Integrating genomics for chickpea improvement: achievements and opportunities (original) (raw)
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Advances in Chickpea Genomic Resources for Accelerating the Crop Improvement
Compendium of Plant Genomes
Chickpea plays a major role in food and nutritional security worldwide. Its productivity is severely affected by various biotic and abiotic stresses; hence development of stress resilience varieties that can yield higher under stress environment remains the call of the hour. Conventional breeding approaches clubbed with the genome information, commonly known as genomic-assisted breeding (GAB) have the potential to accelerate the crop improvement efforts. In order to deploy the GAB for crop improvement in chickpea, there was need to convert an orphan crop chickpea into the genomic resource-rich crop. Advent of sequencing technology has resulted in reduction of cost and led to development of huge genomic resources in chickpea. A variety of markers have been developed, used for various mapping studies including linkage mapping and association mapping and finally deployed for developing the superior varieties using GAB approached such as marker assisted backcrossing and genomic selection. The chapter reviews the journey of chickpea status from orphan crop with almost no marker resources to a genome resource-rich crop, which are being used for achieving the genetic gains at a momentum.
Springer eBooks, 2013
Chickpea (Cicer arietinum L.), the second largest consumed pulse crop of the world after common bean, is grown in over 50 countries and traded across 140 countries. The beneficial effects of chickpea on soil health and human health are well recognized. There has been a slow progress in improving average global productivity of chickpea, which continued to remain below 1.0 ton ha-1. The breeding efforts in chickpea have mainly focused on improving its adaptation to different growing conditions. The changing scenario of chickpea cultivation, particularly the large shift in its area to warmer growing environments, and expected effects of climate change further impose challenges on chickpea breeding programs. After several decades of slow progress, the recent years have witnessed extraordinary growth in development of genetic (mapping populations) and genomic resources (structural and functional molecular markers, integrated genetic map, mapping of genes/quantitative trait loci, whole genome sequencing) for chickpea. Now, chickpea is one of the most advanced grain legumes in terms of availability of genomic resources. Efforts have already begun on application of genomics technologies in chickpea improvement. The coming years are expected to have an exponential growth in integration of genomics technologies in chickpea breeding programs. This book chapter provides an update on the development of genetic and genomic resources for chickpea and their current and potential uses in chickpea improvement.
Impact of Genomics on Chickpea Breeding
Compendium of Plant Genomes
Chickpea is an economical source of vegetable protein for the poor living in the semi-arid regions globally. As a consequence of climate change and increasing climate variability, the incidences of drought and heat stresses and severity of some diseases, such as dry root rot and collar rot, have increased in chickpea crop, resulting in poor and unstable yields. By improoving the efficiency of crop breeding programs, climate resilient varieties with traits desired by the farmers, industries and consumers can be developed more rapidly. Excellent progress has been made in the development of genomic resources for chickpea in the recent past. Several national and international chickpea breeding programs have started utilizing these genomic resources and tools for genetic improvement of complex traits. One of such examples includes the introgression of "QTL-hotspot" containing quantitative trait loci (QTLs) for several drought tolerance-related traits, including root traits, through marker-assisted backcrossing (MABC) for enhancing drought tolerance in popular cultivars. Several drought-tolerant introgression lines with higher yield as compared to the popular cultivars have been identified. Multi-parent advanced generation intercross (MAGIC) populations developed from using 8 parents created large genetic diversity consequently several promising lines. Marker-assisted recurrent selection (MARS) has also been explored for yield improvement in chickpea. Development of diagnostic markers or the identification of candidate genes for several traits is essential for greater use of genomic resources in chickpea improvement.
Impact of Genomic Technologies on Chickpea Breeding Strategies
Agronomy, 2012
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.
Chickpea molecular breeding: New tools and concepts
Euphytica, 2006
Chickpea is a cool season grain legume of exceptionally high nutritive value and most versatile food use. It is mostly grown under rain fed conditions in arid and semi-arid areas around the world. Despite growing demand and high yield potential, chickpea yield is unstable and productivity is stagnant at unacceptably low levels. Major yield increases could be achieved by development and use of cultivars that resist/tolerate abiotic and biotic stresses. In recent years the wide use of early maturing cultivars that escape drought stress led to significant increases in chickpea productivity. In the Mediterranean region, yield could be increased by shifting the sowing date from spring to winter. However, this is hampered by the sensitivity of the crop to low temperatures and the fungal pathogen Ascochyta rabiei. Drought, pod borer (Helicoverpa spp.) and the fungus Fusarium oxysporum additionally reduce harvests there and in other parts of the world. Tolerance to rising salinity will be a future advantage in many regions. Therefore, chickpea breeding focuses on increasing yield by pyramiding genes for resistance/tolerance to the fungi, to pod borer, salinity, cold and drought into elite germplasm. Progress in breeding necessitates a better understanding of the genetics underlying these traits. Marker-assisted selection (MAS) would allow a better targeting of the desired genes. Genetic mapping in chickpea, for a long time hampered by the little variability in chickpea’s genome, is today facilitated by highly polymorphic, co-dominant microsatellite-based markers. Their application for the genetic mapping of traits led to inter-laboratory comparable maps. This paper reviews the current situation of chickpea genome mapping, tagging of genes for ascochyta blight, fusarium wilt resistance and other traits, and requirements for MAS. Conventional breeding strategies to tolerate/avoid drought and chilling effects at flowering time, essential for changing from spring to winter sowing, are described. Recent approaches and future prospects for functional genomics of chickpea are discussed.
Functional Plant Biology, 2007
Chickpea is a valuable and important agricultural crop, but yield potential is limited by a series of biotic and abiotic stresses, including Ascochyta blight, Fusarium wilt, drought, cold and salinity. To accelerate molecular breeding efforts for the discovery and introgression of stress tolerance genes into cultivated chickpea, functional genomics approaches are rapidly growing. Recently a series of genetic tools for chickpea have become available that have allowed high-powered functional genomics studies to proceed, including a dense genetic map, large insert genome libraries, expressed sequence tag libraries, microarrays, serial analysis of gene expression, transgenics and reverse genetics. This review summarises the development of these genomic tools and the achievements made in initial and emerging functional genomics studies. Much of the initial research focused on Ascochyta blight resistance, and a resistance model has been synthesised based on the results of various studies....
Genomics-assisted breeding for drought tolerance in chickpea
Functional Plant Biology, 2014
Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomicsassisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73 Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15 360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10-24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea. (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the J Functional Plant Biology M. Thudi et al. L Functional Plant Biology M. Thudi et al.
Genomic tools and germplasm diversity for chickpea improvement
Plant Genetic Resources, 2011
Chickpea is the third most important grain legume grown in the arid and semi-arid regions of the world. In spite of vast germplasm accessions available in different genebanks, there has been very limited use of these accessions in genetic enhancement of chickpea. However, in recent years, specialized germplasm subsets such as global composite collection, core collection, mini core collection and reference set have been developed. In parallel, significant genomic resources such as molecular markers including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), diversity arrays technology (DArT) and transcript sequences, e.g. expressed sequence tags, short transcript reads, have been developed. By using SSR, SNP and DArT markers, integrated genetic maps have been developed. It is anticipated that the use of genomic resources and specialized germplasm subsets such as mini core collection and reference set will facilitate identification of trait-specific germplasm, tr...
Scientific Reports, 2018
We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars. Chickpea (Cicer arietinum) is a self-pollinated, diploid (2n = 16) and economically important legume food crop rich in human dietary proteins 1. The chickpea is primarily represented by its desi and kabuli cultivars exhibiting a distinct differentiation in both agro-morphological and architecture traits, which genomes have been sequenced recently 2-5. Substantial enhancement of its yield and productivity by developing high-yielding a/biotic stress tolerant and climate-ready cultivars is essential at present to sustain the global food security. To accomplish these objectives, many significant efforts involving classical genetics as well as genomics-assisted breeding strategies like quantitative trait loci (QTL) mapping, fine-mapping/map-based cloning and association analysis have been made to decipher the inheritance pattern and quantitative dissection of complex yield and stress tolerance traits for genetic improvement of chickpea 6-30. However, these are constrained by narrow genetic base and low intra-specific marker polymorphism among desi and kabuli accessions due to combined strong impact of four major domestication bottlenecks in chickpea as compared to other food crop plants 2,3,31-35. To overcome the aforesaid limitations, development and high-throughput genotyping of large-scale sequence-based informative markers like single nucleotide polymorphism (SNPs) exhibiting a higher potential of polymorphism among cultivated desi and kabuli accessions is a prerequisite for their use in genomics-assisted breeding applications and genetic improvement of chickpea. The next-generation sequencing (NGS)-led genome and transcriptome sequencing of multiple cultivated (desi and kabuli) and wild accessions are found efficient in fast discovery of numerous SNPs at a genome-wide scale in chickpea 2,3,13,18,30,36-44. The large-scale validation and high-throughput genotyping of these SNPs mined from limited number of sequenced accessions using diverse array-based genotyping assays commonly exhibit
Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses
Frontiers in Genetics
Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wi...