pangenomic map for chickpea<\/a> using sequencing data from 3,366 genomes. Along the way, they identified superior haplotypes for desirable crop traits, and 56 germplasm lines that could be used for bringing novel haplotypes into the elite germplasm through haplotype-based breeding.<\/p>\n\u201cNow that we have identified superior haplotypes for agronomic traits such as seed size, we can develop assays for those haplotypes,\u201d says Varshney. \u201c[This means] chickpea breeding programmes like Chickpea Breeding Australia can start using this information to introgress superior haplotypes in commercial chickpea varieties.\u201d This he says will provide higher yield and revenues to chickpea growers in Australia.<\/p>\n
So, pangenomics lets us take stock of the diversity across an entire species, enabling us to approach crop improvement from a truly global perspective.<\/p>\n
HapCat analysis, on the other hand, usually focuses on a smaller population of individuals. Instead of trying to describe all possible genetic variants, HapCat analysis creates a \u201ccatalogue of haplotypes\u201d. This is basically a database of all individuals in a population, and the genetic variants they carry on each chromosome. This fine-scale information helps plant breeders select parents to cross together in order to produce superior offspring.<\/p>\n
Varshney\u2019s aim for the Chickpea PanGenome & HapCat Hub is to develop and refine data tools and pipelines for using HapCat and pangenomics for crop improvement.<\/p>\n
\u201cAt present, different research groups have specialized data analytical tools and pipelines that need specialized bioinformatics skills to run pangenome and HapCat analysis, he says. \u201cWe would like to refine those tools and pipelines so that they can be used by researchers with minimum bioinformatics skill.\u201d<\/p>\n
Developing user-friendly analytical tools is important, he says, because it helps to \u201cdemocratize\u201d the genomic sequencing era, and to bring its benefits to developing countries as well.<\/p>\n
Beyond refining the toolkit and making it more accessible, Varshney also hopes to raise awareness for these methods and to educate the wider plant genetic resources community, through targeted capacity-building workshops and webinars.<\/p>\n
Written by: <\/strong>Kiri Marker<\/p>\nCorresponding author: <\/strong>Rajeev Varshney<\/p>\n <\/p>\n
<\/p>\n
<\/p>\n
<\/p>\n
<\/p>\n
<\/p>\n
<\/p>\n
<\/p>\n
<\/p>\n
<\/p>\n
<\/p>\n","protected":false},"excerpt":{"rendered":"
\u00a0 Recent advances in genomics technologies are providing plant breeders with new tools to improve crop yield, quality, and disease resistance. Two approaches that have been gaining increased attention in recent years are pangenomics and haplotype catalogue (HapCat) analyses. These analytic methods are the primary focus of DivSeek\u2019s Chickpea PanGenome & HapCat Hub, which is […]<\/p>\n","protected":false},"author":2,"featured_media":4413,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_et_pb_use_builder":"","_et_pb_old_content":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":"","_wp_stack_schedule":false,"_links_to":"","_links_to_target":""},"categories":[14],"tags":[],"yoast_head":"\n
Here\u2019s how pangenomics can help fast-track crop improvement | DivSeek Intl<\/title>\n \n \n \n \n \n \n \n \n \n \n \n\t \n\t \n\t \n \n \n \n\t \n\t \n\t \n