Progress 10/01/03 to 09/30/09
Outputs
OUTPUTS: Molecular genetics of legumes (mostly common bean) was the primary research objective of this project. In one study, gene-based markers were used to develop a transcriptional map using the community wide BAT93 x Jalo EEP558 recombinant inbred (RI) mapping population of Phaseolus vulgaris L. To develop the map, sequence information, including introns and 3' UTR, was generated for over 550 genes in the two genotypes. Over 1800 single nucleotide polymorphisms (SNPs) and indels were found, 300 of which were screened in the RI population and mapped. The completed LOD 2.0 map is 1587 cM in length and consists of 273 gene-based markers, as well as previously mapped core markers. Parents for other popular common bean mapping populations were screened with these polymorphisms to discover the degree of diversity and facilitate further mapping. Syntentic regions were discovered with two other model legumes, Medicago truncatula and Lotus japonicus. This has greatly added to the genomic resources available for P. vulgaris and legumes in general. In preparation for future association mapping experiments, we analyzed 180 common landraces, which represent the diversity found from northern Mexico to northern Argentina, 55 microsatellite (SSR) distributed among all 11 chromosomes. They were selected in a manner that minimizes repetition and maximizes phenotypic diversity. As with previous research, the diversity was organized in gene pools along a north to south arc. The diversity was best defined by eight different populations. The first electronic transcript (gene-based) map of common bean was developed based on the extensive (over partial arms of chromosomes) synteny between soybean and common bean. All totaled an additional 15,000 gene-based contigs and singletons were placed relative to the low density map. The feasibility of using the electronic map was demonstrated by the addition of 9 other markers more tightly linked markers to the major disease resistance locus on Pv7. This linkage was then used to discover tightly linked to determinacy and green cotyledon phenotypes. Iron deficiency chlorosis (IDC) is a major production problem in the North Central states. Yield is reduced up to 20% with IDC susceptible varieties. This translates into a $210 million loss. An experiment was performed to discover markets linked to IDC. Once discovered, these markers could be coupled with field IDC ratings to pick the best advanced lines for future release. Two SSRmarkers were significantly associated with IDC in both the 2002 and 2003 populations. Candidate gene analysis discovered that three SNPs in GmNAS1 that were associated with IDC. Lines containing the arginine SNP along with the two SSR tolerance alleles had significantly lower IDC scores. This experiment was expanded by evaluating with 1536 SNP markers. Five additional SNP loci were discovered to be associated with IDC. Each of these was closely linked with the following genes known to be involved in iron metabolism: NAS, AtREG1, FRO. Both NAS and FRO genes mapped at synentic regions in the duplicated soybean genome. PARTICIPANTS: Phillip McClean, North Dakota State University; leader for the entire project. Rian Lee, North Dakota State University; research associate assisting with all aspects of the project. Sujan Mamidi, North Dakota State University; graduate student, duplication history of common bean. Melody McConnell, North Dakota State University; graduate student, transcript map development. Shireen Chikara; North Dakota State University; graduate student, transcript map development Phil Miklas; USDA/ARS, Prosser, Washington; collaborator, application of transcript and electronic map to common bean improvement. Jim Myers; Oregon State University; collaborator, application of transcript and electronic map to common bean improvement. North Dakota Soybean Council, financial support of soybean iron deficiency chlorosis research North Central Soybean Research Programs; financial support of soybean iron deficiency chlorosis research. Jay Goos, North Dakota State University; collaborator, soybean iron deficiency chlorosis research. Ted Helms, North Dakota State Unviersity; collaborator, soybean iron deficiency chlorosis research. Randy Shoemaker, USDA/ARS, Ames, Iowa; collaborator, soybean iron deficiency chlorosis research. Carroll Vance, USDA/ARS, St. Paul, Minnesota; collaborator, soybean iron deficiency chlorosis research. Scott Jackson, Purdue University; collaborator, development of physical/genetic map of common bean. Jessica Schlueter, Purdue University; collaborator, development of physical/genetic map of common bean and evolutionary history of common bean. TARGET AUDIENCES: Common bean geneticists, Common bean plant breeders, Common bean producers, Soybean geneticists, Soybean plant breeders, Soybean producers, Plant geneticists in general, Plant breeders in general, Students of plant genetics, Students of plant breeding. PROJECT MODIFICATIONS: None.
Impacts
The transcript and electronic maps of common bean are being used: 1) to improve plant breeding efforts by fine-mapping loci required for a successful new variety; 2) to extend the physical map of common bean; to correlate the physical and genetic maps of common bean; 3) to serve as a reference gene set to build contigs from high throughput sequence data; 4) to determine the evolutionary synteny between common bean and other legumes; 5) to facilitate the development of a low density single nucleotide polymorphism map of common bean; and 6) as a new tool for marker-assisted selection in common bean. Association mapping and candidate gene analysis allow scientists to more accurately define the genes responsible for agronomic traits of interest. In general, the iron deficiency chlorosis experiments that addressed a significant production problem in the North Central states, demonstrated the utility of this approach for the first time in soybean. These approaches require a detailed understanding of the potential genes involved and knowledge of the organization of genetic diversity in the cultivated form of the species. The iron deficiency chlorosis markers are available to industry for the selection of potentially IDC tolerant varieties of soybean. This selection will increase tolerance, and thus increase yield and profitability, in those regions with soils that induce IDC.
Publications
- Todd A, Melmaiee, Russo A, McClean P, Schlueter J, Jackson S, Manoharan M, Lee R, Kalavacharla. 2009. Progress in BAC contig development for the Ur-3 rust resistance locus in common bean (Phaseolus vulgaris). Plant and Animal Genome XVI Abstracts. (http://www.intl-pag.org/17/abstracts/P05f_PAGXVII_388.html).
- Jackson SA, Schlueter J, McClean P, Gepts P, Blair M, Vallejos E. 2009. Genomics in common bean: leveraging the soybean genome for bean improvement. Plant and Animal Genome XVI Abstracts. (http://www.intl-pag.org/17/abstracts/W29_PAGXVII_235.html).
|
Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: Molecular genetics experiments of legumes (mostly common bean) were performed in the past year. These include the development of the first electronic transcript (gene-based) map of common bean, the development of a low-density SNP map of common bean, a determination of the duplication history of legumes, a characterization of the chromosomal structure of soybean based on common bean as a model diploid Phaseoleae species, and high density mapping of the major disease-resistance locus on chromosome Pv7 of common bean. An association mapping study using candidate genes rather than random genomic loci to discover additional molecular markers linked to iron-deficiency chlorosis loci in soybean was initiated this year. Work continued on the development of software that designs primers to be used for the PCR amplification of orthologs in a new species to genes known in other plant species. Training of graduate and undergraduate students continued. Products include: an extended transcript map of common bean with specific information for its utilization; an electronic map of common bean, based on the syntentic relationship with soybean, containing 15,009 loci; 9 additional markers more tightly linked to the major disease resistance locus on Pv7; a catalog of the ancestral chromosome arrangement in the diploid progenitor of soybean; and new markers associated with iron-deficiency chlorosis in soybean. The outputs have been disseminated through talks and posters at professional meetings, peer-reviewed journal articles, and informal discussion with peers. PARTICIPANTS: Phillip McClean, North Dakota State University; leader for the entire project. Rian Lee, North Dakota State University; research associate assisting with all aspects of the project. Sujan Mamidi, North Dakota State University; graduate student, duplication history of common bean. Francesca Anne Denton, North Dakota State University; leader developer of primer design software. North Dakota Soybean Council, financial support of soybean irondeficiency chlorosis research. Jay Goos, North Dakota State University; collaborator, soybean iron-deficiency chlorosis research. Ted Helms, North Dakota State Unviersity; collaborator, soybean iron-deficiency chlorosis research. Scott Jackson, Purdue University; collaborator, development of physical/genetic map of common bean. Jessica Schlueter, Purdue University; collaborator, development of physical/genetic map of common bean and evolutionary history of common bean. TARGET AUDIENCES: Common bean geneticists; Common bean plant breeders; Common bean producers; Soybean geneticists; Soybean plant breeders; Soybean producers; Plant geneticists in general; Plant breeders in general; Students of plant genetics; Students of plant breeding. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The transcript and electronics of common bean is being used: to improve plant breeding efforts by fine-mapping loci required for a successful new variety; to extend the physical map of common bean; to correlate the physical and genetic maps of common bean; to serve as a reference gene set to build contigs from high-throughput sequence data; to determine the evolutionary synteny between common bean and other legumes; to facilitate the development of a low-density single-nucleotide polymorphism map of common bean; and as a new tool for marker-assisted selection in common bean. The iron-deficiency chlorosis markers are being used by industry to select for tolerant varieties of soybean. The primer software is being used to facilitate gene cloning in species with limited genomic resources.
Publications
- McClean, P.E., Cannon, S., Gepts, P., Hudson, M., Jackson, S., Rokshar, D., Schmutz, J., and Vance, C. 2008. Towards a whole genome sequence of common bean (Phaseolus vulgaris): Background, approaches and applications. Stakeholder Input Sources: Plant and Plant Products. Published on-line August 31, 2008. http://www.csrees.usda.gov/business/reporting/stakeholder/pl_stakehol der.html (verified 12/31/2008)
- Schlueter, J.A., Goichochea, J.L., Gill, V., Lin, J-Y., Yu, U., Collura, K., Vallejos, T.J., Blair, M., McClean, P., Wing, R., and Jackson, S.A. 2008. BAC-end sequence and a draft physical map of the common bean (Phaseolus vulgaris L.) genome. Tropical Plant Biology 1:40-48.
- McClean P.E., Lavin, M., Gepts, P., and Jackson, S.A. 2008. Phaseolus vulgaris; a diploid model for soybean. In: Stacey, G. (ed.), Genetics and Genomics of Soybean, Springer, New York, pp. 55-78.
|
Progress 10/01/06 to 09/30/07
Outputs
OUTPUTS: Molecular genetics experiments of common bean were performed in the past year. These include the development of the first transcript (gene-based) map of common bean, the evaluation of the genome duplication history of Phaseolus species, a study of the synteny between common bean and other plant species, and the completion of an extensive microsattelite study of the landrace diversity. An association mapping study to discover molecular markers linked to iron deficiency chlorosis loci in soybean was completed this year. Work continued on the development of software that designs primers to be used for the PCR amplification of orthologs in a new species to genes known in other plant species. Training of graduate and undergraduate students continued. Products include: a transcript map of common bean with specific information for its utilization; a definition of gene families known to have undergone duplication during the evolutionary history of common bean; a collection of microsattelite markers that can distinguish among races of common bean; and a list of microsatellite markers associated with iron deficiency chlorosis in soybean. The outputs have been disseminated through talks and posters at professional meetings, peer-reviewed journal articles, and informal discussion with peers. PARTICIPANTS: Phillip McClean, North Dakota State University; leader for the entire project. Rian Lee, North Dakota State University; research associate assisting with all aspects of the project. Sujan Mamidi, North Dakota State University; graduate student, duplication history of common bean. Melody McConnell, North Dakota State University; graduate student, transcript map development. Anne Denton, North Dakota State University; leader developer of primer design software. North Dakota Soybean Council, financial support of soybean iron deficiency chlorosis research. Jay Goos, North Dakota State University; collaborator, soybean iron deficiency chlorosis research. Ted Helms, North Dakota State Unviersity; collaborator, soybean iron deficiency chlorosis research. Scott Jackson, Purdue University; collaborator, development of physical/genetic map of common bean. Jessica Schlueter, Purdue University; collaborator, development of physical/genetic map of common bean and evolutionary history of common bean. TARGET AUDIENCES: Common bean geneticists Common bean plant breeders Common bean producers
Impacts
The transcript map of common bean is being used: to improve plant breeding practice by identifying genetic regions required for a successful new variety; to anchor the emerging physical map of common bean with this genetic map; to study the evolutionary synteny between common bean, other legumes, and model plant species; to facilitate the development of a low density single nucleotide polymorphism map of common bean; and as a new tool for marker-assisted selection in common bean. The iron deficiency chlorosis markers are being used by industry to select for tolerant varieties of soybean. The primer software is being used to facilitate gene cloning in species with limited genomic resources.
Publications
- Gelin JR, Forster S, Grafton KF, McClean PE, and Rojas-Cifuentes GA. 2007. Analysis of seed-zinc and other nutrients in a recombinant inbred population of navy bean (Phaseolus vulgaris L.) Crop Science 47: 1361-1366.
- McClean PE, Lavin M, Gepts P, and Jackson SA. 2007. Phaseolus vulgaris L.: A diploid model for soybean. In: Stacey G (ed), Genomics of Soybean. Springer Science+Business Media, LLC, New York (in press).
- McClean PE, and Lee RK. 2007. Genetic architecture of chalcone isomerase non-coding regions in common bean (Phaseolus vulgaris L.) Genome 50:203-214.
- Rossi M, Mamidi S, Bellucci E, McConnell MD, Lee RD, Papa R, McClean PE. (2007) The effect of selection on loci within close proximity of domestication loci in common bean (Phaseolus vulgaris L.) Phaseomic V Abstracts. p. 9.
- Gepts P, Aragao F, de Barros E, Blair, MW, Brondani R, Broughton WJ, Galasso I, Hernandez G, Kami J, Lariguet P, McClean P, Melotto M, Miklas P, Pauls P, Pedrosa-Harand A, Porch T, Sanchez F, Sparvoli F and Yu K. 2007. Genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the Tropics. In: Moore PH, and Ming R (Eds), Genomics of Tropical Crop Plants. Springer, Berlin. (in press)
- Wang J, MccClean P, Lee R, Goos RJ, and Helms T. 2008. Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theoretical and Applied Genetics (accepted).
- McConnell MD, Mamidi S, Rossi M, Lee RK, and McClean PE. A gene-based linkage map of common bean (Phaseolus vulgaris L.). 2007. Plant and Animal Genome XV Abstracts. (http://www.intl-pag.org/15/abstracts/PAG15_P05f_414.html)
- Mamidi S, Rossi M, McConnell MD, Lee RK, Papa R, McClean PE, and Bellucci E. 2007. Investigation of the domesticatin process in common bean (Phaseolus vulgaris L.) using multilocus data. Plant and Animal Genome XV Abstracts. (http://www.intl-pag.org/15/abstracts/PAG15_P05f_416.html)
- Buchfink DJ, Denton A, McClean P. 2007. Database and tools for primer design. 2007. Plant and Animal Genome XV Abstracts. (http://www.intl-pag.org/15/abstracts/PAG15_P08a_843.html)
|
Progress 10/01/05 to 09/30/06
Outputs
Study 1. Molecular linkage mapping is an important strategy in any species for use in gene discovery and cloning, crop improvement via marker assisted selection, further genetic studies on the inheritance of important agronomic traits, diversity studies to reveal the germplasm structure, which aids parental selection for plant breeding programs, and evolutionary history, and cross-species comparisons. In this study, gene-based markers were used to develop transcriptional map using the community wide BAT93 x Jalo EEP558 recombinant inbred (RI) mapping population of Phaseolus vulgaris L. Gene-based markers were found in genes chosen based on characteristics of their homologues in other species, including a mutant phenotype in Arabidopsis, selection during domestication in maize, and function in a biochemical pathway in Arabidopsis. Sequence information, including introns and 3' UTR, was generated for over 550 genes in the two genotypes. Over 1800 single nucleotide
polymorphisms (SNPs) and indels were found, 300 of which were screened in the RI population and mapped. The completed LOD 2.0 map is 1587 cM in length and consists of 273 gene-based markers, as well as previously mapped core markers. Parents for other popular common bean mapping populations were screened with these polymorphisms to discover the degree of diversity and facilitate further mapping. Several syntentic regions were discovered with two other model legumes, Medicago truncatula and Lotus japonicus. This has greatly added to the genomic resources available for P. vulgaris and legumes in general. Study 2. Identifying regions of the genome that are targets of selection provides important insights into the evolutionary history of the species and facilitates the identification of important agronomic genes for further crop improvement. Little is known about the effect of the separation of common bean into Middle American and Andeqan gene pools and the subsequent domestication
process on genetic diversity at the DNA sequence level. Our objective is to study these effects in this highly self pollinated species. Specifically, we are studying the effects of domestication and improvement on loci near and far from mapped domestication loci by sequencing 3' portions of genes in three genotype groups: wild, landraces and cultivars. A total of 72 different genotypes were surveyed. P. coccineus was used as a reference outgroup. Of the seven genes studied to date: 1) the wild genotypes are more diverse than the landraces; 2) landraces and cultivars have equivalent levels of diversity; 3) the diversity among Andean genotypes is reduced relative to the Middle American genotypes; and 4) the reduction in diversity from the wild state was greater for the Andean (45%) than the Middle American (25%) landraces. Diversity for two genes was completely lost among the Andean landraces. In the future, several evolutionary scenarios will be modeled using coalescent simulations to
better understand the domestication process in common bean.
Impacts
Association mapping and candidate gene analysis allow scientists to more accurately define the genes responsible for agronomic traits of interest. These approaches require a detailed understanding of the potential genes involved and knowledge of the organization of genetic diversity in the cultivated form of the species. The gene-based molecular map we are developing will be a valuable resource that potentially links specific traits to genes that may control those traits. This will be accomplished by linking known quantitative trait loci to specific mapped genes. This will focus plant improvement efforts on specific genes rather than portions of the genome defined by anonymous markers. By discovering genes associated with both domestication and crop improvement, it will be possible to design high throughput screening procedures to will facilitate the selection of the best lines derived from wide-cross whose goals is to incorporate beneficial traits from wild germplasm
into cultivated materials.
Publications
- Wang, J. 2006. Association Mapping of IDC Loci in Soybean. Ph.D. Thesis. North Dakota State University, Fargo, North Dakota.
|
Progress 10/01/04 to 09/30/05
Outputs
Common bean research. We are developing a new gene-based molecular map of common bean. Primers specific to 600 genes were designed, and fragments from BAT93 and Jalo EEP558, the parents of the community-wide molecular map were amplified and sequences. Comparing these two genotypes, we have discovered single nucleotide polymorphisms (SNP) and insertion/deletion (indels) in over 200 genes. We tested several procedures to efficiently and economically detect these polymorpphisms. The cleaved amplified polymorphic DNA (CAPS) procedure was the most reliable. To date we have mapped 18 genes using the CAPS (12) or our previously described indel (6) procedure. Along with 18 other genes, we have constructed the core of what will a new map for the Phaseolus research community. In preparation for future association mapping experiments, we analyzed molecular diversity among 180 common landraces that represent the diversity found from northern Mexico to northern Argentina. These
180 represent a subset of the core collection of landraces found in the USDA Phaseolus collection. They were selected in a manner that minimizes repetition and maximizes phenotypic diversity. The lines were screened with 55 microsatellite (SSR) distributed among all 11 chromosomes. Generally, the diversity was organized in gene pools along a north to south arc. The diversity was best defined by eight different populations. Soybean research (collaborators Drs. Ted Helms, NDSU Plant Sciences and Dr. Jay Goos, NDSU Soil Science). Iron deficiency cholorsis (IDC) is a major yield limiting factor for soybean production. IDC rating data was collected on two soybean populations consisting of advanced breeding lines in a multi-site, replicated field trial. SSR marker data was also collected. Lines with the extreme phenotypes were used to identify markers putatively associated with the IDC. Based on the logistic regression analysis over all locations, two markers were significantly associated
with IDC in both the 2002 and 2003 populations. For both populations, those lines with the tolerance allele at both marker loci had significantly lower IDC scores than lines with one or no tolerant alleles. Candidate gene analysis was also performed on two the independent soybean populations. Two nicotianamine synthase (NAS) genes were discovered in soybean. GmNAS2 showed not variants among the lines. We discovered three SNP in GmNAS1 that were in complete linkage disequilibirium. One SNP resulted in a non-synonymous substitution of arginine for lysine. This substitution was in a 20 amino acid domain highly conserved among all plant species analyzed. In 2002, a strong association was detected between the arginine variant and IDC tolerance. This association was not as strong in the 2003 population. Lines containing the arginine SNP along with the two SSR tolerance alleles had significantly lower IDC scores.
Impacts
Common bean research: Association mapping and candidate gene analysis allow scientists to more accurately define the genes responsible for agronomic traits of interest. These approaches require a detailed understanding of the potential genes involved and knowledge of the organization of genetic diversity in the cultivated form of the species. The gene-based molecular map we are developing will be a valuable resource that potentially links specific traits to genes that may control those traits. This will focus plant improvement efforts on specific genes rather than portions of the genome defined by anonymous markers. The genetic diversity analysis provided the proper statistical framework necessary for accurate association mapping experiments necessary to confirm the role of a candidate gene in the expression of a specific agronomic trait. Soybean research: Iron deficiency cholorosis (IDC) is a major yield limiting factor for soybeans grown in the northern tier of
states. Previous experiments defined molecular markers that were population specific. These experiments described here discovered markers that were associated IDC tolerance in soybean lines from over 30 breeding programs. The fact that the markers were confirmed in a second independent population substantiates their usefulness. The discovery of variants of the nicotianamine synthase gene associated with IDC tolerance provides a direct link between a gene and this important trait and sets the stage for targeted soybean improvement efforts.
Publications
- No publications reported this period
|
Progress 10/01/03 to 09/30/04
Outputs
The project to clone gene fragments from gene fragments continued this year and has been extended to other crops than common bean (Phaseolus vulgaris). We have sequenced additional fragments of 31 different genes in common bean. Many of these have polymorphisms. These polymorphisms are being converted into single nucleotide polymorphism or insertion/deletion-based markers. The study of the evolutionary divergence of introns in Phaseolus genera was extended to now include 29 species, mostly from Mexico and Central America. Unique evolutionary patterns are being uncovered for different genes. Next year, we will focus on additional genes for cloning with a special emphasis on genes known to cause phenotypic mutants in other plant species. Our microsatellite analysis of cultivated common bean focused on landrace diversity. The germplasm relationships previously defined (Middle American vs. Andean gene pools; races within genepools) appear to be consistent using
microsatellite markers. We will survey a large set (n=225) next year in preparation for future association mapping studies. We continued our experiments to uncover genes associated with iron chlorosis deficiency (IDC) tolerance in soybean. This is a joint project with Drs. Ted Helms (NDSU Plant Sciences) and Jay Goos (NDSU, Soil Science). We completed our association mapping analysis by performing an extensive statistical analysis that allowed us to hypothesize that four markers are associated with tolerance. We then confirmed those results by analyzing a second independent population. Our future goals are to perform candidate gene cloning of genes previously shown to be involved in iron/mineral uptake in plants and determine if specific polymorphisms are associated with the alternate phenotypes.
Impacts
A full understanding of the genetic components of disease resistance will inform those develop new approaches to plant protection. A new marker class that is easy to apply and recognizes the major polymorphisms in common bean will aid with the development of improved cultivars for production purposes. Markers for iron deficiency chlorosis tolerance will improve the selection process for this important agronomic trait.
Publications
- McClean PE, Lee RK, and Miklas PM. 2004. Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean. Genome 47:266-280.
- McClean, P.E., Lee, RL, and Miklas, PN. 2004. Intron-based sequence diversity studies in Phaseolus. Annu. Rep. Bean Improv. Coop. 47:85-86.
- McClean, PE, Gepts, P, and Kami J. 2004. Genomics and genetic diversity in common bean. in Genomics for Legume Crops (RF Wilson and C Brummer, eds), AOCS Press.
|
|