PROGRESS IN FP5: PRE-BREEDING AND TRAIT DISCOVERY

Exploiting the untapped genetic variation in GLDC crops by developing and using cutting-edge tools and techniques for pre-breeding, trait discovery, mapping of diagnostic markers and their validation was the main focus of accelerating the rate of realized genetic gains. Research activities centered around trait discovery/mapping/dissection, functional validation of traits and pre-breeding. These enable the exploitation of natural and/or systematically induced variations for prioritized traits in combination with modern genomics, transgenics, phenomics, and breeding tools for accelerated, precise, cost-effective and efficient breeding of new varieties in future.

Pre-breeding focused on advancing prioritized traits through ongoing activities on exploring the natural diversity in wild/unadapted germplasm. Work related to Botrytis grey mould (BGM) in chickpea and blast/heat tolerance in pearl millet using the wild germplasm in ongoing activities was partially supported by bilateral projects. In addition, the focus was on the characterization and advancement of already created transgenic events for traits (such as insect resistance in pigeonpea, chickpea and cowpea, and aflatoxin resistance in groundnut) where natural diversity is not available. Insect bioassays for Helicoverpa resistance in pigeonpea resulted in the identification of at least 12 transgenic events with the Bt genes showing over 90% insect mortality.

Some of the major achievements include: The use of crop wild relatives (CWR) in breeding programs conducted by ICRISAT, IITA, and CIRAD/CERAAS (Centre d’étude régional pour l’amélioration de l’adaptation à la sécheresse). For examples, in pigeonpea, a total of 2,321 introgression lines previously developed using C. scarabaeoides and C. acutifolius as wild donors were screened for pod borer infestation and tolerant lines were identified. In pearl millet, 9 introgression lines were identified from advanced backcross populations involving 2 Pennisetum violaceum accessions for flowering stage heat tolerance. In cowpea, 250+ wild relative accessions were screened that led to the identification of ca. 15 potential sources of drought and heat tolerance. In terms of genetic resources characterization and population genomics, whole genome sequencing of 8, 7, and 34 wild relative species of chickpea, pigeonpea and groundnut, respectively, have been conducted by ICRISAT and draft assemblies generated.

Towards broadening the elite germplasm base, new backcross nested association mapping (BCNAM) sorghum populations targeting post-flowering drought tolerance are being developed with 17 diverse donor parents and 2 elite recurrent parents. Markers were developed and validated for high oleic trait in groundnut and stay green/shoot fly in sorghum. In addition, significant advances were made in the development and validation of genomic selection (GS) in chickpea. Training populations in groundnut, chickpea, pearl millet and sorghum were identified for optimizing the GS models. Advancing the introgression (molecular breeding) lines in groundnut (high oleic trait), chickpea (drought tolerant) and pearl millet (for downy mildew and blast) was a major achievement. ICRISAT scientists in collaboration with other institutes co-led (together with China) the genome sequence of tetraploid groundnut and participated in the US-led genome sequencing initiative. The 58k SNP arrays in chickpea, pigeonpea and groundnut were developed. The Enabling technologies cluster mainly focused on standardizing protocols, establishing the proof-of-concept in genome editing, second-generation transformation (QuickCrop from Corteva), systematic mutant population and rapid generation advancement (RGA) in at least 2 GLDC crop. Expertise and learnings from private partners (e. g., recent MoAs with Corteva and KeyGene) are being leveraged. Significant progress in refinement of genome assembly in one legume was achieved using HiC approach in collaboration with a leading group expert (Dr Erez Liebermann Aiden, Baylor College of Medicine, TX) in this area in the USA. Briefly, the major achievements include:

  • Provided genotyping support to some NARS partners through High Throughput Genotyping (HTPG) platform.
  • Started optimization of Rapid cycling methods for sorghum.
  • Fully sequenced sorghum TILLING population.
  • Decision support tools such as Flapjack and Galaxy to undertakemarker-assisted backcrossing (MABC) and genomic selection analysis are being developed in some GLDC crops such as chickpea and sorghum.
  • Significant progress has been made in experimental designs, digital data capture data analyses/ management through the Breeding Management System(BMS).

Activities in capacity development of students and researchers (especially NARS partners) were supported by organizing training courses, seminars, workshops, symposiums, supporting exchange visits, data management, etc. The knowledge generated will not only be applied in crop improvement but also be disseminated in the form of reports, datasets, scientific publications, presentations at various scientific platforms, sharing knowledge with partners, etc. Briefly, the major achievements in the area of capacity development include:

  • A Ph.D. student received training at Corteva Labs in Johnston, IA, USA.
  • Over 30 Ph.D. students are being trained.
  • More than 100 high-quality research articles were published (link to the Annual Report 2018).
  • A training course on Advanced R, Mixed Models, and R/QTL was held during 3-7 December 2018 at ICRISAT, where over 35 participants from 14 countries of SA and SSA participated.
  • Basic and advanced training courses on Molecular Markers for Crop Improvement were organized during 10-21 December 2018 at ICRISAT. A total of 89 scientists representing national programs and the private sector from 10 countries (Burkina Faso, Ethiopia, Ghana, India, Kenya, Mali, Morocco, Nigeria, Tanzania, and Uganda) were trained.
  • A Symposium on “Advances in Genomics & Breeding Technologies for Accelerating Genetic Gains” was held during 20 December 2018, at ICRISAT, Patancheru. It brought together 270 participants from 12 countries (Australia, Burkina Faso, Ethiopia, Ghana, India, Kenya, Mali, Morocco, Nigeria, Tanzania, The Philippines, and Uganda) and 71 institutions.
  • A two-day joint workshop with GLDC and Innovation et amélioration variétale en Afrique de l’Ouest (IAVAO) (https://www.IAVAO.org) partnership platform was organized from 18-20 November 2018 on Sorghum and Peanut Breeding Product Profiles (BPP). Sixty sorghum and peanut breeders from WCA and ESA explored the concept of BPP, the methods and tools to define product profiles.
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