PROGRESS IN FP5: Pre-Breeding and Trait Discovery - 2019

The activities of FP5 involve exploiting untapped genetic variation (both natural and induced) by developing and using cutting-edge tools and techniques for pre-breeding and trait discovery, mapping, characterization, and validation of priority traits as per Product Profiles in order to accelerate the rate of realized genetic gains in GLDC crops.

The pre-breeding activities focused on advancing prioritized traits through ongoing activities on exploring the natural diversity in wild and unadapted germplasm. At IITA, 274 cowpea wild relatives were tested for seedling stage drought tolerance alongside six cultivated lines leading to the identification of 44 wild lines as the most drought tolerant. Seven wild accessions and four landraces were identified in finger millet that were immune to blast disease after screening with an isolate from western Kenya. All the wild and landrace materials identified to harbor novel genes will be used as donors for introgression. Previously developed introgression lines (IL) were advanced, as in the case of groundnut developed by CERAAS/CIRAD (A. ipaensis x A. correntina or A. villosa), or further screened, as in pearl millet and pigeonpea. In pearl millet, heat-tolerant introgression lines (ILs) were identified, and a select number evaluated alongside other drought tolerant ILs for their reaction to different pathotypes of the blast pathogen with promising results. A total of 2,321 ILs were screened for pod borer infestation in pigeonpea and 71 ILs rated as tolerant to moderately tolerant based on visual rating (http://oar.icrisat.org/11335/). Towards further characterization of the donors and development of markers for introgression, eight chickpea annual wild species, seven wild Cajanus species and 13 wild diploid groundnut were re-sequenced using Illumina platform and de novo assemblies performed where the gene model prediction and identification of non-coding genes is in progress.

Marker development/deployment resulted in the generation of more than 700K marker data points combined in all GLDC crops through the HTPG platform. The utilization of these molecular markers led to the release of varieties and identification of several QTLs of interest. Two high oleic groundnut varieties and two chickpea varieties were released in India, besides the release of one chickpea variety in Ethiopia. The importance of addressing drought tolerance in pearl millet in WCA was addressed at IRD, where root growth QTLs linked to early drought stress tolerance were identified on LG1 and LG2 and validated using Bulk Segregant Analysis. Additional seven and three markers were identified in pearl millet for resistance to Striga hermonthica, and downy mildew disease respectively for two of the most important biotic stresses in pearl millet in WCA. Striga resistance was also studies in sorghum, and 10 markers identified through GWAS in WCA. Molecular breeding for other stress-related traits in chickpea and pigeonpea resulted in the identification of five and four QTLs respectively. Towards improving quality assurance/check in routine breeding programs of FP4, SNP panels for QC were developed and partially validated in pearl millet, groundnut and chickpea.

The establishment of protocols and generation of proof-of-concepts in genome editing, second-generation transformation (QuickCrop from Corteva), systematic mutant population, developing genomic selection models, phenotypic screening protocols, and rapid generation turnover (RGT) were some of the enabling technologies that resulted in the following achievements:

RGT platforms were established for use in breeding programs of pearl millet and sorghum.
A protocol was optimized for the screening of early stage finger millet leaf blast disease.
High quality draft genome assemblies were refined for chickpea and pigeonpea.
Six genomic prediction models were built from genome-wide marker genotyping and the phenotyping data for sorghum across 3 locations in India.
Decision support tools such as Galaxy-GS pipeline and Flapjack-MABC with improved features were developed to enable user-friendly line selection and deployment in sorghum breeding programs.
Significant progress was made in experimental designs for the capture, analyses, and management of digital data through BMS. All 2017 advanced trial data for cowpea were uploaded on BMS.
Genotyping and phenotyping support was provided to NARS partners in Sudan, India, Turkey, Egypt and Morocco through MABC and genomic selections in chickpea.
Gene edits in sorghum were developed for strigolactone pathway genes including Max1, CCD8, DUF, and ST4 using CRISPR/Cas9 tools to provide durable pre-germination resistance to the parasitic weed Striga hermonthica.
A fundamental advance in sorghum and pearl millet transformation methods (QuickCrop from Corteva) was possible by employing morphogenic genes such as Baby boom (Bbm) and Wuschel (Wus) to stimulate somatic embryogenesis utilizing immature embryos and leaf explants.
To establish a double haploidy system in sorghum to rapidly introgress high-value breeding traits, the development of a haploid inducing pollinator (HIP) was attempted by knocking out the mtl gene that encodes for a sperm-specific phospholipase. Four sequence-confirmed edited events obtained with mutations in the heterozygous state are being advanced to the next generation for attaining homozygosity and use in crossing studies.
A set of modular cloning (MoClo) vectors, based on the Golden Gate method were developed in partnership with Rothamsted Research, UK, for developing quick tools and easy cloning procedures to apply CRISPR-associated protein (CRISPR/Cas) in legume systems.
Robust forewarning models for Helicoverpa armigera outbreak and incidence were developed based on 20-year historical climate data (temperature, RH, rainfall and sunshine) at ICRISAT, Hyderabad to determine the first appearance of disease or pest, crop age at maximum disease severity/pest population and maximum disease severity /pest populations.
In addition, the focus was also on characterization of transgene expression and insect feeding bio-assays in already developed transgenic events of pigeonpea with various combinations of Bt genes from Bacillus thuringiensis for resistance to the legume podborer where diversity for resistance is not available in the natural germplasm.

Capacity development of students and researchers from NARS partners, organizing training courses, seminars, workshops, symposia, supporting exchange visits, data management, etc. were routine activities. Knowledge generated is being applied for crop improvement besides its dissemination and knowledge sharing in the form of reports, datasets, scientific publications, and presentations at various scientific platforms. Briefly, major achievements specific to FP5 are listed below:

Training course on Next Generation Genomics for Crop Improvement, 6-17 May 2019, ICRISAT, with 50 participants (30 males, 20 females) representing NARS from India
International workshop on Genomic selection for crop improvement, 15 May 2019, ICRISAT, with about 80 participants (50 males, 30 females) representing NARS from India, Australia and UK
Joint workshop of ICRISAT-Chinese Academy of Agricultural Sciences (CAAS) – Zhejiang Academy of Agricultural Sciences (ZAAS) on Genomics-assisted crop improvement, 11 July 2019, ICRISAT, with 44 participants (28 males, 16 females) representing NARS from China and India.
International course on Artificial Intelligence & Machine Learning and its application in genomic selection in plant breeding, 18-22 November 2019, ICRISAT, with 32 participants (18 males, 14 females) representing NARS from Ethiopia, India, Mexico, Nigeria, Philippines and Uganda.
Regional expert consultation meeting on gene editing technologies in agriculture and its biosafety, 10-11 October 2019, ICRISAT, with 70 participants (55 males, 15 females) representing Indian NARS, The Asia-Pacific Association of Agricultural Research Institutions (APAARI) country representatives, NGOs, industry, and regulators from Japan and Australia.
International hands-on training on Genome editing technologies, 14-25 October 2019, ICRISAT, with 20 participants (13 males, 7 females) representing partners from India, Philippines, Kenya, Malaysia, Taiwan, Vietnam, Thailand, Rwanda and Senegal.
Industry training on Next generation (QuickCrop) transformation of pearl millet, 1 October-15 December 2019, Corteva , USA, with 1 female participant from India.
Over 30 PhD students are currently being trained.
Published over 100 high-quality research articles.

Since most of the FP5 activities on pre-breeding, trait discovery and novel tools and technologies feed into FP4; its contribution to SDGs and SLOs are also represented by FP4.

Main achievements with gender-specific relevance

Generally, broadening the base of cultivated diversity using CWRs or genetic resources can provide new traits with gender relevance. Mapping of seed protein content in pigeonpea and Zn/Fe in pearl millet are relevant outcomes for women and children due to the benefits of more efficient selection for high protein content. It should lead to the development of new varieties that reduce the amount of work by women and result in higher nutritional qualities and market value, thereby improving the health and economy of small farmer households. The development of demand-led breeding approaches (BPP workshop) is expected to generate varieties with better attributes reflecting the needs of end users, especially women who are involved in the transformation process. Finally, balanced gender representation in capacity building activities in FP5 will lead to a higher representation of women in research staff.

PROGRESS IN FP5: Pre-Breeding and Trait Discovery – 2019