Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) 1. Analyze the BAC and BIBAC libraries resulted from our previous BARD project and the BAC library generated by your group (~60,000 clones together) and assemble from the clones into a genome-wide BAC/BIBAC physical map. 2. Develop a physical/genetic map of chickpea unifying all genetic maps developed so far for chickpea using the BAC/BIBAC map as the platform and SSR markers. 3. High-resolution map the genes and QTLs of interest by using SSR markers to be developed from the BAC/BIBAC contigs of the chickpea BAC/BIBAC physical map and develop molecular tools (e.g., SSRs and/or SNP) for chickpea genetics and breeding. Approach (from AD-416) We will develop the integrated map of the chickpea genome use the map to approach QTLs for flowering time and for resistance to ascochyta blight. We will fingerprint ~50,000 (~10x) BACs from the three chickpea BAC libraries and assemble them into a genome-wide contig map of chickpea. We will anchor the contigs to the chickpea genetic maps, to which the above and many other traits were mapped, by screening the source BACs with the mapped markers. This will unify the genetic maps and locate all mapped QTLs and genes to the BAC contigs. Finally, the BAC contigs containing the QTLs for Ascochyta blight resistance and early flowering will be selected and used to develop new DNA markers that will be used to further fine map these QTLs. In conjunction with field screening, the new DNA markers will be used to facilitate incorporation of resistance genes into high-yielding early-flowering genetic backgrounds. Documents BARD grant. Log 29832.. Formerly 5348-21000-014-11R (5/08) A robust linkage map of chickpea was constructed. This linkage map has 8 linkage groups covering 486 cM. All the markers in each of eight linkage groups remain linked using LOD values ranging from 2-10 except for linkage group IV. We targeted a quantitative trait locus (ABR- QTL1) for QTL cloning. The QTL accounted for 35% of variation and was identified using both interspecific and intraspecific crosses. Genetic characterization of this ABR-QTL1 by enriching the marker density identified more tightly linked markers with increased contribution (56%) to the ABR. These new markers will have direct application in marker- assisted breeding. We discovered 15 candidate genes at ABR-QTL1 and none of them resembled the typical NBS-LRR type genes. The novel discovery is the presence of EIN4-receptor (Ethylene insensitive) gene at this agronomically important genomic region.
Impacts
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) 1. Analyze the BAC and BIBAC libraries resulted from our previous BARD project and the BAC library generated by your group (~60,000 clones together) and assemble from the clones into a genome-wide BAC/BIBAC physical map. 2. Develop a physical/genetic map of chickpea unifying all genetic maps developed so far for chickpea using the BAC/BIBAC map as the platform and SSR markers. 3. High-resolution map the genes and QTLs of interest by using SSR markers to be developed from the BAC/BIBAC contigs of the chickpea BAC/BIBAC physical map and develop molecular tools (e.g., SSRs and/or SNP) for chickpea genetics and breeding. Approach (from AD-416) We will develop the integrated map of the chickpea genome use the map to approach QTLs for flowering time and for resistance to ascochyta blight. We will fingerprint ~50,000 (~10x) BACs from the three chickpea BAC libraries and assemble them into a genome-wide contig map of chickpea. We will anchor the contigs to the chickpea genetic maps, to which the above and many other traits were mapped, by screening the source BACs with the mapped markers. This will unify the genetic maps and locate all mapped QTLs and genes to the BAC contigs. Finally, the BAC contigs containing the QTLs for Ascochyta blight resistance and early flowering will be selected and used to develop new DNA markers that will be used to further fine map these QTLs. In conjunction with field screening, the new DNA markers will be used to facilitate incorporation of resistance genes into high-yielding early-flowering genetic backgrounds. Documents BARD grant. Log 29832.. Formerly 5348-21000-014-11R (5/08) Significant Activities that Support Special Target Populations The recombinant inbred population developed from the cross between FLIP84- 92C and PI599072 was used for marker development and phenotyping. ABR- QTL1 which accounts for 35% of the total phenotypic variation in ascochyta blight resistance (ABR), was targeted for QTL cloning. Genetic characterization of this ABR-QTL1 identified tightly linked markers which contribute 56% of the total variation in ABR. We discovered 15 candidate genes at ABR-QTL 1, none of which resembled Nucleotide Binding Sites and Leucine Rich Repeat (NBS-LRR)type genes. A novel discovery was the presence of a EIN4-receptor (Ethylene insensitive) gene in this important genomic region. The research resulted in development of several tools such as single nucleotide polymorphism (SNP)markers, a reference linkage map, Heterogeneous Inbred Family (HIF) lines, Agrobacterium mediated transformation and TILLING mutants for the chickpea research community. Functional correlation of candidate genes with ABR using TILLING mutants is underway. The work has increased the understanding of ABR and laid a strong foundation for further advanced research in chickpea.
Impacts
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Progress 10/01/07 to 09/30/08
Outputs
Progress Report Objectives (from AD-416) 1. Analyze the BAC and BIBAC libraries resulted from our previous BARD project and the BAC library generated by your group (~60,000 clones together) and assemble from the clones into a genome-wide BAC/BIBAC physical map. 2. Develop a physical/genetic map of chickpea unifying all genetic maps developed so far for chickpea using the BAC/BIBAC map as the platform and SSR markers. 3. High-resolution map the genes and QTLs of interest by using SSR markers to be developed from the BAC/BIBAC contigs of the chickpea BAC/BIBAC physical map and develop molecular tools (e.g., SSRs and/or SNP) for chickpea genetics and breeding. Approach (from AD-416) We will develop the integrated map of the chickpea genome use the map to approach QTLs for flowering time and for resistance to ascochyta blight. We will fingerprint ~50,000 (~10x) BACs from the three chickpea BAC libraries and assemble them into a genome-wide contig map of chickpea. We will anchor the contigs to the chickpea genetic maps, to which the above and many other traits were mapped, by screening the source BACs with the mapped markers. This will unify the genetic maps and locate all mapped QTLs and genes to the BAC contigs. Finally, the BAC contigs containing the QTLs for Ascochyta blight resistance and early flowering will be selected and used to develop new DNA markers that will be used to further fine map these QTLs. In conjunction with field screening, the new DNA markers will be used to facilitate incorporation of resistance genes into high-yielding early-flowering genetic backgrounds. Documents BARD grant. Log 29832. Significant Activities that Support Special Target Populations Research efforts of this research agreement were on fine mapping of the quantitative trait loci in chickpea for resistance to Ascochyta blight. Previous research showed that resistance to Ascochyta blight in chickpea is recessive and there are at least two quantitative trait loci (QTLs) that are responsible for the resistance. To increase marker density at the QTLs of ascochyta blight resistance we incorporated 155 SSR markers, 6 EST markers and 3 RGA markers from chickpea, 1 SSR marker from lentil and 2 SSR markers from Medicago truncatula with previous 170 markers. We analyzed the segregation using 142 recombinant inbred lines developed from an interspecific cross (FLIP84-92C and PI599072). The development of a linkage map with the total of 337 markers and the marker-trait association is now complete. Our final goal of integration of genetic and physical map will have long term application to isolate the genes by chromosome walking and also to develop new markers that are tightly linked to Ascochyta blight resistance for marker assisted selection (MAS). Research progress addresses component 2 of the NP 301 Action Plan (Crop Informatics, Genomics and Genetic Analysis) and problem statement 2c (Genetic Analysis and Mapping of Important Traits). Research progress is monitored via monthly progress and planning meetings.
Impacts
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) 1. Analyze the BAC and BIBAC libraries resulted from our previous BARD project and the BAC library generated by your group (~60,000 clones together) and assemble from the clones into a genome-wide BAC/BIBAC physical map. 2. Develop a physical/genetic map of chickpea unifying all genetic maps developed so far for chickpea using the BAC/BIBAC map as the platform and SSR markers. 3. High-resolution map the genes and QTLs of interest by using SSR markers to be developed from the BAC/BIBAC contigs of the chickpea BAC/BIBAC physical map and develop molecular tools (e.g., SSRs and/or SNP) for chickpea genetics and breeding. Approach (from AD-416) We will develop the integrated map of the chickpea genome use the map to approach QTLs for flowering time and for resistance to ascochyta blight. We will fingerprint ~50,000 (~10x) BACs from the three chickpea BAC libraries and assemble them into a genome-wide contig map of chickpea. We will anchor the contigs to the chickpea genetic maps, to which the above and many other traits were mapped, by screening the source BACs with the mapped markers. This will unify the genetic maps and locate all mapped QTLs and genes to the BAC contigs. Finally, the BAC contigs containing the QTLs for Ascochyta blight resistance and early flowering will be selected and used to develop new DNA markers that will be used to further fine map these QTLs. In conjunction with field screening, the new DNA markers will be used to facilitate incorporation of resistance genes into high-yielding early-flowering genetic backgrounds. Documents BARD grant. Log 29832. Significant Activities that Support Special Target Populations This is a reimbursable agreement between ARS and BARD. Additional details of research can be found in the report for the parent CRIS 5348-21000-014- 00D, Germplasm Enhancement, Genetics and Disease Management of Cool Season Food Legumes. Research efforts of this research agreement were on fine mapping of the quantitative trait loci in chickpea for resistance to Ascochyta blight. Previous research showed that resistance to Ascochyta blight in chickpea is recessive and there are at least two quantitative trait loci (QTLs) that are responsible for the resistance. To increase marker density at the QTLs of ascochyta blight resistance we analyzed segregation of 157 markers of simple sequence repeats (SSR), six markers of expressed sequence tags (EST), three markers of resistance gene analogs (RGA) from chickpea and two SSR markers from Medicago truncatula using a mapping population of 142 recombinant inbred lines (RILs). This mapping population was developed from an interspecific cross (FLIP84-92C and PI599072). Our preliminary marker analysis identified one of EST markers to be linked to ABR-QTL2. Current research is on developing an inter- specific linkage map with increased marker density and also marker-trait association. This research progress on integration of genetic and physical map will have long term application for isolating the genes by chromosome walking and also for developing new markers that are tightly linked to ascochyta blight resistance for marker assisted selection to be used in our breeding programs.
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