Article

Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
Plant Biotechnology Journal (Impact Factor: 5.68). 05/2011; 9(8):922-31. DOI: 10.1111/j.1467-7652.2011.00625.x
Source: PubMed

ABSTRACT Chickpea (Cicer arietinum L.) is an important legume crop in the semi-arid regions of Asia and Africa. Gains in crop productivity have been low however, particularly because of biotic and abiotic stresses. To help enhance crop productivity using molecular breeding techniques, next generation sequencing technologies such as Roche/454 and Illumina/Solexa were used to determine the sequence of most gene transcripts and to identify drought-responsive genes and gene-based molecular markers. A total of 103,215 tentative unique sequences (TUSs) have been produced from 435,018 Roche/454 reads and 21,491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49,437 (47.8%) of the TUSs, and gene ontology assignments were determined for 20,634 (41.7%) of the TUSs. Comparison of the chickpea TUSs with the Medicago truncatula genome assembly (Mt 3.5.1 build) resulted in 42,141 aligned TUSs with putative gene structures (including 39,281 predicted intron/splice junctions). Alignment of ∼37 million Illumina/Solexa tags generated from drought-challenged root tissues of two chickpea genotypes against the TUSs identified 44,639 differentially expressed TUSs. The TUSs were also used to identify a diverse set of markers, including 728 simple sequence repeats (SSRs), 495 single nucleotide polymorphisms (SNPs), 387 conserved orthologous sequence (COS) markers, and 2088 intron-spanning region (ISR) markers. This resource will be useful for basic and applied research for genome analysis and crop improvement in chickpea.

4 Followers
 · 
504 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: To detect more credibly the changes in the crystal structure of chickpea starch during processing treatments, two methods, a deconvolution method based on X-ray diffraction (XRD) pattern of starch and a moisture analysis method based on starch moisture content, were applied to determine the relative crystallinity (RC) of A- and B-type polymorphs (RCA and RCB) in the same chickpea starch sample. It was found that the values of RCA for chickpea starch samples determined by these two methods were close and showed similar trend. The results suggested that these two methods could be used to estimate RCA in the same chickpea starch sample and provide mutual corroboration. Based on the deconvolution method, it was observed that the crystalline region of chickpea starch was less susceptible to α-amylase hydrolysis than its amorphous region, and B-type polymorph in chickpea starch was more resistant to α-amylase hydrolysis than A-type polymorph. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Carbohydrate Polymers 05/2015; 121:169-74. DOI:10.1016/j.carbpol.2014.12.048 · 3.92 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The large-scale validation and high-throughput genotyping of numerous informative genic microsatellite markers are required for association mapping to identify candidate genes for complex quantitative traits in chickpea. However, the screening and genotyping of such informative markers in individual genotypes/whole association panels for trait association mapping involves massive costs in terms of resources, time and labour due to low genetic polymorphism in chickpea. We have developed an alternative time-saving and cost-effective pool-based trait association mapping approach by combining pooled DNA analysis (with 616 genic microsatellite markers) and individual genotype (large structured association panel) genotyping. Using this approach we have identified seven seed weight-associated transcription factor gene-derived microsatellite markers (with minor allele frequency >15 %) in desi and kabuli chickpea. Strong marker allele effects of these five transcription factors with increasing seed weight in the contrasting desi and kabuli genotypes were evident. Bi-parental linkage mapping using 241 of the informative gene-based microsatellite markers resulted in the identification and mapping of nine such markers linked with three major quantitative trait loci (explaining a total phenotypic variance of 23.5–34.7 %) on chromosomes 1 (CaqSW1.1: 73.5–74.5 cM and CaqSW1.2: 79.3–81.3 cM) and 2 (CaqSW2.1: 65.7–67.5 cM) controlling 100-seed weight in chickpea. The integration of pool-based trait association mapping with differential expression profiling, traditional bi-parental linkage mapping and high-resolution microsatellite-single nucleotide polymorphism marker-based haplotyping/linkage disequilibrium mapping delineated four transcription factor genes (DUF3594, bZIP, DUF1635 and SBP) controlling seed weight in desi and kabuli chickpea. The strategies implemented in our study can be used in large-scale trait association mapping for the rapid identification of candidate genes and in the development of functional markers for traits of agricultural importance in crop species including chickpea.
    Molecular Breeding 06/2014; 34(1):241-265. DOI:10.1007/s11032-014-0033-3 · 2.28 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Legumes are the third largest family of flowering plants, known for their unique capacity of symbiotic nitrogen fixation. The draft genome sequences of three important food legumes [soybean (Glycine max), pigeonpea (Cajanus cajan) and chickpea (Cicer arietinum)] have been completed. Coupled with a deluge of information on transcriptomics, proteomics and metabolomics, they present a huge amount of genomic resources for the genetic improvement of legume crops. Developed molecular markers, structurally and functionally annotated genes/quantitative trait loci/alleles and regulatory sequences can be utilized in improvement breeding programmes. Further, the genetic transformation of two valuable pulses (chickpea and pigeonpea) has now taken centre stage, realizing the potential of genetically modified soybean, for enhanced prospects of food production. Together, the advances in biotechnological tools and the research community’s capacity to develop imaginative strategies will help in framing a legume development programme for ensuring the nutritional security of the world.
    Plant Biotechnology Reports 03/2013; 8(2):83-99. DOI:10.1007/s11816-013-0299-7 · 1.59 Impact Factor

Full-text (36 Sources)

Download
2,966 Downloads
Available from
Jun 10, 2014

View other sources