A consensus genetic map of chickpea (Cicer arietinum L.) based on 10 mapping populations

Millán, Teresa; Winter, Peter; Jüngling, Ruth; Gil, J.; Rubio, J.; Cho, S.; Cobos, María José; Iruela, M.; Rajesh, P. N.; Tekeoglu, M.; Kahl, Günter; Muehlbauer, F. J.

doi:10.1007/s10681-010-0157-4

Cited by 103 publications

(100 citation statements)

References 67 publications

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“…This signature of purifying selection was evident in dark-colored desi but not light-colored kabuli genotypes, consistent with ongoing purifying selection for seed color. Interestingly, Ca4 is the most differentiated between kabuli and desi types and Ca4 also contains most of the mapped traits that distinguish kabuli from desi genotypes 26 . Establishing precise genetic correlations and testing the biological significance of the underlying genes represent key opportunities for chickpea breeding and biotechnology.…”

Section: Genetic Diversity Among Cultivated Varieties and Germplasmmentioning

confidence: 99%

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

et al. 2013

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Section: Genetic Diversity Among Cultivated Varieties and Germplasmmentioning

confidence: 99%

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

et al. 2013

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“…A consensus map based on five interspecific (C. arietinum × C. reticulatum) and five intraspecific (Desi × Kabuli types) populations was developed [71]. It integrated 555 marker loci including, RAPDs (251), STMSs (149), AFLPs (47), 33 cross-genome markers, 28 gene-specific markers, 10 isozyme markers, 10 inter-simple sequence repeats (ISSRs) and 7 RGA loci.…”

Section: Linkage Mappingmentioning

confidence: 99%

Impact of Genomic Technologies on Chickpea Breeding Strategies

2012

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Abstract:The major abiotic and biotic stresses that adversely affect yield of chickpea (Cicer arietinum L.) include drought, heat, fusarium wilt, ascochyta blight and pod borer. Excellent progress has been made in developing short-duration varieties with high resistance to fusarium wilt. The early maturity helps in escaping terminal drought and heat stresses and the adaptation of chickpea to short-season environments. Ascochyta blight continues to be a major challenge to chickpea productivity in areas where chickpea is exposed to cool and wet conditions. Limited variability for pod borer resistance has been a major bottleneck in the development of pod borer resistant cultivars. The use of genomics technologies in chickpea breeding programs has been limited, since available genomic resources were not adequate and limited polymorphism was observed in the cultivated chickpea for the available molecular markers. Remarkable progress has been made in the development of genetic and genomic resources in recent years and integration of genomic technologies in chickpea breeding has now started. Marker-assisted breeding is currently being used for improving drought tolerance and combining resistance to diseases. The integration of genomic technologies is expected to improve the precision and efficiency of chickpea breeding in the development of improved cultivars with enhanced resistance to abiotic and biotic stresses, better adaptation to existing and evolving agro-ecologies and traits preferred by farmers, industries and consumers.

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“…Mapping kabuli isolated chromosome sequence reads to kabuli reference genome assembly demonstrated the correspondence with pseudomolecule. Chromosome F and G reads mapped to Ca2 and Ca1, respectively, which is opposite to earlier assignments (Millan et al, 2010;Thudi et al, 2011;Zatloukalová et al, 2011).…”

Section: Isolation and Sequencing Of Chickpea Chromosomescontrasting

confidence: 91%

“…For heterozygous SNPs across all varieties, Ca 4 exhibited the highest heterozygosity (2.6 SNPs/Kbp) and chromosome 8 the least heterozygosity (2.0 SNPs/Kbp) (Table 4-1). Since Ca4 shows great divergence between desi and kabuli types (Millan et al, 2010;Varshney et al, 2013), the high SNP density in this chromosome is expected.…”

Section: Snp Discoverymentioning

confidence: 99%

Analysis of the Chickpea genome using next generation sequencing data

Ruperao¹

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Chickpea is an annual, self-pollinating, diploid (2n=2x=16) and the second most important food legume crop with major production areas in the Indian sub-continent, West Asia and North Africa. Australia is the largest exporter of chickpea and yield for 2015 has been forecasted at 990,000 tonnes (http://www.agriculture.gov.au/abares/media-releases/2015). The main constraint for increasing yield is the susceptibility of the plant to foliar disease, ascochyta blight, fusarium wilt. Chickpea breeding aims at high yielding cultivars that combine longlasting resistance against both biotic and abiotic stress. Emerging sequencing technologies have enhanced the availability of crop genomic resources. Analysis of huge amounts of genomic data comes with major computational challenges.This thesis describes a new method for assessing the quality of reference genome assembly by flow sorting and isolating chromosomes based on size. This chromosomal DNA was sequenced and mapped to the reference genome assembly.This approach will reduce the genome DNA complexity to a chromosome level and is expect to correspond to only one chromosome assembly. Appling this approach on both released desi and kabuli reference genomes has shown miss-assembly. The desi genome was of poor quality compared to the kabuli genome. To fix these misassemblies, we developed a novel method called skimGBS for rearranging the fragmented sequences. In this approach, genotypes were called from population individuals to construct haplotype blocks. Based on the haplotype block signature, contigs/fragmented sequences were reordered as new assemblies. Using this approach, both desi and kabuli genomes were improved by placing unplaced contig sequences into chromosomes. Furthermore, these improved reference assemblieswere assessed and annotated.This thesis also reports identification of more than 800,000 high quality SNPs by sequencing 69 diverse Australian chickpea accessions. Gene loss, genetic relatedness, population structure and diversity analysis was also performed. The public accessibility of the data and above results provides a valuable resource to support chickpea research.iiThe developed methodology can also apply to other genomics studies, and will therefore be a valuable approach to assist crop improvement and further breeding approaches.iii

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A consensus genetic map of chickpea (Cicer arietinum L.) based on 10 mapping populations

Cited by 103 publications

References 67 publications

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Impact of Genomic Technologies on Chickpea Breeding Strategies

Analysis of the Chickpea genome using next generation sequencing data

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