Young Choi, Eun-Young Hwang, Marcial Pastor-Corrales, Perry B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Background: Next generation sequencing has significantly increased the speed at which single nucleotide polymorphisms (SNPs) can be discovered and subsequently used as molecular markers for research. Unfortunately, for species such as common bean (Phaseolus vulgaris L.) which do not have a whole genome sequence available, the use of next generation sequencing for SNP discovery is much more difficult and costly. To this end we developed a method which couples sequences obtained from the Roche 454-FLX system (454) with the Illumina Genome Analyzer (GA) for high-throughput SNP discovery. Results: Using a multi-tier reduced representation library we discovered a total of …

Inoculation With Arbuscular Mycorrhizal Fungi Or Crop Rotation With Mycorrhizal Plants Improves The Growth Of Maize In Limed Acid Sulfate Soil, Hasao Higo, Katsunori Isobe, Dong-Jin Kang, Kazuhiro Ujie, Rhae A. Drijber, Ryuichi Ishii

Department of Agronomy and Horticulture: Faculty Publications

Arbuscular mycorrhizal fungi (AMF) improve the uptake of immobile mineral nutrients such as phosphate, thereby improving plant growth. In acid sulfate soil (ASS), AMF spore density is generally low which impacts root colonization and phosphate uptake. Thus, inoculation may help increase AMF colonization of crops grown in ASS. AMF spore density decreases after cultivation of a non-host crop or bare fallow. In addition, preceding crops affect the growth and yield of subsequent crops. The production of AMF inocula requires AMF-compatible plants. The objective of the present study is to elucidate the effect of preceding crops on the persistence of inoculated …

Fine Mapping Of The Soybean Aphid-Resistance Gene Rag2 In Soybean Pi 200538, Ki-Seung Kim, Curtis B. Hill, Glen L. Hartman, D. L. Hyten, Matthew E. Hudson, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

The discovery of biotype diversity of soybean aphid (SA: Aphis glycines Matsumura) in North America emphasizes the necessity to identify new aphid-resistance genes. The soybean [Glycine max (L.) Merr.] plant introduction (PI) 200538 is a promising source of SA resistance because it shows a high level of resistance to a SA biotype that can overcome the SA-resistance gene Rag1 from ‘Dowling’. The SA-resistance gene Rag2 was previously mapped from PI 200538 to a 10-cM marker interval on soybean chromosome 13 [formerly linkage group (LG) F]. The objective of this study was to fine map Rag2. This fine mapping …

Abundance Of Ssr Motifs And Development Of Candidate Polymorphic Ssr Markers (Barcsoyssr_1.0) In Soybean, Qijian Song, Gaofeng Jia, Youlin Zhu, David Grant, Rex T. Nelson, Eun-Young Hwang, D. L. Hyten, P. B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among …

Nebline, November/December 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Middle School Youth on a “Nutrition Mission”
Roasts – Easy to Make for the Holidays and Any Other Time, Too!
Family & Community Education (FCE) Clubs: Presidents’ Notes—Bonnie’s Bits
FCE News & Events
Household Hints: Get a Handle on Holiday Cleaning
Radon—A Health Hazard
Computer Cleaning—Hotspots for Germs
Flexible Cash Lease Provisions
Thistle Control Still Possible This Fall — but Hurry
Use Season-Long Records to Assess Pumping Plant Performance
Diversity is the Key to Attracting Wildlife
Provide Basic Needs to Attract Birds
Relocating Problem Wild Animals: Not as Humane as Most People Think
Evergreen Colors for Winter
Fall Vegetable Garden …

Nebline, October 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Extension Helps Establish a Garden at City Mission
Nutrition Classes Focus on Produce from Garden
How to Reduce Energy Cost for Grain Drying
Tree Planting for Success
Successful Composting
$tretch Your Food Dollar by Making Your Own Mixes
Slow Cookers and Food Safety
Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Household Hints: End-of-Summer Cleanup
10 Tips for Parent-Teacher Conferences
Drying Gourds
Growing American Bittersweet
Storing Vegetables
Praying Mantids: Garden Carnivores
Problem Squirrels in Buildings
October's Heart of 4-H Award Winner: Jennifer Cusick-Rawlinson
Nebraska State Fair 4-H Results
Free Speech: UNL Speakers Bureau in 15th …

Nebline, September 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

September is Preparedness Month
Overseeding Lawns
Water Young Trees to Prevent Winter Damage
Winterizing Your Home
Propagating Plants from Cuttings
Just Like Kids, Head Lice are Back in School
When a Bat Gets Indoors
Eating Locally Grown Foods in the Fall
Get Your Grains
Laundry Tips for Back-to-School Garments and Stains
Parent-Teacher Communication
Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Household Hints: Recognize Symptoms of Stress
Ten Tips for Welcoming Wildlife into Your Landscape
Weedy Vines: Identification and Control
Winter Annual Weeds in Lawn
Fall is a Good Time to Control Weeds
September's Heart …

Nebline, August 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Landscape Water Saving Methods
Natural Sources of Nitrogen for Plant Growth
Commercial Nitrogen Fertilizer Sources
Pumping Water For Ponds
Canning Fruits and Vegetables
Heating With Wood
Fall Prairie Seeding Site Preparation
Handling Food Safely on the Road $tretch Your Food Dollar by Packing Your Lunch Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Household Hints
Financial Security: Consumer Credit
Running Out of Time for Bagworm Control
Harvesting and Preserving Herbs
Summertime Bug Bites
Taking Insect Photos at Spring Creek Prairie
4-H’ers Test Animal Science Skills at PASE
4-H’ers Test Family and Consumer Sciences Skills at …

Nebline, July 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Lancaster Rural Water District: Providing Water to Acreages and Villages for 35 Years
Watch for Blister Beetles in Alfalfa
Use of Copper Compounds to Control Algae in Farm Ponds
Two-Spotted Spider Mites
Water Conservation at Home Begins in the Bathroom, Laundry Room
Harvesting Rainwater Helps Conserve Water and Save Money
What to Do with Zucchini!
Fruits Are Good Source of Nutrients
Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Household Hints: Environmental and Energy Saving Tips When Washing Dishes
Learn the Signs/Act Early Autism Awareness
Summer Safety Tips
There is Still Time to Control Bagworms …

Nebline, June 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Proper Timing Crucial for Bagworm Control
Enjoy Eating Locally Grown Foods!
Drink Your “D” with Dairy
Resurgence in Farmers’ Markets is Good News
Follow Guidelines when Selling Crops Directly to Consumers
Ten Lawn Irrigation Tips
Determining and Sharing Irrigation Costs
When to Harvest Bromegrass Hay
Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Household Hints: Air Conditioner Maintenance
June — National Safety Month
Ten Tips for Fertilizing Your Lawn
Bagworms on a Variety of Plants
Bed Bug Bites
Bed Bug Interceptors
4-H Life Challenge Contests
Lancaster County 4-H Horse VIPS Pre-Districts Format Clinic/Show/Fundraiser
4-H Clover …

Nebline, May 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Bed Bugs Come Back with a Vengeance: Controlling Them Quickly is Key to Slowing Their Spread
Bird Watching: A Little Backyard Therapy
May is Time to Control Leafy Spurge
Recognize/Control Phragmites
Getting the Most Out of CRP
Gluten-Free Sorghum Recipes
Eat a Variety of Vegetables
Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Household Hints: Removing Pollen Stains
May is Clean Air Month: Important Asthma Triggers
Encourage Communication Within the Family
Hand Picking Bagworms an Effective Control
ReTree Nebraska: Important to Diversify When Replanting
Managing Aquatic Plant Life
Using Animal Manure in the Garden
Control …

Nebline, April 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Urban Youth Learn About Agriculture at Local Ag Awareness Festivals
Renting Livestock Facilities
Is Sainfoin Right For You?
Wind Energy Seminars Archived on the Web
Backyard Organic Gardens Need Work but Have Increased Benefits
Pre-emergent Herbicide Application Time
Act Early to Control Musk Thistles
Study Shows Transplanted Trees Grow Better Without Grass Nearby
Eat Your Breakfast— Your Body will Thank You!
Easter Egg Tips
Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Household Hints: Housekeeping Organization
Wring Out the Old; Bring in the New: Debunking Some Common Cleaning Practices
Boost Your Child’s Brain Power
Children …

Nebline, March 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

4-H Embryology: More Than Just a Science Project!
How to Account for Differences in Moisture Content in Commodities
Controlling Winter Annual Brome with Herbicides
Canada Geese Populations are Increasing
Managing Pocket Gophers
Do a “Don’t Do” List!
5 More Main Dishes—Each Using Only 5 Ingredients
Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Household Hints: Removing Soot from Carpet
Tips to Help Parents Talk to Their Kids About Sex and Technology
Local Bagworm Control Initiative
2009 Great Plants Selections
Early Detection is Key to Minimizing Insecticide Use in Home Gardens
Bird House Care Is Important …

Nebline, February 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

13 Fun Ways to Eat More Fruites and Vegetables!
Farmland Leasing Workshop, Feb. 11
Soil Fertility and Phosphorus
Private Pesticide Applicator Certification Opportunities
The Value of Landscaping
Are You Winning the “Fruit & Vegetable Bowl Game”?
5 Main Dishes—Each Using Only 5 Ingredients
Family & Community Education (FCE) Clubs: Presidents’ View—Bonnie’s Bits
FCE News & Events
Beltline FCE Club: 1931–2008
Household Hints: How to Keep Red Clothes from Turning Pink
Small Steps to Health and Wealth
2009 All-America Selections
Starting Tender Perennials Indoors
Garden Guide: Things to Do This Month
Tree Squirrels and Rabbits are Active in Winter
Beginning Beekeeping …

Nebline, January 2009

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Creating a Strong Family: Strong Families Have Six Common Characteristics
Ways to Spend Time With Your Family in January
Private Pesticide Applicator Certification Opportunities
Soybean Cyst Nematode Spreading in Nebraska: Free Soil Sampling Kits at Extension Offices
Mystery “Bites”: Unidentifiable Skin Problems Usually Have Non-Insect Causes
Raccoons in the City
2009 Wall Calendar
Beginning Beekeeping 2-Day Workshop
2009 All-America Rose Selections
Shopping for Plants and Seeds
Garden Guide: Things to Do This Month
Birds Need Water In Winter
Attract Winter Birds With Feeders
Top 10 Myths of Entrepreneurship
Winter Houseplant Care
Wishing You a Healthy H-A-P-P-Y N-E-W Y-E-A-R!
$tretch Your …

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Bulked Segregant Analysis Using The Goldengate Assay To Locate The Rpp3 Locus That Confers Resistance To Soybean Rust In Soybean, D. L. Hyten, James R. Smith, Reid D. Frederick, Mark L. Tucker, Qijian Song, P. B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Few resistance loci to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd., have been genetically mapped and linked to molecular markers that can be used for marker assisted selection. New technologies are available for single nucleotide polymorphism (SNP) genotyping that can be used to rapidly map traits controlled by single loci such as resistance to SBR. Our objective was to demonstrate that the highthroughput SNP genotyping method known as the GoldenGate assay can be used to perform bulked segregant analysis (BSA) to fi nd candidate regions to facilitate effi cient mapping of a dominant resistant locus to SBR designated Rpp3 …

Mapping And Confirmation Of A New Allele At Rpp1 From Soybean Pi 594538a Conferring Rb Lesion–Type Resistance To Soybean Rust, Nanda Chakraborty, Joe Curley, Reid D. Frederick, D. L. Hyten, Randall L. Nelson, Glen L. Hartman, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

Soybean rust, caused by Phakopsora pachyrhizi (H. Sydow & Sydow), is a destructive soybean [Glycine max (L.) Merr.] disease and identification of new resistance genes is essential for effective rust management. Our research objectives were to map and confirm the location of resistance gene(s) in PI 594538A using a population of 98 F_3:4 lines from across between PI 594538A (reddish-brown [RB] lesions) and the susceptible cultivar Loda (tan [TAN] lesions). The lines were inoculated with the P. pachyrhizi isolate ZM01-1 from Zimbabwe. The RB resistance in PI 594538A mapped on linkage group G as a single dominant gene. …

Detection And Validation Of Single Feature Polymorphisms Using Rna Expression Data From A Rice Genome Array, Sung-Hyun Kim, Prasanna R. Bhat, Xinping Cui, Harkamal Walia, Jin Xu, Steve Wanamaker, Abdelbagi M. Ismail, Clyde Wilson, Timothy J. Close

Department of Agronomy and Horticulture: Faculty Publications

Background: A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent. Results: Expression data obtained by hybridizing RNA to an oligonucleotide array …