PROGRESS IN FP5: Pre-Breeding and Trait Discovery – 2020

The Flagship Program 5 (FP5) focused on prioritized trait discovery/mapping/dissection, functional validation and deployment of traits and pre-breeding by exploiting natural and/or systematically induced variations for prioritized traits in combination with modern genomics, transgenics, genome editing, phenomics and breeding tools for accelerated, precise, cost-effective and efficient breeding of new varieties in the future.

Prioritized traits for pre-breeding were advanced through ongoing activities on exploring the natural diversity in wild/unadapted germplasm. Activities using the crop wild relatives (CWRs) in breeding programs were continued by ICRISAT, IITA and CIRAD/CERAAS. At IITA, several lines of cross-compatible cowpea CWRs including those consistently exhibiting seedling stage drought tolerance across different screenhouse trials were crossed with some of the elite cultivated varieties and incorporated into pre-breeding activities. Pre-breeding activities in exotic germplasm of soybean were conducted with the introduction of 63 lines sourced from the Colombian private sector, Semillas Panorama to Nigeria and Zambia.  In Nigeria, four Colombian lines yielded over 2 tons, greater than the popular variety, whereas in Zambia, four lines performed well both under normal and reduced P application. Based on these trials, most of the Colombian lines were found to be well adapted to Nigeria than to Southern Africa with a potential to contribute enormously to the West African soybean breeding community. A set of exotic germplasm of 205 soybean lines was received from the USA through the Soybean Innovation Lab that will will be evaluated in Lusaka and the highlands environment in Kenya. In chickpea, introgression lines showed high levels of Botrytis grey mold resistance and good agronomic performance at ICRISAT. A pre-breeding population was developed using botrytis gray mold (BGM)-resistant Cicer reticulatum as donor and popular chickpea variety ICCV 10 as recipient and the BC2F2 population was genotyped using the SNP genotyping platform. In addition, the focus was on the characterization and advancement of stacked transgenic events with multiple Bt genes for resistance to the legume pod borer in pigeonpea and chickpea and events in groundnut for reduced aflatoxin  where natural durable resistance sources to this insect pest are not available.

CoA5.2 (trait discovery) targets important traits in alignment with breeding Product Profiles related to yield and yield stability under various biotic and abiotic stresses, in addition to those related to nutritional quality.  Among the main achievements were the molecular breeding lines that were advanced in GLDC crops including groundnut, chickpea, pearl millet. The deployment of molecular markers in routine breeding programs in most GLDC crops resulted in more than 300K marker data points generated at HTPG (High Throughput Genotyping Platform) in Intertek in 2020  Identification and assay development was done for a small set of unique and polymorphic SNPs and initial validation for QC panels for breeding applications in groundnut, pearl millet, sorghum, pigeonpea and chickpea, in addition to the generation and validation of 10 trait-linked SNP panels for breeder preferred traits in sorghum, pearl millet, chickpea, pigeonpea, finger millet, soybean and cowpea. The selection of SNPs for mid-density panel was achieved with support for EiB in sorghum, pigeonpea, groundnut, which would significantly change genomic selection (GS) and genomics-assisted breeding in future. Significant progress was made in the development of GS models in GLDC crops such as chickpea, groundnut, sorghum, pigeonpea and pearlmillet; identification of QTLs/MTAs for priority traits in GLDC crops and introgression and pyramiding of already identified QTLs in breeding elite lines for release to breeders and farmers. Accessions from eight annual wild species of Cicer and seven wild species of Cajanus were sequenced using Illumina platform to identify various haplotypes. In groundnut, 34 accessions from 13 wild diploid species were resequenced where the mapping percentage ranged from 88.7% to 99.2% on the reference genome that resulted in the identification of 19.81 million genome-wide SNPs for further analysis.

CoA5.3 (Enabling technologies) mainly focused on establishing protocols for proof of concept in genome editing, second-generation transformation (QuickCrop from Corteva), systematic mutant population, phenotypic screening protocols, and rapid generation turnover (RGT) with the following major achievements:

  • Hi-C approach was deployed to develop new de novo assemblies in order to improve the existing draft genome assemblies of chickpea, pigeonpea and groundnut.
  • All field experiments were designed using BMS in 2020.
  • Data for the ICRISAT mandate crops were loaded on GOBii and complete DNA sampling workflow was done by connecting BMS and GOBii.
  • Diversity in virulence was studied among 10 isolates of grisea (blast disease) collected from Bengaluru, Mandya and Vizianagaram districts in India. Of the 15 breeding lines screened against 10isolates, 4 lines and one germplasm accession (IE 2911) were found resistant to both neck and finger blast.
  • In collaboration with Corteva Agriscience, QuickCrop expression constructs for gene editing were developed to target primary SL pathway genes in two sorghum and one pearl millet lines. These plants were advanced to T1 generation to select for homozygous plants.
  • Using reverse genetics approaches utilizing the TILLING population of sorghum, mutation in the candidate genes for strigolactone exudation were validated using root exudate analysis. The selected mutant lines were sent to Niger and Mali to evaluate their efficacy under Striga infestation. Simultaneously, gene editing is being carried out in elite backgrounds for accelerated trait deployment.
  • Transformative RapidGen methodologies for accelerated breeding cycles in cowpea were developed using a range of 10 genotypes. Overall, 4-6 generations may be taken in a year, thereby offering tremendous opportunities to enhance the rate of genetic gain and accelerate breeding pipelines for this important crop.

The following Capacity building activities were carried out mostly online due to the COVID-19 pandemic situation:

  • The 15th training course and International Workshop on Next Generation Genomics for Developing Climate Resilient Agriculture, 10-15 Feb, ICRISAT headquarters (60 participants).
  • Workshop for early career researchers during the annual general assembly of TIGR2ESS, 20-24 Jan, ICRISAT, HQ (50 participants).
  • Virtual webinar in the series of Next Generation Genomics and Integrated Breeding for Crop Improvement on Genomics for food, health and nutrition, 14 May 2020 (~3000 virtual participants).
  • One CGIAR Global webinar series (5 webinars) on Genome Editing in Agriculture: Innovations for Sustainable Production and Food Systems, 22 September-20 October 2020 (600-700 virtual participants in each webinar).
  • Several Ph.D. students and Post-doctoral fellows were trained.
  • Over 100 high-quality research articles in peer-reviewed journals.
2020 2019 2018
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