Project on Market-Class Specific Markers in Beans
This project, funded by the USDA National Institute of Food and Agriculture, focuses on identifying market-class specific markers in various types of beans. Through the use of polymorphic SNPs and indel markers, the project aims to enhance understanding of genetic variations in different bean varieties, such as Snap Bean, Pinto, Navy, Black, and others. The project management involves regular updates, steering committee meetings, and the addition of new members to the advisory board. The research has resulted in the discovery of new markers for common bean varieties, contributing to the ongoing advancement of bean genetics research.
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Project Sponsor This project is funded by the USDA National Institute of Food and Agriculture. Project number 2009-01929.
Project Management Highlights Monthly conference calls Participants Steering committee Advisory committee members Any project participant Goal Up-date everyone on recent project activity Plan upcoming activities Minutes provided on-line Advisory Board resignation Dr. Chuck Hibberd, Purdue Extension resigned Dr. Christine Bruhn agreed to serve on board Dr. Fred Bliss, resigned Dr. Steve Beebe agreed to serve on board
Objective 1: Market-class specific markers % polymorphic SNPs 59.6 50.3 48.7 45.5 41.5 39.2 36.4 33.0 30.3 23.8 17.6 14.3 Market class Snap Bean Pinto Small red Pink Great Northern Small White Navy Black Light red kidney Dark red kidney White kidney Cranberry n 134 91 29 17 48 6 43 42 32 15 8 19
Objective 1: Market-class specific markers Linkage group Pv01 Pv02 Pv03 Pv04 Pv05 Pv06 Pv07 Pv08 Pv09 Pv10 Pv11 Total SNPs mapped in 2011 760 518 531 708 666 199 192 824 449 763 923 6553 SNPs mapped previously 73 48 55 47 29 28 30 38 41 42 54 485 LG length (cM) 143.7 197.0 175.9 154.8 135.1 103.8 141.1 196.8 159.7 135.4 122.3 1665.5 Total SNPs 833 566 586 755 695 227 222 862 490 805 977 7018
Objective 1: Market-class specific markers Indels (>7 nt) preprocessing 9,634 1,515 1,954 5,524 1,378 20,005 Indels (>7 nt) postprocessing 1,358 339 299 649 Market Class Pinto Navy Black Light red kidney Dark red kidney Total 66 2,711 Current catalog of common bean markers 10,453 SNP markers 2,711 indel markers 13,164 new markers for common bean
Objective 1: Market-class specific markers Pinto indel markers useful in other market classes PBN-3187434 Great Northern Black Navy Small red Pink Pinto PBN-411737 Great Northern Black Navy Small red Pink Pinto
Objective 1: Market-class specific markers Newer, upright pintos Fst = 0.25 Older, prostrate pintos
Objective 2: Nutritional Phenotyping Elements Macro (mg/g DW) Ca K Mg P S Micro ( g/g DW) Cu Fe Mn Na Ni Se Zn BeanCAP range Fold range 0.40 3.75 10.50 15.78 1.21 2.40 3.25 6.52 1.50 2.60 9.5 x 1.5 x 2.0 x 2.0 x 1.7 x 6.59 13.86 47.16 101.39 10.05 19.98 not detected 0.62 6.28 0.28 1.01 31.03 68.54 2.1 x 2.1 x 2.0 x 10.2 x 3.6 x 2.2 x
Objective 3: PhaseolusGenes Database MAPPED MARKERS Type/Source STS Hougaard et al. 2008 Various Murray et al. 2002 Kami et al. , unpubl. Kim et al. 2006 McConnell et al. 2010 David et al. 2008 Total STS Genes SCARS SSRs Blair et al. , various Yu et al. 2000 Buso et al. 2006, Grisi et al. 2007 Hanai et al. 2010 Hanai et al. 2007 Benchimol et al. 2007, Oblessuc et al. 2009 Cardoso et al. 2008 Total SSR Total Name Total Mapped Leg 195 12 130 113 120 302 114 986 25 78 105 11 89 Bng D COS g 9 0 295 114 623 15 69 B4 BACs BM Pv PVBR PVM FJ 692 37 81 140 40 173 99 1,262 2,351 210 19 55 45 0 0 0 IAC, IAC-SSR SSR-IAC 329 1,036
Objective 3: PhaseolusGenes Database Name Bean01 Parents BJ Pop Type RI Source Freyre et al. 1998 Type of markers Phenotypic, RFLP, RAPD, AFLP; SCAR;Allozyme STS: g, CAPS, dCAPS, indel; SCAR; RAPD, AFLP STS: g, Leg, Bng, D, RFLP; STS: Leg; SNP: g # markers 234 MA Bean02 BJ RI MA McClean 2007; McConnell et al. 2010 MA Navarro Gomes & Gepts 2011 MA Galeano et al. 2011 MM Galeano et al. 2011 MA Galeano et al. 2011 NA Galeano et al. 2011 450 Bean03 BJ RI 485 Bean04 BJ RI 424 Bean05 DOR364 x BAT477 RI SSR, SSR-BES, RAPD, AFLP SSR, SNP, STS: RFLP, Leg SSR; SNP; STS: Leg, g, Bng 291 Bean06 DOR364 x G19833 RI 499 Bean07 Consensus NA 1,010
Objective 4: Early Breeder Training Two graduates of program are in graduate plant breeding programs 19 student interns for 2010 ~170 high school students visited during 2010
Objective 5: Multimedia Development 2011 Outcomes Spillin the Beans (Julie Garden-Robinson) Bean nutrition curriculum Mineral transport animation (Christina Johnson) Recruiting documentary, Part 2 (Bree Reetz, Shane Reetz) How to make a difference: Norman Borlaug Story Root biology documentary (Shane Reetz) Shovelomics How-to (Shane Reetz) New techniques for screening root traits 2012 Plans Genetic Diversity Documentary (Part 3) How plant breeding solves problems: US wheat stem rust story Young Plant Breeders Documentary (Part 4) Why students are interested in plant breeding Minerals and human nutrition animation(s)
85 Active Participants North Dakota State Univ: Phillip McClean, PD; Juan Osorno, Co-PD, education lead, breeding; Julie Garden-Robinson, Co- PD, extension; Michelle Grant, Administrative assistant; Bradley Bisek, intern; Nicole Dallman, intern; Kataryna Cookman, intern; Mitchell Bauske, intern; Lyndsie Park, intern; Peter Totten, intern; Christina Johnson, Artistic lead; Shane Reetz, Documentary lead; Bree Malingnen, Infrographics artist; Samira Mafi Moghaddam, Marker development; Rian Lee, Marker development; Sujan Mamidi, Statistical analysis; Stacy Halvorson, extension associate; Leah Whigham, nutrition researcher; Deb Habedank, childcare director; Todd Weinmann, extension agent; Steve Sagaser, extension agent; Chelsea Langus, intern; Alexandra Idso, intern; Aimee Henning, intern, Kendra Otto, intern; Emily Westrom, intern; Amy Hutchinson, intern; Kayla Bahtiraj, intern. Univ Nebraska, Lincoln: Carlos Urrea, , Co-PD; Nicole Schnitger, intern; Misty Griffitts, intern; Scout Wilson, intern; Charity Berkey, intern; Danielle Becker, intern; USDA/Houston: Michael Grusak, Co-PD, nutritional analysis; Paz Etcheverry, cooperator; David Dworak, technician; Lori Center, technician; William Carter, intern; Oregon State Univ: Jim Myers,; Co-PD, Nutritional analysis, breeding; Annie Chozinski, faculty research assistant; Kara Young, intern; Katrina Maguelli, intern. Univ California, Davis: Paul Gepts, Co-PD, data base development; Shelby Repinski, Graduate student, QTL entry to database; Adriana Navarro Gomez, Graduate student, QTL entry to database; Sun Lei, Graduate student; Tania Gioia, Graduate Student; Dawei Lin, Bioinformatics and database lead; Jose Boveda, Database/web programmer; Joe Fass, Lead programmer; Nikhil Joshi, Bioinformatics programmer; Monica Britton, Bioinformatics analyst; Zhi-Wei Lu, Bioinformatics analyst. Michigan State Univ: Jim Kelly, Co-PD, Breeding, education; Evan Wright, technician; Amy Lasley, MSU, graduate student; Valerio Hoyos Villegas, graduate student; Rosa Castanon, intern; Brittany Lane, intern. USDA/Prosser: Phil Miklas, Co-PD, Field increase of core population; Susan Swanson, technician; Jennifer Trapp, technician; Jeff Coulson, technician. USDA/Beltsville: Perry Cregan, Co-PD, Marker development and screening; David Hyten, Marker development and screening; Edward Fickus, Marker development technician; Qijiain Song, Bioinformatics analysis; Gaofeng Jia, marker and bioinformatics analysis; Josaine Rodriques, Federal University of Vicosa, Brazil, SSR analysis, graduate; Charles Quigley, research DNA sequencing. Seminis: Ken Kmecik, Greenhouse/field increase of core population. Colorado State Univ: Mark Brick, Breeding, education, nutrition analysis; Henry Thompson, Nutrition analysis; Soni Hueftle, intern; Griffin Carpenter, intern; Keera Brown, intern; Alyssa Bollig, intern; Dimas Echeveria Moreno, Research associate, nutrition analysis. USDA/East Lansing: Karen Cichy, Co-PD, Nutritional analysis; Nicole Butler, graduate student; USDA/Mayquez, PR: Tim Porch, Co-PD, Field stress analysis; Abraham Montes, technician; Franquie Colon, research assistant; Gregory Howard, research; Edlin Gonzalez, research.
