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Advances in genomics research / projects

1. Chickpea

(I) Improved chickpea productivity for marginal environments in sub-Saharan Africa (Tropical Legumes I - Objective 4- Phase II (Funded by Bill & Melinda Gates Foundation (BMGF) thorough the CGIAR-Generation Challenge Program)

(II) Accelerating development of genomic resources and strengthening NARS partner capacities for enhancing adoption of molecular breeding for drought tolerance in chickpea (Funded by CGIAR-Generation Challenge Program)

(III) Marker-assisted back crossing (MABC) for drought tolerance in chickpea-Students for analysis of drought tolerance in chickpea (TLI- Kenyan student) (Funded by the CGIAR-Generation Challenge Program)

Overview: These three complementary projects, based on the genetic and genomic resources developed during TLI (2006-2009), is developing and deploying genomic tools in molecular breeding for developing superior chickpea lines for drought tolerance in sub-Saharan Africa (Kenya, Ethiopia) and Asia (India).

Achievements:

Large-scale SNPs in chickpea using various approaches like allele re-sequencing, sequencing of transcritome etc( Plant Biotechnology Journal (2012) 10, 716–732 ).

Cost-effective and low to mid throughput SNP genotyping platforms such as 2005 KASPar assays, 768-SNP assay for GoldenGate assays and 96-SNP assay for BeadXpress system.

Genome-wide physical map in collaboration with National Institute of Plant Genetic Research (NIPGR), New Delhi and University of California -Davis, USA (http://probes.pw.usda.gov:8080/chickpea/).

Introgression of a genomic region harouring various drought tolerance related QTLs contributing >30% phenotypic variation in some elite cultivars from Africa and Asia in collaboration with Egerton University (EU) - Kenya, Ethiopian Institute of Agricultural Research (EIAR) - Ethiopia, Indian Institute of Pulses Research (IIPR) - India, Indian Agricultural Research Institute (IARI)- New Delhi.

Deployment of marker-assisted recurrent selection (MARS) approach for pyramiding drought tolerance alleles in collaboration with EU, EIAR, IARI and IIPR.

Organization of a workshop on modern breeding technologies for chickpea improvement (October 25 - November 19, 2010; ) in which sixteen chickpea scientists from both TLI and TLII initiatives as well as others, twelve from Africa (Ethiopia, Kenya, Tanzania, Malawi, Algeria) and four from Asia (India, Nepal, Bangladesh, Myanmar) participated.

Training the next-generation of breeders by hosting PhD and MSc students from Africa: Ms Serah Songok (EU, Kenya), Mr Musa Jarso (Addis Ababa University; AAU, Ethiopia), Ms Alice Koskie (West Africa Centre for Crop Improvement; WACCI, Ghana), Mr Kebede Teshome (Haramaya University; HU, Ethiopia), Mr Abebe Sori (HU, Ethiopia), Mr Moses Oyier (EU, Kenya), Mr Getachew Tilahun (AAU, Ethiopia).


(IV) Deployment of molecular markers in chickpea breeding for developing superior cultivars with enhanced disease resistance (Funded by Department of Biotechnology Government of India under Accelerated Crop Improvement Program)

Overview: The project is deploying molecular markers to develop the superior lines of chickpea with enhanced resistance to fusraium wilt (FW) and also ascochyta blight (AB). ICRISAT has been leading these efforts with four other collaborating centres Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur; IIPR, Kanpur; Mahatma Phule Krishi Vidyapeeth (MPKV), Rahuri and ARS-Gulburga.

Achievements:

C 214 genotype has been selected to pyramid resistance to race 1 and race 3 of FW and two QTLs for AB by using two donor genotypes namely WR 315 (for FW resistance) and ILC 3279 (AB resistance).

Two crosses C 214 (FWS) × WR315 (FWR) and C 214 (ABS) × ILC 3279 (ABR) have been made and BC3F3 progenies have been developed from each of two crosses by deploying foreground and background selection.

Marker genotyping for crosses developed at ARS-Gulbarga and MPKV-Rahuri is in progress.


(V) Biotechnological approaches to improve chickpea crop productivity for farming community and industry (Funded by Indo-German Science and Technology Center, IGSTC)

Overview: Under IGSTC, ICRISAT in collaboration with University of Frankfurt (Germany), GenXPro (Germany) and BenchBio (India) is developing tools for molecular breeding such as the Illumina BeadXpress arrays, validated gene expression microarrays, qRT-PCR assays, high-density gene-based expression marker maps, eQTLs and candidate genes/QTLs associated with drought related traits. Use of these tools in chickpea breeding programs should eventually lead to development of chickpea varieties with enhanced drought tolerance that will enhance chickpea production in drought prone environment.

Achievements:

RNA-seq approach is being used on drought stressed root tissues of two chickpea genotypes, ICC 4958 and ICC 1882, parents of a mapping population segregating for drought tolerance were selected along with 5 best RILs each from tolerant and sensitive sets based on selective phenotyping.

Reference set comprising of 300 lines have been genotyped with DArT and KASPar assays and association genetics approach for mapping drought tolerance trait is in progress.

RAD-Sequencing of 48 genotypes is underway.


(VI) Overcoming the Domestication Bottleneck for Symbiotic Nitrogen Fixation in Legumes (Funded by National Science Foundation (NSF), USA under Basic Research to Enable Agricultural Development)

Overview: In collaboration with University of California- Davis (USA),The goal of the project is to characterize the genetic mechanisms that underlie phenotypic plasticity for symbiosis through elucidating the molecular genetic basis of phenotypic variation for symbiotic nitrogen fixation efficiency in Cicer spp, including C. ariteinum (cultivated chickpea) and C. reticulatum (the wild progenitor); to quantify the impact of domestication on the potential for symbiotic nitrogen fixation in chickpea; to examine genetic potential for efficient nitrogen fixation in chickpea.

Achievements:

To understand the genetic bottleneck of domestication in chickpea, 18 cultivars and 12 wild accessions, were analyzed in field trials to phenotype in no treatment, rhizobium and nitrogen treatment.

To evaluate the effect of drought stress on symbiotic nitrogen fixation a gradient of chickpea genotypes including 4 species arietinum, reticulatum, echinospermum and bijugum were exposed to terminal drought stress. 13 genotypes were subjected to irrigated and stressed conditions under 3 treatments viz. no treatment, nitrogen and rhizobium treatment.

Phenological parameters such as shoot biomass, root biomass, nodule weight, nodule number and leaf surface area were recorded to elucidate the elevation of stress effect on tolerant and susceptible genotypes.

 

2. Pigeonpea

(I) Pigeonpea improvement using molecular breeding (Funded by United States Agency for International Development; USAID)

Overview: Because of exposure of the crop with several biotic (Fusarium wilt, sterility mosaic disease) and abiotic (water logging, salinity) stresses, the crop productivity is very low. With an objective of closing this yield gap through genomics-assisted breeding approaches, this project plans to develop and utilize specialized genetic resources with genome sequence to harness the potential of genomics and genetic diversity in crop improvement in following ways:

Achievements:

Genetic diversity present in elite gene pool is being utilized by linkage mapping and nested association mapping (NAM) approaches for trait mapping.

Multi-parents advanced generation inter-cross (MAGIC) population and introgression libraries (ILs) are being developed to generate genetic resources with enhanced genetic diversity after bringing the superior alleles from landraces and wild species, respectively.

Superior alleles for traits of interest to the breeders, present in unadapted germplasm (e.g. reference set), are being identified through genome-wide association study (GWAS) approach.

Genetic material, available at present and being developed, will be used for multi-location phenotyping for traits of interest to breeders and will be used for high-density genotyping (e.g. GBS). Detailed analysis of these large-scale data should provide useful information on marker(s)/ gene(s)/ haplotype(s)- trait association as well as the superior lines for target traits as well as with enhnaced genetic diversity that can be used in future molecular breeding programmes.


(II) Identification of candidate genes associated with growth habit in pigeonpea (Cajanus cajan (L) Millsp.) (Funded by CGIAR-GCP)

Overview: It is believed that determinate growth habit has long been selected during pigeonpea domestication and some of the mutation may be responsible for this transition from indeterminate to determinate growth habit. Keeping the above in view efforts have been made to identify the genes responsible for this transition in pigeonpea.

Achievements:

Both genome-wide association analysis and candidate gene based approaches were employed to identify candidate markers and SNPs responsible for determinacy in pigeonpea.

For genome-wide association analysis, GoldenGate assay (768 SNPs) by Illumina and 15,360 features developed by DArT Pty Ltd, Australia was used. For candidate gene sequencing, a set of 12 candidate genes were initially selected from Kwak et al. 2008 (J Heredity 99: 283-291).

Association analysis using the TASSEL program showed significant (p= <0.01) association of determinacy trait with 19 SNP and 6 DArT markers explaining 8.1-8.6% and 7.3-14.5% of phenotypic variation respectively.

One SNP identified in TFL1 showed the strongest association with determinacy, flowering time and plant height.

Two candidate genes, GI and TFL1 were mapped to LG7 and LG4 of ICPA 2039 × ICPL 2447, F2 mapping population where the growth habit phenotype segregates.

 

3. Groundnut

(I) QTL analysis for drought tolerance related traits and construction of reference genetic map in groundnut (Arachis hypogaea L.) (Funded by Bill & Melinda Gates Foundation (BMGF) thorough the CGIAR, Generation Challenge Program)

Overview: Terminal drought has high adverse impact on yield worldwide in groundnut. Identification and development of tolerant/resistant breeding material is one of the challenging objectives in groundnut breeding.

Achievements:

Two genetic linkage maps based on two RILs namely ICGS 76 × CSMG 84-1 and ICGS 44 × ICGS 76 were constructed with 82 and 188 marker loci, respectively.

A consensus genetic map with 293 SSR loci (2,840.8 cM) were prepared for drought tolerance related traits based on three RILs (TAG 24 × ICGV 86031, ICGS 76 × CSMG 84-1, ICGS 44 × ICGS 76).

Identification of a total of 153 main effect QTLs (M-QTLs) and 25 epistatic QTLs (E-QTLs) for drought tolerance related traits. Sixteen key genomic regions were selected on the basis of QTLs identified for their expected role towards drought adaptation. (Molecular Breeding (2012) 30, 757-772).

Development of reference consensus maps using marker segregation data for 10 RILs and one BC population from the international groundnut community comprising 897 marker loci spanning a map distance of 3863.6 cM with an average map density of 4.4 cM (PLoS ONE (2012) 7, e41213a>).

Integration of available genomic tools for genetic enhancement of cultivated groundnut in collaboration with several international partners (Biotechnology Advances (2012) 30, 639-651).


(II) Molecular breeding for enhancing rust resistance in elite varieties of groundnut (Arachis hypogaea L.) (Funded by Bill & Melinda Gates Foundation (BMGF) thorough the CGIAR, Generation Challenge Program)

Overview: Rust, caused by Puccinia arachidis, is widespread in most of the tropical countries and severely affects the crop productivity and quality of the groundnut seed/oil. Despite the fact that several fungicides are available to control, host-plant resistance is considered as the best approach to manage this disease and to overcome hazardous effect of fungicides. Furthermore, since the trait is governed by recessive genes, use of tightly linked markers will enhance precision in selection of the trait as well as shorten the breeding duration.

Achievements:

Tightly linked SSR markers for rust resistance using a RIL population (TAG 24 × GPBD 4) was identified and validated among a diverse set of germplasm and alternate mapping population (TG 26 × GPBD 4).

Successful marker-assisted introgression of major QTL (QTLrust01) into three elite cultivars (TAG 24, JL 24 and ICGV 91114) using the donor (GPBD 4).

Identification of several promising lines based on initial screening for rust resistance showing remarkable reduction in disease spread.

 

(III) Molecular breeding for improving quantity and quality of groundnut (Arachis hypogaea L.) oil (Funded by Department of Agriculture and Co-operation (DOAC), Ministry of Agriculture, GOI)

Overview: Groundnut (Arachis hypogaea L.) is a major oilseed legume crop in India as meets >30% of the edible oil requirements. Newer groundnut varieties with oil content (OC) and oleic/linoleic acid ratio (O/L ratio) higher than that of the varieties currently cultivated by farmers are needed to boost the edible oil production and correspondingly increase the income levels of the poor groundnut farmers. The project aims at improving the quality and quantity of groundnut oil employing molecular breeding approaches.

Achievements:

Crosses were made to develop mapping populations to identify QTLs for high oil content (OC) and oleic/linoleic acid (O/L) ratio.

Linked markers i.e., cleaved amplified polymorphic sequence (CAPS) and allele-specific PCR-based markers reported elsewhere were validated among a diverse set of 22 parental genotypes. The existing genotyping protocol has been modified to amplify these markers and to get clear separation of alleles.

The validated markers for O/L ratio using modified protocol are being used currently for introgression of high oleate trait through marker-assisted backcrossing (MABC) in the genetic background of elite high OC groundnut cultivars.

Completed Projects in recent years

1. Chickpea

(I) Improved chickpea productivity for marginal environments in sub-Saharan Africa -Phase I (Funded by Bill & Melinda Gates Foundation (BMGF) thorough the CGIAR, Generation Challenge Programme)

Overview: With an objective to develop the superior cultivars of chickpea for drought tolerance and with enhanced resistance to Helicoverpa, concerted efforts have been made by Objective 4 Team of Tropical Legume I (TL-I ) in Phase I.

Achievements:

Screening of the germplasm has provided drought tolerant and Helicoverpa resistant lines.

Significant genomic tools like SSRs (simple sequence repeats), SNPs (single nucleotide polymorphisms) and DArT (Diversity Array Technologies) arrays have been developed. Several of these have been documented in (Theoretical and Applied Genetics (2010) 120, 1415-1441; Gujaria etal (2011) 122, 1577-1589; PLoS ONE (2011) 6, e27275)

A few putative QTLs have been identified for resistance to Helicoverpa and drought tolerance

Genomic region harbouring drought tolerance QTLs introgressed into three elite Indian cultivars ICCV 92318, ICCV 92311 and ICCV 93954. Marker assisted recurrent selection initiated for accumulating drought tolerance alleles.

(II) Evaluating candidate gene towards enhancement of drought tolerance in chickpea (Cicer arietinum.) (Funded by Department of Biotechnology, Government of India, under National Fund for Basic and Strategic Research in Agricultural sciences)

Overview: In collaboration with NRCPB and IARI.The main aim of this project was, to identify candidate genes (or expressed sequence tags) and molecular markers (SSR, SNP) associated drought tolerance. The project has good collaboartion with NRCPB and IARI.

Achievements:

A comprehenisve set of 20,162 Sanger ESTs was developed from drought and salinity challenged tissues (BMC Genomics (2009) 10, 523)

In collaboartion with Generation Challenge Program, a transcriptome assembly based on 454 transcript reads were developed (Plant Biotechnology Journal (2011) 9, 922-931;)

In collaboartion with Generation Challenge Programme, about 2900 differentially expressed genes were identified following Illumina 1G sequencing approach (Plant Biotechnology Journal (2012) 10, 716-732)

Selected genes were validated through quantitative real time PCR (qRT-PCR).

In collaboartion with TLI-Phase I proposal, a genetic map was developed on the intra-specific mapping population ICC 4958 × ICC 1882.

In collaboartion with TLI-Phase I proposal, a genomic region containing several QTLs for root traits wad identified.

A TILLING population comprising of 5236 lines from ICC 4958 genotype was developed.

(III) Construction of the transcript map and development of functional markers for chickpea (Arachis hypogaea L.) oil (Funded by Department of Biotechnology, Government of India)

Overview: ICRISAT in collaboration with NIPGR, developed functional markers and the first transcript map for chickpea.

Achievements:

Novel set of gene-based molecular markers (GMMs) including 143 CGMMs, 87 CISRs and 51 ICCeMs were developed

By using above developed molecular markers along with additional set of genic markers, a genetic map comprising a total of 300 loci including 126 GMM loci with a coverage of 766.56 cM and an average inter-marker distance of 2.55 cM was developed (Theoretical and Applied Genetics (2011) 122, 1577-1589)

 

2. Pigeonpea

(I) Pigeonpea Genomics Initiative (PGI) project (Funded by Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative US National Science Foundation's Plant Genome Research Program and the Generation Challenge Program)

Overview: To enable genomics-assisted breeding in pigeonpea, the pigeonpea genomics initiative (PGI) was initiated in late 2006, as a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries.

Achievements:

Twenty five mapping populations segregating for a number of biotic and abiotic stresses have been developed/ are under development (Molecular Breeding (2010) 26, 393-408)

Bacterial artificial chromosome (BAC) library with 11X-genome coverage comprising of 69,120 clones have been developed and 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). A set of 3072 SSRs were developed from BES

About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated (DNA Research (2011) 18, 153–164)

(II)Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in Pigeonpea (Funded by Indo-US Agricultural Knowledge Initiative Indo-US AKI)

Overview: In order to enhance the genomic resources for pigeonpea, the study was designed to large scale development of SSR markers from BAC-end sequences (BESs) and their subsequent use for genetic mapping and hybridity testing in pigeonpea.

Achievements:

Two BAC libraries were developed from pigeonpea cultivar "Asha", based on partial digestion with HindIII and BamHI restriction enzymes.

A set of 88,860 BAC (bacterial artificial chromosomes)-end sequences (BESs) were generated from two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes.

BESs were searched for microsatellites or simple sequence repeats (SSRs) and a total of 18,149 SSRs were identified, from which a set of 6,212 SSRs were selected for downstream analysis.

A total of 3,072 SSRs were successfully used for primer pairs synthesis and tested for polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, 842 polymorphic SSRs were identified.

Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed. SSR markers were also used for identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment (BMC Plant Biology (2011) 11, 56)

(III) Genetic mapping and quantitative trait locus analysis of resistance to sterility mosaic disease in pigeonpea (Funded by Department of Biotechnology, Government of India)

Overview: Sterility mosaic disease (SMD), known as the "green plague of pigeonpea" and caused by Pigeonpea Sterility Mosaic Virus (PPSMV), is one of the major biotic factor which leads to heavy yield losses. The project aims at identification of the genomic segments related to SMD resistance.

Achievements:

Two F2populations i.e. ICP 8863 × ICPL 20097 and TTB 7 × ICP 7035 were developed and F2:3 families were phenotyped by using leaf stapling method for resistance to SMD.

Intra-specific genetic maps comprising of 11 linkage groups and 120 and 78 SSR loci were developed for ICP 8863 × ICPL 20097 and TTB 7 × ICP 7035 populations, respectively.

QTLs for SMD identified. One QTL identified within an interval of 2.8 cM on LG 7 explaining 24.72 % of phenotypic variance (Field Crop Research (2011) 123, 53-61)

(IV) Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Funded by CGIAR, Generation Challenge Programme, GCP)

Overview: The main goal of this project is to identify the potential polymorphic markers for drought tolerance in pigeonpea using Affymetrix Genome Arrays of soybean (Glycine max), on cRNA of six parental genotypes of three mapping populations of pigeonpea segregating for agronomic traits like drought tolerance and pod borer (Helicoverpa armigiera) resistance.

Achievements:

Expression data were generated by hybridizing pigeonpea cRNA to the soybean genome array.

A total of 5,692 potential SFPs were identified by using robustified projection pursuit (RPP) on 15 pair-wise comparisons for six parental lines.

Based on good quality sequence data for 75 genes, true positives were found for 37.73% predicted SFPs for ICPL 151 × ICPL 87, 40% for ICPL 8755 × ICPL 227 and 86.11% for ICP 28 × ICPW 94 parental combinations.

A set of 397 candidate genes that may have association with drought tolerance identified based on gene ontologies (Functional Integrative Genomics (2011) 11, 651-657)

(V) Decoding the genome of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor smallholder farmers in Asia and Africa (Funded by CGIAR-Generation Challenge Programme, NSF-USA, BGI and ICRISAT)

Overview: To accelerate the application of genomics to improve yield and quality draft genome sequence has been generated.

Achievements:

Next generation sequencing (Illumina) was used to generate the raw sequence reads that, along with Sanger-based BAC end sequences and a genetic map, was assembled into scaffolds. Genome annotation and downstream analysis were conducted by using standard bioinformatics tools.

By using Next generation sequencing a total of 237.2 Gb of sequence were generated that, along with Sanger-based BAC end sequences and a genetic map, was assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome (Nature Biotechnology (2011 30, 83-89)

Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role of some gene families during evolution/domestication, e.g. drought tolerance related genes.

Although a few segmental duplication events were found, recent genome-wide duplication events, such as seen in soybean, were not observed.

(VI) Developing genomic resources for pigeonpea using next-generation sequencing (NGS) technologies (Funded by CGIAR, Generation Challenge Programme)

Overview: The large scale sequence information generated using NGS technologies utilized for generation of molecular markers (SSR, SNPs) and construction of genetic maps using the genomic resources developed.

Achievements:

A total of 494,353 short transcript reads (STRs) generated from normalized cDNA pool prepared from 31 tissues employing Roche/FLX 454 sequencing.

A total of 150.8 million Illumina sequence tags were generated from 10 pigeonpea genotypes. For identification of SNPs, tags for two genotypes of a given mapping population were aligned with 127,754 TAs (DNA Research (2011) 18, 153–164), (Molecular Plant (2012) 5, 1020-1028)

The number of SNPs in an individual cross ranged from 704 to 6,263. In total, 12,141 SNPs were identified across these genotypes. In terms of developing the marker platforms, CAPS markers could not be validated at a good rated

As a result, a total of 1,834 SNPs were attempted for KASPar assays and successful assays were developed for 1,616 SNPs and tested on a set of 94 genotypes. In addition, four genetic maps were developed based on SSR markers and by using these maps, in addition to two earlier maps, a consensus genetic linkage map was developed that includes a total of 339 SSR marker loci (DNA Res (2012) doi: 10.1093/dnares/dss025)


3. Groundnut

(I) Gene-based Genetic Maps and Molecular Markers for Biotic and Abiotic Stress Tolerance in Groundnut (Funded by Department of Biotechnology, Government of India)

Overview: The project aimed at developing novel set of markers, construction of several genetic maps and identification of genes/QTL associated with resistance to foliar diseases (rust and late leaf spot) and drought tolerance related traits.

Achievements:

For the first time, SSR based linkage map was developed for cultivated groundnut using a RIL population derived from the cross between cultivated genotypes (TAG 24 × ICGV 86031) (AABB genome). (Theoretical and Applied Genetics (2009) 118, 729-739)

Four populations (RIL-2: ICGS 76 × CSMG 84-1, RIL-3: ICGS 44 × ICGS 76, RIL-4: TAG 24 × GPBD 4, RIL-5: TG 26 × GPBD 4) were used to construct four more new individual genetic linkage maps ranging from 82 (RIL-3) to 188 (RIL-4) marker loci. Total map length ranged from 831.4 (RIL-3) to 2208.0 cM (RIL-2).

Two consensus genetic maps were prepared for drought tolerance based on three RILs (RIL 1-3) with 293 SSR loci (2,840.8 cM) and for foliar diseases based on two RILs with 225 SSR loci (1152.9 cM), respectively.

Extensive phenotyping and comprehensive QTL analysis in all the five populations detected a total of 153 main effect QTLs (M-QTLs) and 25 epistatic QTLs (E-QTLs) for drought tolerance related traits while 43 QTLs for foliar diseases (LLS and rust). Sixteen key genomic regions were selected on the basis of QTLs identified for their expected role towards drought adaptation. Similarly, in case of foliar diseases, a major QTL each for LLS (62.34% PVE) and rust (82.96% PVE) resistive were identified. (Theoretical and Applied Genetics (2009) 118, 729-739); Theoretical and Applied Genetics (2011) 122, 1119-1132; Field Crops Research (2011) 122, 49-59; Molecular Breeding (2012) 30, 757-772)

A total of 244 SSR markers have been developed at ICRISAT and accessed primer sequence information for 4485 SSR markers from different sources. All the SSRs are being used to screen parental genotypes of different mapping populations to identify polymorphic markers between different parental crosses. Screening led to identification of 199 highly informative SSR markers with PIC >0.50 (Plant Breed (2012) 131, 139-147)

 

4. Pearl Millet

(I) Enhancement of the set of microsatellite (SSR) markers for improving Pearl Millet breeding efficiency in Africa and Asia (Funded by Syngenta Foundation for Sustainable Agriculture)

Overview: Enrich genomic resources for genetics and breeding of pearl millet through development of SSR markers from microsatellite enriched library

Achievements:

Microsatellite enriched (CA, GA, CAA and AGA repeats) gDNA library was constructed from the pearl millet genotype "Tift 23D2B1-P5".

Among different classes of SSRs, di-nucleotide repeat motifs were found to be the most abundant (830; 36.5%) followed by compound (767; 32.4%), mono-(370; 16.3%) and tri-nucleotide SSRs (305; 13.4%).

A total of 454 primer pairs were designed of which 226 produced scorable amplicons and 69 markers were found polymorphic across of the panel of 22 pearl millet inbred lines studied. Further a set of 45 markers polymorphic were genotyped on the RIL population ICMB 841-P3 × 863B-P2, of a set of 22 markers could be integrated on to the genetic map.

Please contact : Dr Rajeev Varshney, Director-Center of Excellence in Genomics, ICRISAT, Patancheru, 502 324, India;
Office: +91 40 3071 3305; Email : r.k.varshney@cgiar.org
© Center of Excellence in Genomics. 2008